=>> Building biology/p5-BioPerl build started at Wed Mar 27 14:41:23 GMT 2024 port directory: /usr/ports/biology/p5-BioPerl package name: p5-BioPerl-1.007008 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: sunpoet@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1912 Oct 15 13:25 /usr/ports/biology/p5-BioPerl/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 0567b2de2c Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for p5-BioPerl-1.007008: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- sunpoet@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- INSTALLDIRS="site" CC="cc" CCFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " LD="cc" 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 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work/.cache HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/p5-BioPerl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/p5-BioPerl/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work/.cache HOME=/wrkdirs/usr/ports/biology/p5-BioPerl/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/p5-BioPerl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/p5-BioPerl/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" PORTEXAMPLES="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 DOCSDIR="share/doc/BioPerl" EXAMPLESDIR="share/examples/BioPerl" DATADIR="share/BioPerl" WWWDIR="www/BioPerl" ETCDIR="etc/BioPerl" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/BioPerl DOCSDIR=/usr/local/share/doc/BioPerl EXAMPLESDIR=/usr/local/share/examples/BioPerl WWWDIR=/usr/local/www/BioPerl ETCDIR=/usr/local/etc/BioPerl --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> p5-BioPerl-1.007008 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> p5-BioPerl-1.007008 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-BioPerl-1.007008 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by p5-BioPerl-1.007008 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by p5-BioPerl-1.007008 for building => SHA256 Checksum OK for BioPerl-1.7.8.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by p5-BioPerl-1.007008 for building ===> Extracting for p5-BioPerl-1.007008 => SHA256 Checksum OK for BioPerl-1.7.8.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for p5-BioPerl-1.007008 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> p5-BioPerl-1.007008 depends on package: p5-Data-Stag>=0 - not found ===> Installing existing package /packages/All/p5-Data-Stag-0.14_2.pkg [pkg-builder.dan.net.uk] Installing p5-Data-Stag-0.14_2... [pkg-builder.dan.net.uk] `-- Installing p5-IO-String-1.08_1... [pkg-builder.dan.net.uk] | `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] | `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting p5-IO-String-1.08_1: ... done [pkg-builder.dan.net.uk] Extracting p5-Data-Stag-0.14_2: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-Data-Stag>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Error>=0 - not found ===> Installing existing package /packages/All/p5-Error-0.17029.pkg [pkg-builder.dan.net.uk] Installing p5-Error-0.17029... [pkg-builder.dan.net.uk] Extracting p5-Error-0.17029: ..... done ===> p5-BioPerl-1.007008 depends on package: p5-Error>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Graph>=0 - not found ===> Installing existing package /packages/All/p5-Graph-0.9727,1.pkg [pkg-builder.dan.net.uk] Installing p5-Graph-0.9727,1... [pkg-builder.dan.net.uk] `-- Installing p5-Heap-0.80_1... [pkg-builder.dan.net.uk] `-- Extracting p5-Heap-0.80_1: .......... done [pkg-builder.dan.net.uk] `-- Installing p5-Set-Object-1.42... [pkg-builder.dan.net.uk] `-- Extracting p5-Set-Object-1.42: ........ done [pkg-builder.dan.net.uk] Extracting p5-Graph-0.9727,1: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-Graph>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-HTTP-Message>=0 - not found ===> Installing existing package /packages/All/p5-HTTP-Message-6.45.pkg [pkg-builder.dan.net.uk] Installing p5-HTTP-Message-6.45... [pkg-builder.dan.net.uk] `-- Installing p5-Clone-0.46... [pkg-builder.dan.net.uk] `-- Extracting p5-Clone-0.46: ..... done [pkg-builder.dan.net.uk] `-- Installing p5-Encode-Locale-1.05... [pkg-builder.dan.net.uk] `-- Extracting p5-Encode-Locale-1.05: ... done [pkg-builder.dan.net.uk] `-- Installing p5-HTTP-Date-6.06... [pkg-builder.dan.net.uk] | `-- Installing p5-TimeDate-2.33,1... [pkg-builder.dan.net.uk] | `-- Extracting p5-TimeDate-2.33,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting p5-HTTP-Date-6.06: ... done [pkg-builder.dan.net.uk] `-- Installing p5-IO-HTML-1.004... [pkg-builder.dan.net.uk] `-- Extracting p5-IO-HTML-1.004: ... done [pkg-builder.dan.net.uk] `-- Installing p5-LWP-MediaTypes-6.04... [pkg-builder.dan.net.uk] `-- Extracting p5-LWP-MediaTypes-6.04: .... done [pkg-builder.dan.net.uk] `-- Installing p5-URI-5.27... [pkg-builder.dan.net.uk] `-- Extracting p5-URI-5.27: .......... done [pkg-builder.dan.net.uk] Extracting p5-HTTP-Message-6.45: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-HTTP-Message>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-IO-Stringy>=0 - not found ===> Installing existing package /packages/All/p5-IO-Stringy-2.113.pkg [pkg-builder.dan.net.uk] Installing p5-IO-Stringy-2.113... [pkg-builder.dan.net.uk] Extracting p5-IO-Stringy-2.113: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-IO-Stringy>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-IPC-Run>=0 - not found ===> Installing existing package /packages/All/p5-IPC-Run-20231003.0.pkg [pkg-builder.dan.net.uk] Installing p5-IPC-Run-20231003.0... [pkg-builder.dan.net.uk] `-- Installing p5-IO-Tty-1.20... [pkg-builder.dan.net.uk] `-- Extracting p5-IO-Tty-1.20: ........ done [pkg-builder.dan.net.uk] Extracting p5-IPC-Run-20231003.0: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-IPC-Run>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-List-MoreUtils>=0 - not found ===> Installing existing package /packages/All/p5-List-MoreUtils-0.430.pkg [pkg-builder.dan.net.uk] Installing p5-List-MoreUtils-0.430... [pkg-builder.dan.net.uk] `-- Installing p5-Exporter-Tiny-1.006002... [pkg-builder.dan.net.uk] `-- Extracting p5-Exporter-Tiny-1.006002: .......... done [pkg-builder.dan.net.uk] `-- Installing p5-List-MoreUtils-XS-0.430... [pkg-builder.dan.net.uk] `-- Extracting p5-List-MoreUtils-XS-0.430: .... done [pkg-builder.dan.net.uk] Extracting p5-List-MoreUtils-0.430: ....... done ===> p5-BioPerl-1.007008 depends on package: p5-List-MoreUtils>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Module-Build>=0 - not found ===> Installing existing package /packages/All/p5-Module-Build-0.4234.pkg [pkg-builder.dan.net.uk] Installing p5-Module-Build-0.4234... [pkg-builder.dan.net.uk] Extracting p5-Module-Build-0.4234: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-Module-Build>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Set-Scalar>=0 - not found ===> Installing existing package /packages/All/p5-Set-Scalar-1.29.pkg [pkg-builder.dan.net.uk] Installing p5-Set-Scalar-1.29... [pkg-builder.dan.net.uk] Extracting p5-Set-Scalar-1.29: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-Set-Scalar>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Test-Most>=0 - not found ===> Installing existing package /packages/All/p5-Test-Most-0.38.pkg [pkg-builder.dan.net.uk] Installing p5-Test-Most-0.38... [pkg-builder.dan.net.uk] `-- Installing p5-Exception-Class-1.45... [pkg-builder.dan.net.uk] | `-- Installing p5-Class-Data-Inheritable-0.09... [pkg-builder.dan.net.uk] | `-- Extracting p5-Class-Data-Inheritable-0.09: ... done [pkg-builder.dan.net.uk] | `-- Installing p5-Devel-StackTrace-2.05... [pkg-builder.dan.net.uk] | `-- Extracting p5-Devel-StackTrace-2.05: ..... done [pkg-builder.dan.net.uk] `-- Extracting p5-Exception-Class-1.45: ..... done [pkg-builder.dan.net.uk] `-- Installing p5-Test-Deep-1.204... [pkg-builder.dan.net.uk] `-- Extracting p5-Test-Deep-1.204: .......... done [pkg-builder.dan.net.uk] `-- Installing p5-Test-Differences-0.650,1... [pkg-builder.dan.net.uk] | `-- Installing p5-Text-Diff-1.45... [pkg-builder.dan.net.uk] | | `-- Installing p5-Algorithm-Diff-1.1903... [pkg-builder.dan.net.uk] | | `-- Extracting p5-Algorithm-Diff-1.1903: ......... done [pkg-builder.dan.net.uk] | `-- Extracting p5-Text-Diff-1.45: ....... done [pkg-builder.dan.net.uk] `-- Extracting p5-Test-Differences-0.650,1: ... done [pkg-builder.dan.net.uk] `-- Installing p5-Test-Exception-0.43... [pkg-builder.dan.net.uk] | `-- Installing p5-Sub-Uplevel-0.2800... [pkg-builder.dan.net.uk] | `-- Extracting p5-Sub-Uplevel-0.2800: ... done [pkg-builder.dan.net.uk] `-- Extracting p5-Test-Exception-0.43: ... done [pkg-builder.dan.net.uk] `-- Installing p5-Test-Warn-0.37... [pkg-builder.dan.net.uk] `-- Extracting p5-Test-Warn-0.37: ... done [pkg-builder.dan.net.uk] Extracting p5-Test-Most-0.38: ..... done ===> p5-BioPerl-1.007008 depends on package: p5-Test-Most>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-Test-RequiresInternet>=0 - not found ===> Installing existing package /packages/All/p5-Test-RequiresInternet-0.05.pkg [pkg-builder.dan.net.uk] Installing p5-Test-RequiresInternet-0.05... [pkg-builder.dan.net.uk] Extracting p5-Test-RequiresInternet-0.05: ... done ===> p5-BioPerl-1.007008 depends on package: p5-Test-RequiresInternet>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-URI>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-DOM>=0 - not found ===> Installing existing package /packages/All/p5-XML-DOM-1.46.pkg [pkg-builder.dan.net.uk] Installing p5-XML-DOM-1.46... [pkg-builder.dan.net.uk] `-- Installing p5-XML-Parser-2.47... [pkg-builder.dan.net.uk] | `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] | `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting p5-XML-Parser-2.47: .......... done [pkg-builder.dan.net.uk] `-- Installing p5-XML-RegExp-0.04_1... [pkg-builder.dan.net.uk] `-- Extracting p5-XML-RegExp-0.04_1: ... done [pkg-builder.dan.net.uk] `-- Installing p5-libwww-6.70... [pkg-builder.dan.net.uk] | `-- Installing p5-Authen-NTLM-1.09_1... [pkg-builder.dan.net.uk] | | `-- Installing p5-Digest-HMAC-1.04... [pkg-builder.dan.net.uk] | | `-- Extracting p5-Digest-HMAC-1.04: ....... done [pkg-builder.dan.net.uk] | `-- Extracting p5-Authen-NTLM-1.09_1: ..... done [pkg-builder.dan.net.uk] | `-- Installing p5-File-Listing-6.16... [pkg-builder.dan.net.uk] | `-- Extracting p5-File-Listing-6.16: ... done [pkg-builder.dan.net.uk] | `-- Installing p5-HTML-Parser-3.81... [pkg-builder.dan.net.uk] | | `-- Installing p5-HTML-Tagset-3.20_1... [pkg-builder.dan.net.uk] | | `-- Extracting p5-HTML-Tagset-3.20_1: ... done [pkg-builder.dan.net.uk] | `-- Extracting p5-HTML-Parser-3.81: .......... done [pkg-builder.dan.net.uk] | `-- Installing p5-HTTP-CookieJar-0.014... [pkg-builder.dan.net.uk] | `-- Extracting p5-HTTP-CookieJar-0.014: ..... done [pkg-builder.dan.net.uk] | `-- Installing p5-HTTP-Cookies-6.11... [pkg-builder.dan.net.uk] | `-- Extracting p5-HTTP-Cookies-6.11: ....... done [pkg-builder.dan.net.uk] | `-- Installing p5-HTTP-Negotiate-6.01_1... [pkg-builder.dan.net.uk] | `-- Extracting p5-HTTP-Negotiate-6.01_1: ... done [pkg-builder.dan.net.uk] | `-- Installing p5-Net-HTTP-6.23... [pkg-builder.dan.net.uk] | | `-- Installing p5-IO-Socket-SSL-2.085... [pkg-builder.dan.net.uk] | | `-- Installing p5-IO-Socket-IP-0.42... [pkg-builder.dan.net.uk] | | `-- Extracting p5-IO-Socket-IP-0.42: ... done [pkg-builder.dan.net.uk] | | `-- Installing p5-Mozilla-CA-20231213... [pkg-builder.dan.net.uk] | | `-- Extracting p5-Mozilla-CA-20231213: .... done [pkg-builder.dan.net.uk] | | `-- Installing p5-Net-SSLeay-1.94... [pkg-builder.dan.net.uk] | | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting p5-Net-SSLeay-1.94: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting p5-IO-Socket-SSL-2.085: .......... done [pkg-builder.dan.net.uk] | `-- Extracting p5-Net-HTTP-6.23: ......... done [pkg-builder.dan.net.uk] | `-- Installing p5-Try-Tiny-0.31... [pkg-builder.dan.net.uk] | `-- Extracting p5-Try-Tiny-0.31: ... done [pkg-builder.dan.net.uk] | `-- Installing p5-WWW-RobotRules-6.02_1... [pkg-builder.dan.net.uk] | `-- Extracting p5-WWW-RobotRules-6.02_1: ..... done [pkg-builder.dan.net.uk] `-- Extracting p5-libwww-6.70: .......... done [pkg-builder.dan.net.uk] `-- Installing p5-libxml-0.08_1... [pkg-builder.dan.net.uk] `-- Extracting p5-libxml-0.08_1: .......... done [pkg-builder.dan.net.uk] Extracting p5-XML-DOM-1.46: .......... done ===> p5-BioPerl-1.007008 depends on package: p5-XML-DOM>=0 - found ===> Returning to build of p5-BioPerl-1.007008 ===> p5-BioPerl-1.007008 depends on package: p5-XML-LibXML>=0 - not found ===> Installing existing package /packages/All/p5-XML-LibXML-2.0210,1.pkg [pkg-builder.dan.net.uk] Installing p5-XML-LibXML-2.0210,1... [pkg-builder.dan.net.uk] `-- Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... 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Looks good Generating a Unix-style Makefile Writing Makefile for BioPerl Writing MYMETA.yml and MYMETA.json =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for p5-BioPerl-1.007008 cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm cp lib/Bio/Range.pm blib/lib/Bio/Range.pm cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp bin/bp_aacomp blib/script/bp_aacomp "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp cp bin/bp_bioflat_index blib/script/bp_bioflat_index "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index cp bin/bp_biogetseq blib/script/bp_biogetseq "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq cp bin/bp_dbsplit blib/script/bp_dbsplit "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq 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 cp bin/bp_fetch blib/script/bp_fetch "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch 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 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 cp bin/bp_gccalc blib/script/bp_gccalc "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 cp bin/bp_index blib/script/bp_index "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index 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 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 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 cp bin/bp_mrtrans blib/script/bp_mrtrans "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans cp bin/bp_mutate blib/script/bp_mutate "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate cp bin/bp_nexus2nh blib/script/bp_nexus2nh "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh cp bin/bp_nrdb blib/script/bp_nrdb "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb 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 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 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 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 cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks cp bin/bp_search2gff blib/script/bp_search2gff "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff cp bin/bp_search2table blib/script/bp_search2table "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe cp bin/bp_seq_length blib/script/bp_seq_length "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert cp bin/bp_seqcut blib/script/bp_seqcut "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut cp bin/bp_seqpart blib/script/bp_seqpart "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart cp bin/bp_seqret blib/script/bp_seqret "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret cp bin/bp_seqretsplit blib/script/bp_seqretsplit "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit 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 cp bin/bp_sreformat blib/script/bp_sreformat "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat cp bin/bp_taxid4species blib/script/bp_taxid4species "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree 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 cp bin/bp_tree2pag blib/script/bp_tree2pag "/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag 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 Manifying 40 pod documents Manifying 471 pod documents =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> p5-BioPerl-1.007008 depends on package: p5-Data-Stag>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Error>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Graph>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-HTTP-Message>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-IO-Stringy>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-List-MoreUtils>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Module-Build>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Set-Scalar>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Test-Most>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-Test-RequiresInternet>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-URI>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-DOM>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-LibXML>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-SAX>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-SAX-Base>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-SAX-Writer>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-XML-Writer>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-YAML>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-libwww>=0 - found ===> p5-BioPerl-1.007008 depends on package: p5-libxml>=0 - found ===> p5-BioPerl-1.007008 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for p5-BioPerl-1.007008 ===> Generating temporary packing list Manifying 40 pod documents Manifying 471 pod documents Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/BioPerl.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Range.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnnotatableI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Taxon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqUtils.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SimpleAlign.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/LocatableSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisResultI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/PrimarySeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/LocationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisParserI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DBLinkContainerI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Species.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/PrimarySeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/IdCollectionI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/UpdateableSeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/WebAgent.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DescribableI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationCollectionI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/ParameterBaseI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/IdentifiableI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/PullParserI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DasI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/RangeI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/FeatureHolderI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeatureI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqAnalysisParserI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SimpleAnalysisI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AnalysisI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/HandlerBaseI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/EncodedSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/RichSeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/RichSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/SeqFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/BaseSeqProcessor.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/LargePrimarySeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/PrimaryQual.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/MetaI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/SequenceTrace.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/LargeLocatableSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/SeqBuilder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/LargeSeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/LargeSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/SeqFastaSpeedFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/TraceI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/Quality.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/PrimedSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/Meta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/SimulatedRead.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/QualI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Seq/Meta/Array.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/NodeI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/AnnotatableNode.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/Node.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/RandomFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/TreeFunctionsI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/NodeNHX.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/Statistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/Tree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/TreeI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/DistanceFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tree/Compatible.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/DatabaseI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/SearchUtils.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/BlastStatistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/GenericStatistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/GenericDatabase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/StatisticsI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Processor.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/BlastUtils.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/WABAResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/ResultI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/BlastResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/ResultFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/BlastPullResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/GenericResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/INFERNALResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/CrossMatchResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Result/PullResultI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Iteration/IterationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Iteration/GenericIteration.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/HSPFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/PsiBlastHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/FastaHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/HSPI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/GenericHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/ModelHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/PSLHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/WABAHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/PullHSPI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/BlastHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/HSP/BlastPullHSP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Tiling/MapTiling.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Tiling/TilingI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Tiling/MapTileUtils.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/PsiBlastHit.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/HitFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/PullHitI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/BlastPullHit.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/Fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/GenericHit.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/HitI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/BlastHit.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Search/Hit/ModelHit.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/QueryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/FileCache.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/IndexedBase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Registry.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/ReferenceI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/LocationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/SeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/UpdateableSeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/RandomAccessI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/InMemoryCache.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/GenericWebAgent.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/DBFetch.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Qual.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/WebDBSeqI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Failover.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Query/WebQuery.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/GFF/Util/Rearrange.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/GFF/Util/Binning.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy/silva.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy/list.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy/greengenes.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Taxonomy/flatfile.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BDB.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BinarySearch.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BDB/swiss.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BDB/genbank.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BDB/fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/DB/Flat/BDB/embl.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/FuzzyLocationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/SplitLocationI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/Simple.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/CoordinatePolicyI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/WidestCoordPolicy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/NarrowestCoordPolicy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/Fuzzy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/Split.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/AvWithinCoordPolicy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Location/Atomic.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/AnnotationFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Comment.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Relation.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Collection.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/TypeManager.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/TagTree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/StructuredValue.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/DBLink.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/OntologyTerm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Reference.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Tree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/SimpleValue.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Annotation/Target.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/sim4.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/axt.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/wise.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/psl.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/gmap_f9.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/SearchWriterI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/SearchResultEventBuilder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/rnamotif.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/FastHitEventBuilder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/erpin.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/blasttable.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/blast_pull.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/IteratedSearchResultEventBuilder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/infernal.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/exonerate.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/waba.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/megablast.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/blast.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/cross_match.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/EventHandlerI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/HitTableWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/HSPTableWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/TextResultWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/GbrowseGFF.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/HTMLResultWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SearchIO/Writer/ResultTableWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/SequenceProcessorI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/DriverFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ApplicationFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/SequenceFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/FTLocationFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/SeqAnalysisParserFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/TreeFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ObjectFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ObjectFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/LocationFactoryI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/ObjectBuilderI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/SequenceStreamI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/AnalysisI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Factory/SeqAnalysisParserFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/fastq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/gbdriver.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/raw.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/scf.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/tigr.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/MultiFile.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/seqxml.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/tigrxml.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/metafasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/mbsout.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/table.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/msout.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/kegg.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/locuslink.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/swiss.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/gbxml.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/FTHelper.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/gcg.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/bsml.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/phd.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/largefasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/swissdriver.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/bsml_sax.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/pir.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/qual.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/asciitree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/genbank.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/tab.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/embldriver.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/ace.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/embl.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/tinyseq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game/gameSubs.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game/seqHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game/featHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game/gameWriter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/game/gameHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/tinyseq/tinyseqHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqIO/Handler/GenericRichSeqHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/CodonUsage/Table.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/CodonUsage/IO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Root.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Test.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Exception.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Version.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Storable.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/TestObject.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/RootI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/Utilities.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/IO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Root/HTTPget.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/ProteinStatistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/PairwiseStatistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/AlignI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/DNAStatistics.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/StatisticsI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Align/Utilities.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Das/SegmentI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Das/FeatureTypeI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Seg.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/ipcress.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Genemark.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Geneid.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Tmhmm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Lucy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/OddCodes.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/GuessSeqFormat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/GFF.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/MZEF.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/FootPrinter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Genscan.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Est2Genome.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/ECnumber.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Promoterwise.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/EPCR.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/RandomDistFunctions.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Fgenesh.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/isPcr.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Genomewise.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/TandemRepeatsFinder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Profile.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/QRNA.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Grail.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Coil.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Glimmer.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/SeqStats.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/ESTScan.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/IUPAC.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Primer3.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/AmpliconSearch.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Signalp.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Pseudowise.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Eponine.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Match.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/PrositeScan.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/CodonTable.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/SeqPattern.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/tRNAscanSE.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Blat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Sigcleave.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Genewise.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/RepeatMasker.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/AnalysisResult.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Prints.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/pICalculator.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/TargetP.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/SeqWords.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/EMBOSS/Palindrome.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Primer/Pair.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Primer/AssessorI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Primer/Feature.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Primer/Assessor/Base.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Phylo/Molphy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Phylo/Gerp.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Phylo/Molphy/Result.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Phylo/Phylip/ProtDist.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Signalp/ExtendedSignalp.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Sim4/Results.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Sim4/Exon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Spidey/Results.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Spidey/Exon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Analysis/SimpleAnalysisBase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/SeqPattern/Backtranslate.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Alignment/Consed.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Alignment/Trim.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/AnalysisFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/GenericParameters.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/WrapperBase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/ParametersI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Analysis.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PhyloBase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Prediction/Gene.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Prediction/Exon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/MatrixI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/Scoring.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/Mlagan.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/Generic.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/IO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PhylipDist.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/IO/phylip.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/IO/mlagan.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/IO/scoring.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/ProtPsm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/InstanceSiteI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/PsmHeaderI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/PsmI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/SiteMatrixI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/SiteMatrix.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/ProtMatrix.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/PsmHeader.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/InstanceSite.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/Psm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO/psiblast.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO/masta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO/transfac.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO/meme.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Matrix/PSM/IO/mast.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/GOterm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/RelationshipI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/Path.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/RelationshipFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/TermI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/Ontology.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/Relationship.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/OntologyI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/OBOEngine.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/PathI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/InterProTerm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/Term.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/DocumentRegistry.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/SimpleOntologyEngine.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/TermFactory.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/OntologyStore.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/OntologyEngineI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/OBOterm.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/RelationshipType.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/goflat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/soflat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/simplehierarchy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/obo.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/InterProParser.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/dagflat.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/InterProHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/OntologyIO/Handlers/BaseSAXHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/AnnotationAdaptor.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Lite.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/PositionProxy.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Primer.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/CollectionI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/SimilarityPair.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Computation.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Collection.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Similarity.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Amplicon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/TypedSeqFeatureI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/FeaturePair.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Generic.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/SubSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/Promoter.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/GeneStructureI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/TranscriptI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/ExonI.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/Transcript.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/Poly_A_site.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/Intron.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/Exon.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/UTR.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/NC_Feature.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Gene/GeneStructure.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Tools/Unflattener.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Tools/TypeMapper.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Tools/IDHandler.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/SeqFeature/Tools/FeatureNamer.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/EMBL.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Swissprot.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/GenBank.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Abstract.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/BlastTable.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/SwissPfam.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Fastq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/AbstractSeq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Blast.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/Index/Qual.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/NewickParser.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/cluster.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/pag.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/phyloxml.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/nhx.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/tabtree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/TreeEventBuilder.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/newick.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/lintree.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO/nexus.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/emboss.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/bl2seq.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/clustalw.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/msf.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/mega.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/arp.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/metafasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/phylip.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/maf.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/mase.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/po.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/proda.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/xmfa.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/fasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/prodom.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/meme.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/selex.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/largemultifasta.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/psi.pm Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/Bio/AlignIO/nexus.pm 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_process_sgd.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_oligo_count.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_fastam9_to_table.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_sreformat.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_make_mrna_protein.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqret.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_extract_feature_seq.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqpart.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_tree2pag.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2alnblocks.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_nrdb.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2gff.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_fetch.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_index.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqretsplit.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2tribe.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_bioflat_index.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seq_length.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_biogetseq.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqcut.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_find-blast-matches.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_taxid4species.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_revtrans-motif.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2table.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_mutate.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_process_gadfly.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_nexus2nh.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_translate_seq.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_mrtrans.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_local_taxonomydb_query.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_aacomp.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_filter_search.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_gccalc.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_unflatten_seq.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_mask_by_search.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqconvert.1 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::RepeatMasker.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::RelationshipType.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::GFF::Util::Binning.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BDB::fasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::fasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::Transcript.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::qual.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Iteration::GenericIteration.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::MultiFile.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Fgenesh.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::DBFetch.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::GenericStatistics.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::PrimarySeqI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Phylo::Gerp.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::wise.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::ProtPsm.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::Writer::GbrowseGFF.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::Fastq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::embl.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::Promoter.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::Tree.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::mase.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::GeneStructureI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::infernal.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BDB::genbank.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::OntologyTerm.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::SeqFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::SeqBuilder.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Profile.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::CollectionI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Tools::TypeMapper.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::CodonTable.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::SearchUtils.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::WrapperBase::CommandExts.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::SimulatedRead.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::Tree.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Taxonomy::list.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AnalysisResultI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Genemark.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Sim4::Exon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::Utilities.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AnnotationI.3 Installing 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::GenericResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Prints.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Utilities.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::lintree.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO::InterProParser.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::blast.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::IO::mast.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::PrimarySeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::MetaI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::Comment.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::SeqStats.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::UTR.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Exception.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::exonerate.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::LocationI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Query::WebQuery.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::GenericParameters.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::game::seqHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::UpdateableSeqI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::GenericHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::rnamotif.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::metafasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::pag.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::OBOEngine.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::SiteMatrixI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::DriverFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::Path.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::TypeManager.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::gmap_f9.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::HSPI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::PullParserI.3 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::SiteMatrix.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::TermI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqUtils.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Spidey::Exon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::IdCollectionI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Qual.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Species.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::StructuredValue.3 Installing 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::SubSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::clustalw.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::gcg.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::GFF::Util::Rearrange.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::Handler::GenericRichSeqHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Fasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::PSLHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Version.3 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::megablast.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Computation.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::table.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::GFF.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Promoterwise.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::game::gameHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::Meta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::BlastResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::InterProTerm.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::Term.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::tinyseq::tinyseqHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::SimilarityPair.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Grail.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Signalp::ExtendedSignalp.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::BlastStatistics.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::IO::phylip.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::CodonUsage::IO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::bsml_sax.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::StatisticsI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::GenericHit.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO::obo.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::mega.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::Writer::HitTableWriter.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::EventHandlerI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Pseudowise.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::RichSeqI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::MZEF.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::BlastPullResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::SearchWriterI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Phylo::Molphy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::bsml.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::PullHitI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::WrapperBase.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::BlastPullHit.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::PathI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::Handler::GenericAlignHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::StatisticsI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::GOterm.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BDB::embl.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::PrimedSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Eponine.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::OddCodes.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::PsiBlastHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Tools::FeatureNamer.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::TandemRepeatsFinder.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::proda.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::HitFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::TranscriptI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Lite.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::Compatible.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::IteratedSearchResultEventBuilder.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::RangeI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::Fuzzy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::pir.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::psi.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Tiling::TilingI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::cluster.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::seqxml.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::cross_match.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Tools::Unflattener.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::gbxml.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::tabtree.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::Exon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::TypedSeqFeatureI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::InstanceSite.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::ECnumber.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Amplicon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::CrossMatchResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::HandlerBaseI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Test.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::AvWithinCoordPolicy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::game::featHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::PositionProxy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::Writer::TextResultWriter.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::INFERNALResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::tab.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::sim4.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::DBLink.3 Installing 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::EncodedSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::pfam.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::IdentifiableI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::RootI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Analysis.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::BlastPullHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::BlastHit.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::AmpliconSearch.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::SeqFastaSpeedFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::genbank.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::ModelHit.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::WABAHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Root.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::OntologyStore.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Similarity.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::DatabaseI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::TermFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Alignment::Trim.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::metafasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::TreeFactoryI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::swissdriver.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::game.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DBLinkContainerI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::DNAStatistics.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::TraceI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Primer::Assessor::Base.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Prediction::Exon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::SeqPattern.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::IO::masta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::Abstract.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Coil.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Analysis::SimpleAnalysisBase.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::tigr.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::EMBOSS::Palindrome.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Event::EventGeneratorI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::EMBL.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::blasttable.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::nexus.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO::Handlers::BaseSAXHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::CoordinatePolicyI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::Atomic.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::phyloxml.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::SimpleOntologyEngine.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::maf.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::ObjectFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::raw.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Glimmer.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::PrimaryQual.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::ace.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO::simplehierarchy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BinarySearch.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::tinyseq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::GenericDatabase.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::AnnotationFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::InstanceSiteI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::erpin.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::prodom.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::FootPrinter.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::QueryI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::NarrowestCoordPolicy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Tools::IDHandler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::ESTScan.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Primer::Pair.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Alignment::Consed.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::Node.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::Quality.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::psl.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::Storable.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::HTTPget.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::nexus.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::HSPFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::Meta::Array.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::Generic.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::QRNA.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BDB::swiss.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::tigrxml.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Hit::PsiBlastHit.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::SeqWords.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::ModelHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::SequenceTrace.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::LargePrimarySeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SimpleAnalysisI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Primer.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::WebAgent.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::arp.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::GeneStructure.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::Swissprot.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::GuessSeqFormat.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::WidestCoordPolicy.3 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::FastHitEventBuilder.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::isPcr.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::Qual.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::AnalysisResult.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::SeqAnalysisParserFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Primer::AssessorI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Taxonomy::flatfile.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::OBOterm.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::PullHSPI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::ProtMatrix.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Taxonomy::silva.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Event::EventHandlerI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::AnnotatableNode.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::ParametersI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::msf.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::Simple.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::selex.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Generic.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::NC_Feature.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::HSP::BlastHSP.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::Gene::ExonI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::TreeFunctionsI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::LargeLocatableSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Signalp.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Registry.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Taxon.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::AnalysisI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::IO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::pICalculator.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::SplitLocationI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqFeature::FeaturePair.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::blast_pull.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::largefasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::OntologyI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Primer::Feature.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::Ontology.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Location::FuzzyLocationI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::TreeIO::newick.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::LargeSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::PrositeScan.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::locuslink.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::IO::mlagan.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Processor.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::TreeI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::SearchResultEventBuilder.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Sigcleave.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::SequenceStreamI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Prediction::Gene.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Tiling::MapTileUtils.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::IO::scoring.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::largemultifasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::PairwiseStatistics.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Ontology::DocumentRegistry.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::phylip.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::Reference.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::LocationI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::FTLocationFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::SeqPattern::Backtranslate.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tree::DistanceFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Das::FeatureTypeI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::Target.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::EPCR.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::LargeSeqI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::emboss.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::PsmHeader.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Matrix::PSM::IO::meme.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Index::SwissPfam.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SearchIO::fasta.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::ResultFactory.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::xmfa.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Annotation::Collection.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Root::IO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::OntologyIO.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::SeqIO::game::gameWriter.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::AlignIO::meme.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Search::Result::ResultI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Lucy.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Seq::RichSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::ProteinStatistics.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Failover.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::UpdateableSeqI.3 Installing 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/wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::Flat::BDB.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Align::AlignI.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::CodonUsage::Table.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::LocatableSeq.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::FileCache.3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_local_taxonomydb_query Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_nrdb Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_taxid4species Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_search2tribe Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_taxonomy2tree Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_sreformat Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_mrtrans Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_extract_feature_seq Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seqcut Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_mask_by_search Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_index Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_process_gadfly Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_biogetseq Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_search2alnblocks Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_gccalc Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_process_sgd Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_translate_seq Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seqret Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_find-blast-matches Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_make_mrna_protein Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seq_length Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_split_seq Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_genbank2gff3 Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_nexus2nh Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seqconvert Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_revtrans-motif Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seqpart Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_tree2pag Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_search2table Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_search2gff Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_dbsplit Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_mutate Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_fastam9_to_table Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_oligo_count Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_fetch Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_bioflat_index Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_unflatten_seq Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_aacomp Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_filter_search Installing /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/bin/bp_seqretsplit cd /wrkdirs/usr/ports/biology/p5-BioPerl/work/BioPerl-1.7.8 && install -m 0644 AUTHORS Changes MANIFEST README.md /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/share/doc/BioPerl cd /wrkdirs/usr/ports/biology/p5-BioPerl/work/BioPerl-1.7.8/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 . /wrkdirs/usr/ports/biology/p5-BioPerl/work/stage/usr/local/share/examples/BioPerl ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-27T14:41:23+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=0567b2de2c' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for p5-BioPerl-1.007008 ===> Building p5-BioPerl-1.007008 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for p5-BioPerl-1.007008 build of biology/p5-BioPerl | p5-BioPerl-1.007008 ended at Wed Mar 27 14:41:56 GMT 2024 build time: 00:00:34