=> Building biology/p5-BioPerl Started : Wednesday, 6 MAR 2019 at 18:45:44 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for p5-BioPerl-1.007005: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples PGTEST=off: Test PostGreSQL SQLITETEST=off: Test SQLite ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-BioPerl XDG_CONFIG_HOME=/construction/biology/p5-BioPerl HOME=/construction/biology/p5-BioPerl TMPDIR="/tmp" PATH=/construction/biology/p5-BioPerl/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- INSTALLDIRS="site" CC="cc" CCFLAGS="-pipe -O2 -fno-strict-aliasing " LD="cc" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib" -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-BioPerl XDG_CONFIG_HOME=/construction/biology/p5-BioPerl HOME=/construction/biology/p5-BioPerl TMPDIR="/tmp" PATH=/construction/biology/p5-BioPerl/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/p5-BioPerl/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/BioPerl" EXAMPLESDIR="share/examples/BioPerl" DATADIR="share/BioPerl" WWWDIR="www/BioPerl" ETCDIR="etc/BioPerl" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/BioPerl DOCSDIR=/usr/local/share/doc/BioPerl EXAMPLESDIR=/usr/local/share/examples/BioPerl WWWDIR=/usr/local/www/BioPerl ETCDIR=/usr/local/etc/BioPerl -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-1.007005 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> p5-BioPerl-1.007005 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-BioPerl-1.007005 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user => BioPerl-1.7.4.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.4.tar.gz BioPerl-1.7.4.tar.gz 7462 kB 0 Bps ===> Fetching all distfiles required by p5-BioPerl-1.007005 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-1.007005 for building => SHA256 Checksum OK for BioPerl-1.7.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-1.007005 for building ===> Extracting for p5-BioPerl-1.007005 => SHA256 Checksum OK for BioPerl-1.7.4.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-BioPerl-1.007005 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-1.007005 depends on package: p5-DBI>=0 - not found ===> Installing existing package /packages/All/p5-DBI-1.642.txz Installing p5-DBI-1.642... `-- Installing perl5-5.28.1... `-- Extracting perl5-5.28.1: .......... done Extracting p5-DBI-1.642: .......... done Message from perl5-5.28.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> p5-BioPerl-1.007005 depends on package: p5-DBI>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Data-Stag>=0 - not found ===> Installing existing package /packages/All/p5-Data-Stag-0.14_2.txz Installing p5-Data-Stag-0.14_2... `-- Installing p5-IO-String-1.08_1... `-- Extracting p5-IO-String-1.08_1: ....... done Extracting p5-Data-Stag-0.14_2: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-Data-Stag>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Error>=0 - not found ===> Installing existing package /packages/All/p5-Error-0.17027.txz Installing p5-Error-0.17027... Extracting p5-Error-0.17027: ......... done ===> p5-BioPerl-1.007005 depends on package: p5-Error>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-GD>=0 - not found ===> Installing existing package /packages/All/p5-GD-2.71.txz Installing p5-GD-2.71... `-- Installing libgd-2.2.5_1,1... | `-- Installing fontconfig-2.12.6,1... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing freetype2-2.9.1... | | `-- Extracting freetype2-2.9.1: .......... done | `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | `-- Installing jpeg-turbo-2.0.2... | `-- Extracting jpeg-turbo-2.0.2: .......... done | `-- Installing png-1.6.36... | `-- Extracting png-1.6.36: .......... done | `-- Installing tiff-4.0.10... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | `-- Extracting tiff-4.0.10: .......... done | `-- Installing webp-1.0.2... | | `-- Installing giflib-5.1.4... | | `-- Extracting giflib-5.1.4: .......... done | `-- Extracting webp-1.0.2: .......... done `-- Extracting libgd-2.2.5_1,1: .......... done Extracting p5-GD-2.71: .......... done Message from freetype2-2.9.1: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). ===> p5-BioPerl-1.007005 depends on package: p5-GD>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Graph>=0 - not found ===> Installing existing package /packages/All/p5-Graph-0.9704,1.txz Installing p5-Graph-0.9704,1... `-- Installing p5-Heap-0.80_1... `-- Extracting p5-Heap-0.80_1: .......... done Extracting p5-Graph-0.9704,1: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-Graph>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-HTTP-Message>=0 - not found ===> Installing existing package /packages/All/p5-HTTP-Message-6.18.txz Installing p5-HTTP-Message-6.18... `-- Installing p5-Encode-Locale-1.05... `-- Extracting p5-Encode-Locale-1.05: ....... done `-- Installing p5-HTTP-Date-6.02_1... `-- Extracting p5-HTTP-Date-6.02_1: ....... done `-- Installing p5-IO-HTML-1.001_1... `-- Extracting p5-IO-HTML-1.001_1: ....... done `-- Installing p5-LWP-MediaTypes-6.02_1... `-- Extracting p5-LWP-MediaTypes-6.02_1: ........ done `-- Installing p5-URI-1.76... `-- Extracting p5-URI-1.76: .......... done Extracting p5-HTTP-Message-6.18: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-HTTP-Message>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-IO-stringy>=0 - not found ===> Installing existing package /packages/All/p5-IO-stringy-2.111.txz Installing p5-IO-stringy-2.111... Extracting p5-IO-stringy-2.111: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-IO-stringy>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-IPC-Run>=0 - not found ===> Installing existing package /packages/All/p5-IPC-Run-0.99.txz Installing p5-IPC-Run-0.99... `-- Installing p5-IO-Tty-1.12_2... `-- Extracting p5-IO-Tty-1.12_2: .......... done Extracting p5-IPC-Run-0.99: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-IPC-Run>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-List-MoreUtils>=0 - not found ===> Installing existing package /packages/All/p5-List-MoreUtils-0.428.txz Installing p5-List-MoreUtils-0.428... `-- Installing p5-Exporter-Tiny-1.002001... `-- Extracting p5-Exporter-Tiny-1.002001: .......... done `-- Installing p5-List-MoreUtils-XS-0.428... `-- Extracting p5-List-MoreUtils-XS-0.428: ....... done Extracting p5-List-MoreUtils-0.428: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-List-MoreUtils>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Module-Build>=0 - not found ===> Installing existing package /packages/All/p5-Module-Build-0.4224.txz Installing p5-Module-Build-0.4224... Extracting p5-Module-Build-0.4224: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-Module-Build>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Set-Scalar>=0 - not found ===> Installing existing package /packages/All/p5-Set-Scalar-1.29.txz Installing p5-Set-Scalar-1.29... Extracting p5-Set-Scalar-1.29: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-Set-Scalar>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Test-Most>=0 - not found ===> Installing existing package /packages/All/p5-Test-Most-0.35.txz Installing p5-Test-Most-0.35... `-- Installing p5-Exception-Class-1.44... | `-- Installing p5-Class-Data-Inheritable-0.08_1... | `-- Extracting p5-Class-Data-Inheritable-0.08_1: ....... done | `-- Installing p5-Devel-StackTrace-2.03... | `-- Extracting p5-Devel-StackTrace-2.03: ........ done `-- Extracting p5-Exception-Class-1.44: ......... done `-- Installing p5-Test-Deep-1.128... `-- Extracting p5-Test-Deep-1.128: .......... done `-- Installing p5-Test-Differences-0.640,1... | `-- Installing p5-Text-Diff-1.45... | | `-- Installing p5-Algorithm-Diff-1.1903... | | `-- Extracting p5-Algorithm-Diff-1.1903: .......... done | `-- Extracting p5-Text-Diff-1.45: .......... done `-- Extracting p5-Test-Differences-0.640,1: ....... done `-- Installing p5-Test-Exception-0.43... | `-- Installing p5-Sub-Uplevel-0.2800... | `-- Extracting p5-Sub-Uplevel-0.2800: ....... done `-- Extracting p5-Test-Exception-0.43: ....... done `-- Installing p5-Test-Warn-0.36... `-- Extracting p5-Test-Warn-0.36: ....... done Extracting p5-Test-Most-0.35: ......... done ===> p5-BioPerl-1.007005 depends on package: p5-Test-Most>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-Test-RequiresInternet>=0 - not found ===> Installing existing package /packages/All/p5-Test-RequiresInternet-0.05.txz Installing p5-Test-RequiresInternet-0.05... Extracting p5-Test-RequiresInternet-0.05: ....... done ===> p5-BioPerl-1.007005 depends on package: p5-Test-RequiresInternet>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-URI>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-DOM-XPath>=0 - not found ===> Installing existing package /packages/All/p5-XML-DOM-XPath-0.14_1.txz Installing p5-XML-DOM-XPath-0.14_1... `-- Installing p5-XML-DOM-1.44_1... | `-- Installing p5-XML-Parser-2.44... | `-- Extracting p5-XML-Parser-2.44: .......... done | `-- Installing p5-XML-RegExp-0.04_1... | `-- Extracting p5-XML-RegExp-0.04_1: ....... done | `-- Installing p5-libwww-6.36... | | `-- Installing p5-Authen-NTLM-1.09_1... | | `-- Installing p5-Digest-HMAC-1.03_1... | | `-- Extracting p5-Digest-HMAC-1.03_1: .......... done | | `-- Extracting p5-Authen-NTLM-1.09_1: ......... done | | `-- Installing p5-File-Listing-6.04_1... | | `-- Extracting p5-File-Listing-6.04_1: ....... done | | `-- Installing p5-HTML-Parser-3.72... | | `-- Installing p5-HTML-Tagset-3.20_1... | | `-- Extracting p5-HTML-Tagset-3.20_1: ....... done | | `-- Extracting p5-HTML-Parser-3.72: .......... done | | `-- Installing p5-HTTP-Cookies-6.04... | | `-- Extracting p5-HTTP-Cookies-6.04: .......... done | | `-- Installing p5-HTTP-Daemon-6.01_1... | | `-- Extracting p5-HTTP-Daemon-6.01_1: ....... done | | `-- Installing p5-HTTP-Negotiate-6.01_1... | | `-- Extracting p5-HTTP-Negotiate-6.01_1: ....... done | | `-- Installing p5-Net-HTTP-6.18... | | `-- Installing p5-IO-Socket-SSL-2.060... | | | `-- Installing p5-IO-Socket-INET6-2.72_1... | | | `-- Installing p5-Socket6-0.29... | | | `-- Extracting p5-Socket6-0.29: ....... done | | | `-- Extracting p5-IO-Socket-INET6-2.72_1: ....... done | | | `-- Installing p5-Mozilla-CA-20180117... | | | `-- Extracting p5-Mozilla-CA-20180117: ........ done | | | `-- Installing p5-Net-SSLeay-1.85... | | | `-- Installing libressl-2.8.3... | | | `-- Extracting libressl-2.8.3: .......... done | | | `-- Extracting p5-Net-SSLeay-1.85: .......... done | | `-- Extracting p5-IO-Socket-SSL-2.060: .......... done | | `-- Extracting p5-Net-HTTP-6.18: .......... done | | `-- Installing p5-Try-Tiny-0.30... | | `-- Extracting p5-Try-Tiny-0.30: ...... done | | `-- Installing p5-WWW-RobotRules-6.02_1... | | `-- Extracting p5-WWW-RobotRules-6.02_1: ......... done | `-- Extracting p5-libwww-6.36: .......... done | `-- Installing p5-libxml-0.08_1... | `-- Extracting p5-libxml-0.08_1: .......... done `-- Extracting p5-XML-DOM-1.44_1: .......... done `-- Installing p5-XML-XPathEngine-0.14_1... `-- Extracting p5-XML-XPathEngine-0.14_1: .......... done Extracting p5-XML-DOM-XPath-0.14_1: ....... done ===> p5-BioPerl-1.007005 depends on package: p5-XML-DOM-XPath>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-XML-DOM>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-LibXML>=0 - not found ===> Installing existing package /packages/All/p5-XML-LibXML-2.0134,1.txz Installing p5-XML-LibXML-2.0134,1... `-- Installing libxml2-2.9.8... `-- Extracting libxml2-2.9.8: .......... done `-- Installing p5-XML-NamespaceSupport-1.12... `-- Extracting p5-XML-NamespaceSupport-1.12: ....... done `-- Installing p5-XML-SAX-1.00... | `-- Installing p5-XML-SAX-Base-1.09... | `-- Extracting p5-XML-SAX-Base-1.09: .......... done `-- Extracting p5-XML-SAX-1.00: .......... done could not find ParserDetails.ini in /usr/local/lib/perl5/site_perl/XML/SAX Extracting p5-XML-LibXML-2.0134,1: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-XML-LibXML>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX-Base>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX-Writer>=0 - not found ===> Installing existing package /packages/All/p5-XML-SAX-Writer-0.57.txz Installing p5-XML-SAX-Writer-0.57... `-- Installing p5-XML-Filter-BufferText-1.01_1... `-- Extracting p5-XML-Filter-BufferText-1.01_1: ....... done Extracting p5-XML-SAX-Writer-0.57: ......... done ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX-Writer>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-Twig>=0 - not found ===> Installing existing package /packages/All/p5-XML-Twig-3.52.txz Installing p5-XML-Twig-3.52... `-- Installing p5-HTML-Tree-5.07... `-- Extracting p5-HTML-Tree-5.07: .......... done `-- Installing p5-Text-Iconv-1.7_3... | `-- Installing libiconv-1.14_11... | `-- Extracting libiconv-1.14_11: .......... done `-- Extracting p5-Text-Iconv-1.7_3: ......... done `-- Installing p5-Tie-IxHash-1.23_1... `-- Extracting p5-Tie-IxHash-1.23_1: ....... done `-- Installing p5-XML-XPath-1.44... `-- Extracting p5-XML-XPath-1.44: .......... done Extracting p5-XML-Twig-3.52: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-XML-Twig>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-XML-Writer>=0 - not found ===> Installing existing package /packages/All/p5-XML-Writer-0.625_1.txz Installing p5-XML-Writer-0.625_1... Extracting p5-XML-Writer-0.625_1: ...... done ===> p5-BioPerl-1.007005 depends on package: p5-XML-Writer>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-YAML>=0 - not found ===> Installing existing package /packages/All/p5-YAML-1.27.txz Installing p5-YAML-1.27... Extracting p5-YAML-1.27: .......... done ===> p5-BioPerl-1.007005 depends on package: p5-YAML>=0 - found ===> Returning to build of p5-BioPerl-1.007005 ===> p5-BioPerl-1.007005 depends on package: p5-libwww>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-libxml>=0 - found ===> p5-BioPerl-1.007005 depends on package: perl5>=5.28.r1<5.29 - found ===> p5-BioPerl-1.007005 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-BioPerl-1.007005 Warning: prerequisite Test::Memory::Cycle 0 not found. Warning: prerequisite Test::Weaken 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for BioPerl Writing MYMETA.yml and MYMETA.json -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-BioPerl-1.007005 --- blib/lib/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/BioPerl/.exists --- --- blib/arch/auto/BioPerl/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- pm_to_blib --- --- blib/script/bp_aacomp --- --- blib/script/bp_bioflat_index --- --- blib/script/bp_biogetseq --- --- blib/script/bp_bioflat_index --- cp bin/bp_bioflat_index blib/script/bp_bioflat_index --- blib/script/bp_biogetseq --- cp bin/bp_biogetseq blib/script/bp_biogetseq --- blib/script/bp_aacomp --- cp bin/bp_aacomp blib/script/bp_aacomp --- blib/script/bp_bioflat_index --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index --- blib/script/bp_biogetseq --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq --- blib/script/bp_aacomp --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp --- blib/script/bp_chaos_plot --- cp bin/bp_chaos_plot blib/script/bp_chaos_plot "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_chaos_plot --- pm_to_blib --- cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm cp lib/Bio/Symbol/README.Symbol blib/lib/Bio/Symbol/README.Symbol cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm cp lib/Bio/Tools/Run/README blib/lib/Bio/Tools/Run/README cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm cp lib/Bio/Symbol/Symbol.pm blib/lib/Bio/Symbol/Symbol.pm cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp lib/Bio/Seq/SeqWithQuality.pm blib/lib/Bio/Seq/SeqWithQuality.pm cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm cp lib/Bio/Symbol/DNAAlphabet.pm blib/lib/Bio/Symbol/DNAAlphabet.pm cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm --- blib/script/bp_classify_hits_kingdom --- cp bin/bp_classify_hits_kingdom blib/script/bp_classify_hits_kingdom "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_classify_hits_kingdom --- pm_to_blib --- cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/Symbol/AlphabetI.pm blib/lib/Bio/Symbol/AlphabetI.pm cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm cp lib/Bio/Symbol/SymbolI.pm blib/lib/Bio/Symbol/SymbolI.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm cp lib/Bio/SeqIO/interpro.pm blib/lib/Bio/SeqIO/interpro.pm cp lib/Bio/Range.pm blib/lib/Bio/Range.pm cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm --- blib/script/bp_dbsplit --- cp bin/bp_dbsplit blib/script/bp_dbsplit "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit --- pm_to_blib --- cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm cp lib/Bio/Symbol/ProteinAlphabet.pm blib/lib/Bio/Symbol/ProteinAlphabet.pm cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm cp lib/Bio/Symbol/Alphabet.pm blib/lib/Bio/Symbol/Alphabet.pm cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm --- blib/script/bp_extract_feature_seq --- cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq --- blib/script/bp_fastam9_to_table --- cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table --- blib/script/bp_extract_feature_seq --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq --- blib/script/bp_fetch --- cp bin/bp_fetch blib/script/bp_fetch "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch --- blib/script/bp_filter_search --- cp bin/bp_filter_search blib/script/bp_filter_search "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search --- blib/script/bp_find-blast-matches --- cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches --- blib/script/bp_gccalc --- cp bin/bp_gccalc blib/script/bp_gccalc "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc --- blib/script/bp_genbank2gff3 --- cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 --- blib/script/bp_index --- cp bin/bp_index blib/script/bp_index "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index --- blib/script/bp_local_taxonomydb_query --- cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query --- blib/script/bp_make_mrna_protein --- cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein --- blib/script/bp_mask_by_search --- cp bin/bp_mask_by_search blib/script/bp_mask_by_search "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search --- blib/script/bp_mrtrans --- cp bin/bp_mrtrans blib/script/bp_mrtrans "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans --- blib/script/bp_mutate --- cp bin/bp_mutate blib/script/bp_mutate "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate --- blib/script/bp_nexus2nh --- cp bin/bp_nexus2nh blib/script/bp_nexus2nh "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh --- blib/script/bp_nrdb --- cp bin/bp_nrdb blib/script/bp_nrdb "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb --- blib/script/bp_oligo_count --- cp bin/bp_oligo_count blib/script/bp_oligo_count "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count --- blib/script/bp_process_gadfly --- cp bin/bp_process_gadfly blib/script/bp_process_gadfly "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly --- blib/script/bp_process_sgd --- cp bin/bp_process_sgd blib/script/bp_process_sgd "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd --- blib/script/bp_revtrans-motif --- cp bin/bp_revtrans-motif blib/script/bp_revtrans-motif "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_revtrans-motif --- blib/script/bp_search2alnblocks --- cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks --- blib/script/bp_search2gff --- cp bin/bp_search2gff blib/script/bp_search2gff "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff --- blib/script/bp_search2table --- cp bin/bp_search2table blib/script/bp_search2table "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table --- blib/script/bp_search2tribe --- cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe --- blib/script/bp_seq_length --- --- blib/script/bp_seqconvert --- --- blib/script/bp_seqcut --- --- blib/script/bp_seqconvert --- cp bin/bp_seqconvert blib/script/bp_seqconvert --- blib/script/bp_seq_length --- cp bin/bp_seq_length blib/script/bp_seq_length --- blib/script/bp_seqcut --- cp bin/bp_seqcut blib/script/bp_seqcut "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut --- blib/script/bp_seq_length --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length --- blib/script/bp_seqconvert --- "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert --- blib/script/bp_seqpart --- cp bin/bp_seqpart blib/script/bp_seqpart "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart --- blib/script/bp_seqret --- cp bin/bp_seqret blib/script/bp_seqret "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret --- blib/script/bp_seqretsplit --- cp bin/bp_seqretsplit blib/script/bp_seqretsplit "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit --- blib/script/bp_split_seq --- cp bin/bp_split_seq blib/script/bp_split_seq "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq --- blib/script/bp_sreformat --- cp bin/bp_sreformat blib/script/bp_sreformat "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat --- blib/script/bp_taxid4species --- cp bin/bp_taxid4species blib/script/bp_taxid4species "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species --- blib/script/bp_taxonomy2tree --- cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree --- blib/script/bp_translate_seq --- cp bin/bp_translate_seq blib/script/bp_translate_seq "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq --- blib/script/bp_tree2pag --- cp bin/bp_tree2pag blib/script/bp_tree2pag "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag --- blib/script/bp_unflatten_seq --- cp bin/bp_unflatten_seq blib/script/bp_unflatten_seq "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_unflatten_seq --- blibdirs --- --- config --- --- dynamic --- --- linkext --- --- pure_all --- --- pure_all --- --- manifypods --- Manifying 42 pod documents Manifying 479 pod documents --- all --- -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-1.007005 depends on package: p5-DBI>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Data-Stag>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Error>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-GD>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Graph>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-HTTP-Message>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-IO-stringy>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-List-MoreUtils>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Module-Build>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Set-Scalar>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Test-Most>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-Test-RequiresInternet>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-URI>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-DOM-XPath>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-DOM>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-LibXML>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX-Base>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX-Writer>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-SAX>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-XML-Writer>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-YAML>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-libwww>=0 - found ===> p5-BioPerl-1.007005 depends on package: p5-libxml>=0 - found ===> p5-BioPerl-1.007005 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-BioPerl-1.007005 ===> Generating temporary packing list Manifying 42 pod documents Manifying 479 pod documents Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/BioPerl.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/IdentifiableI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/LocationI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/PrimarySeq.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Species.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/ParameterBaseI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DBLinkContainerI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Taxon.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/IdCollectionI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisResultI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/LocatableSeq.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/PrimarySeqI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeatureI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Seq.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DescribableI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/UpdateableSeqI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisParserI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/FeatureHolderI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationCollectionI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/HandlerBaseI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/WebAgent.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO.pm Installing 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/construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqUtils.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/goflat.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/simplehierarchy.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/soflat.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/dagflat.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/InterProParser.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/obo.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/InterProHandler.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/BaseSAXHandler.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ObjectBuilderI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/LocationFactoryI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/FTLocationFactory.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ApplicationFactoryI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ObjectFactory.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Factory/DriverFactory.pm Installing 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Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Exception.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/HTTPget.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Utilities.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Test.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Root.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Storable.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/IO.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/Version.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Root/RootI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DB/DBFetch.pm Installing 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/construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DB/GFF/Util/Binning.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DB/GFF/Util/Rearrange.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/EventHandlerI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/wise.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/IteratedSearchResultEventBuilder.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/sim4.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/SearchWriterI.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/gmap_f9.pm Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/blast_pull.pm Installing 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Installing /construction/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::Writer::HitTableWriter.3 Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_process_sgd Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_index Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_filter_search Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_aacomp Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_nrdb Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_nexus2nh Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_taxonomy2tree Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seqpart Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_dbsplit Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seqcut Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_biogetseq Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_mutate Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_taxid4species Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_oligo_count Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_make_mrna_protein Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_search2tribe Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_search2gff Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_chaos_plot Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_bioflat_index Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_fetch Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_search2alnblocks Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_local_taxonomydb_query Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seqret Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_search2table Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seqconvert Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seqretsplit Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_tree2pag Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_extract_feature_seq Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_mask_by_search Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_mrtrans Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_process_gadfly Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_unflatten_seq Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_sreformat Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_translate_seq Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_genbank2gff3 Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_find-blast-matches Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_fastam9_to_table Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_revtrans-motif Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_split_seq Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_seq_length Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_classify_hits_kingdom Installing /construction/biology/p5-BioPerl/stage/usr/local/bin/bp_gccalc cd /construction/biology/p5-BioPerl/BioPerl-1.7.4 && install -m 0644 AUTHORS Changes MANIFEST README.md /construction/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl cd /construction/biology/p5-BioPerl/BioPerl-1.7.4/examples/ && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/p5-BioPerl/stage/usr/local/share/examples/BioPerl ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for p5-BioPerl-1.007005 file sizes/checksums [1099]: .......... done packing files [1099]: .......... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 6 MAR 2019 at 18:46:30 UTC Duration: 00:00:46