Tue Jan 28 19:12:14 UTC 2025 I: starting to build ruby-bio/trixie/arm64 on jenkins on '2025-01-28 19:11' Tue Jan 28 19:12:14 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/77287/console.log Tue Jan 28 19:12:14 UTC 2025 I: Downloading source for trixie/ruby-bio=2.0.5-1 --2025-01-28 19:12:14-- http://deb.debian.org/debian/pool/main/r/ruby-bio/ruby-bio_2.0.5-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2108 (2.1K) [text/prs.lines.tag] Saving to: ‘ruby-bio_2.0.5-1.dsc’ 0K .. 100% 264M=0s 2025-01-28 19:12:14 (264 MB/s) - ‘ruby-bio_2.0.5-1.dsc’ saved [2108/2108] Tue Jan 28 19:12:14 UTC 2025 I: ruby-bio_2.0.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.5-1 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Nilesh Patra Homepage: https://bioruby.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-bio Vcs-Git: https://salsa.debian.org/ruby-team/ruby-bio.git Testsuite: autopkgtest-pkg-ruby Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Package-List: ruby-bio deb ruby optional arch=all Checksums-Sha1: c5eafc8420a966903759ca1971b56b977d5c19b7 1403239 ruby-bio_2.0.5.orig.tar.gz f481b14185f8a52163cead283563fa8287e4e32f 14388 ruby-bio_2.0.5-1.debian.tar.xz Checksums-Sha256: 9f66cc728e61a0608cba24ccbee03a5c4fd08e8b6a51cd65b608e6a1d6389b1d 1403239 ruby-bio_2.0.5.orig.tar.gz e012d4a27cd47da374f43f35c775f541b645badbb2feeda94836f628534a5086 14388 ruby-bio_2.0.5-1.debian.tar.xz Files: 76215231a9bb1d93a22a0eba24647886 1403239 ruby-bio_2.0.5.orig.tar.gz 9d2401ccde190177cc92465890847141 14388 ruby-bio_2.0.5-1.debian.tar.xz Ruby-Versions: all -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE/t7ByzN7z1CfQ8IkORS1MvTfvpkFAmXkefUACgkQORS1MvTf vpmcDhAAnrwI3Wbj3eGvkYew5UH6Rgau+ritM1SzyzaMftoOhT/RmN96MlWK8I0t BIPwqtsz8QxIcgNtMVqV6TsDz3Cwgkv2ffudm9z6jvnYyJar83HHOnot7hSTWdgU FhxDIpCHnn3G+FHd8KNCfLwlizy/TWhIHVM355FL7wuw3ddzEQmsidn2s+lf44Qj f6dOhvjRspWshnnCUUzcGLpv5a+m2aVZDdjGangK3qjOI30TfoVKwfp7ZwXr2A7H WlNEgz04WE4s1O1dXjfU9l1YWpZ+4qRSr6EpAYpOJS/9uBsLgbj36VE4GHraCHxJ V9YDjfiwdiXARaJ1T2RuvVfbGwOtcM90r44jIyaJrcMJQIy2krKEg8v7t7yVgEHV hEfz5J7JIli77uqPxA37WaD10GzUykY65TKvLhvt27ZheMbS4k8JZ5zS+OfZC8F/ lhk7TSimAOS3mVAbkNEy3cPX3ue7J5H8h0VhOPSDpNAkFyoIV2V6bcnuBccGHjX8 v68T8yJLKMtxJkh9VMlcHtgI9Zg2VK93qZ7rEC0FKXlRzjqYscbD43rqevJumbeG ZFiKNbCngp/cWxNFrTLKEP9eqt8+22In+7qq6aFDqUMjcTB5Yo8MrHtRLNtN/BJa Xvnzdh2UtKaG9vYNrB1AaknU7Knq6sInvVdenAePLpdqCrA4+bY= =z+Qe -----END PGP SIGNATURE----- Tue Jan 28 19:12:14 UTC 2025 I: Checking whether the package is not for us Tue Jan 28 19:12:14 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Jan 28 19:12:14 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Jan 28 19:13:37 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 2 13:35:16 -12 2026 I: pbuilder-time-stamp: 1772501716 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ruby-bio_2.0.5-1.dsc] I: copying [./ruby-bio_2.0.5.orig.tar.gz] I: copying [./ruby-bio_2.0.5-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.5-1.dsc: unsupported subcommand dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.5 dpkg-source: info: unpacking ruby-bio_2.0.5.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable_tests_using_chi2.patch dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1784902/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5019db9ac7694fdb96c71d46568d86bc' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1784902' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/pbuilderrc_b1jX --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/b1 --logfile b1/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1784902/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} gpgv{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libb-hooks-op-check-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgcrypt20{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls30t64{a} libgpg-error0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap2{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libp11-kit0{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libruby3.3{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-quote-perl{a} libtasn1-6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} ruby3.3{a} ruby3.3-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} sopv-gpgv{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato gnupg-utils gpg-wks-client libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpg-error-l10n libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc ruby3.3-doc strace unzip wget zip 0 packages upgraded, 143 newly installed, 0 to remove and 0 not upgraded. Need to get 55.6 MB of archives. After unpacking 228 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libassuan9 arm64 3.0.1-2 [58.1 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 gpgconf arm64 2.2.46-1+b1 [115 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libnpth0t64 arm64 1.8-2 [22.8 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 dirmngr arm64 2.2.46-1+b1 [344 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 gpg arm64 2.2.46-1+b1 [481 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 gpg-agent arm64 2.2.46-1+b1 [231 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 gpgsm arm64 2.2.46-1+b1 [232 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 gnupg all 2.2.46-1 [376 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 gpgv arm64 2.2.46-1+b1 [200 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 74 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 102 http://deb.debian.org/debian trixie/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 wdiff arm64 1.2.2-7 [121 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 devscripts all 2.25.1 [1053 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 docbook all 4.5-11 [126 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libosp5 arm64 1.5.2-15.1 [922 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 opensp arm64 1.5.2-15.1 [441 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 docbook-to-man arm64 1:2.0.0-47+b1 [71.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.19 [5488 B] Get: 119 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libruby3.3 arm64 3.3.6-1.1 [6110 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+support3.3 [4888 B] Get: 125 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b6 [17.9 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.5 [5267 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.5 [664 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+support3.3 [5944 B] Get: 132 http://deb.debian.org/debian trixie/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 gem2deb-test-runner arm64 2.2.5 [17.9 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 ruby3.1-dev arm64 3.1.2-8.5 [1007 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 ruby3.3 arm64 3.3.6-1.1 [820 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 ruby3.3-dev arm64 3.3.6-1.1 [1030 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 ruby-all-dev arm64 1:3.1+support3.3 [5976 B] Get: 140 http://deb.debian.org/debian trixie/main arm64 gem2deb arm64 2.2.5 [48.0 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 ruby-libxml arm64 5.0.3-1+b2 [95.7 kB] Fetched 55.6 MB in 0s (169 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_arm64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:arm64 (3.13.1-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20303 files and directories currently installed.) 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../027-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../034-libgpg-error0_1.51-3_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-3) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../035-libassuan9_3.0.1-2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.1-2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../036-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../037-gpgconf_2.2.46-1+b1_arm64.deb ... Unpacking gpgconf (2.2.46-1+b1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../038-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../039-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../040-libtasn1-6_4.19.0-3+b3_arm64.deb ... Unpacking libtasn1-6:arm64 (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../041-libgnutls30t64_3.8.8-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.8-2) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../042-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../043-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../044-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../045-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../046-libnpth0t64_1.8-2_arm64.deb ... Unpacking libnpth0t64:arm64 (1.8-2) ... Selecting previously unselected package dirmngr. Preparing to unpack .../047-dirmngr_2.2.46-1+b1_arm64.deb ... Unpacking dirmngr (2.2.46-1+b1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../048-gnupg-l10n_2.2.46-1_all.deb ... Unpacking gnupg-l10n (2.2.46-1) ... Selecting previously unselected package gpg. Preparing to unpack .../049-gpg_2.2.46-1+b1_arm64.deb ... Unpacking gpg (2.2.46-1+b1) ... 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Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../062-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../063-libclass-xsaccessor-perl_1.19-4+b4_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b4) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../064-libb-hooks-op-check-perl_0.22-3+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../065-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../066-libdevel-callchecker-perl_0.009-1+b1_arm64.deb ... 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Unpacking libnet-ssleay-perl:arm64 (1.94-2) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../089-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../090-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../091-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../092-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../093-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. 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Setting up libgpg-error0:arm64 (1.51-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up libosp5 (1.5.2-15.1) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Mar 3 01:35:39 UTC 2026. Universal Time is now: Tue Mar 3 01:35:39 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up gnupg-l10n (2.2.46-1) ... Setting up libncurses6:arm64 (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-1) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up gpgv (2.2.46-1+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.4.0-2) ... Setting up readline-common (8.2-6) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:arm64 (1.94-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.5.4-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up opensp (1.5.2-15.1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.46-1+b1) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.46-1+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up gpgsm (2.2.46-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up rubygems-integration (1.19) ... Setting up sopv-gpgv (0.1.1-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.46-1+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gnupg (2.2.46-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.23) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libruby:arm64 (1:3.1+support3.3) ... Setting up libwww-perl (6.77-1) ... Setting up ruby (1:3.1+support3.3) ... Setting up devscripts (2.25.1) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b6) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:arm64 (3.1.2-8.5) ... Setting up ruby3.1 (3.1.2-8.5) ... Setting up ruby3.1-dev:arm64 (3.1.2-8.5) ... Setting up ruby-libxml:arm64 (5.0.3-1+b2) ... Setting up libruby3.3:arm64 (3.3.6-1.1) ... Setting up gem2deb-test-runner (2.2.5) ... Setting up ruby3.3-dev:arm64 (3.3.6-1.1) ... Setting up ruby3.3 (3.3.6-1.1) ... Setting up ruby-all-dev:arm64 (1:3.1+support3.3) ... Setting up gem2deb (2.2.5) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-47+b1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lucas Nussbaum dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.5.gemspec /usr/bin/ruby3.1 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.1 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.1.0:/var/lib/gems/3.1.0:/usr/local/lib/ruby/gems/3.1.0:/usr/lib/ruby/gems/3.1.0:/usr/lib/aarch64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000463) test_dbs: .: (0.000130) test_go_ids: .: (0.000106) test_go_terms: .: (0.000106) test_parser: .: (0.000261) test_set_date: .: (0.000120) test_set_desc: .: (0.000098) test_to_str: .: (0.000205) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.004809) test_mktmpdir_without_block: .: (0.000431) test_remove_entry_secure: .: (0.000515) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.022084) test_call_command_fork: .: (0.000135) test_call_command_open3: .: (0.039632) test_call_command_popen: .: (0.008006) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.012056) test_call_command_fork: .: (0.000258) test_call_command_open3: .: (0.035062) test_call_command_popen: .: (0.028175) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.019632) test_call_command_fork: .: (0.000827) test_call_command_open3: .: (0.042694) test_call_command_popen: .: (0.027866) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.015642) test_call_command_fork_chdir: .: (0.000441) test_call_command_popen_chdir: .: (0.015157) test_query_command_chdir: .: (0.015765) test_query_command_fork_chdir: .: (0.000393) test_query_command_popen_chdir: .: (0.015212) Bio::FuncTestCommandQuery: test_query_command: .: (0.055548) test_query_command_fork: .: (0.012182) test_query_command_open3: .: (0.055276) test_query_command_popen: .: (0.051901) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000913) test_initialize: .: (0.000460) test_path: .: (0.000345) test_path_after_close: .: (0.000526) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.017391) test_output_fasta: .: (0.078952) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.006854) test_accession: .: (0.000371) test_accessions: .: (0.000313) test_comment: .: (0.000248) test_common_name: .: (0.000286) test_definition: .: (0.000673) test_features: .: (0.000399) test_gi: .: (0.000225) test_keywords: .: (0.000244) test_locus: .: (0.000163) test_nid: .: (0.000265) test_organism: .: (0.000248) test_origin: .: (0.000224) test_references: .: (0.001391) test_segment: .: (0.000235) test_source: .: (0.000368) test_taxonomy: .: (0.000251) test_version: .: (0.000230) test_versions: .: (0.000247) Bio::TestAA: test_13: .: (0.000301) test_1n: .: (0.000142) test_name2one: .: (0.000192) test_name2three: .: (0.000176) test_one2name: .: (0.000398) test_one2three: .: (0.000495) test_three2name: .: (0.000162) test_three2one: .: (0.000281) test_to_1_1: .: (0.000152) test_to_1_3: .: (0.000187) test_to_1_name: .: (0.000174) test_to_3_1: .: (0.000142) test_to_3_3: .: (0.000126) test_to_3_name: .: (0.000167) test_to_re: .: (0.000196) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000281) Bio::TestAAindex: test_api: .: (0.000215) test_auto_aax1: .: (0.000339) test_auto_aax2: .: (0.000294) Bio::TestAAindex1: test_author: .: (0.000812) test_comment: .: (0.000298) test_correlation_coefficient: .: (0.000509) test_dblinks: .: (0.000313) test_definition: .: (0.000323) test_entry_id: .: (0.006709) test_index: .: (0.000509) test_journal: .: (0.000358) test_title: .: (0.000278) Bio::TestAAindex2: test_access_A_R: .: (0.000909) test_access_R_A: .: (0.000624) test_author: .: (0.000284) test_cols: .: (0.000628) test_comment: .: (0.000401) test_dblinks: .: (0.000271) test_definition: .: (0.000291) test_entry_id: .: (0.000286) test_journal: .: (0.000358) test_matrix: .: (0.000702) test_matrix_1_2: .: (0.000855) test_matrix_2_2: .: (0.000484) test_matrix_A_R: .: (0.000393) test_matrix_R_A: .: (0.000737) test_matrix_determinant: .: (0.003329) test_matrix_rank: .: (0.002817) test_matrix_transpose: .: (0.000845) test_rows: .: (0.000318) test_title: .: (0.000313) Bio::TestAAindexConstant: test_delimiter: .: (0.000496) test_tagsize: .: (0.000142) Bio::TestAbif: test_complement: .: (0.006578) test_seq: .: (0.006210) test_to_biosequence: .: (0.006657) Bio::TestActsLikeMap: test_mixin: .: (0.000444) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000467) Bio::TestActsLikeMarker: test_mixin: .: (0.000354) Bio::TestAlignment: test_add_seq_no_key: .: (0.000514) test_add_seq_using_seq_with_aaseq_method: .: (0.000220) test_add_seq_using_seq_with_definition_method: .: (0.000164) test_add_seq_using_seq_with_entry_id_method: .: (0.000210) test_add_seq_using_seq_with_naseq_method: .: (0.000185) test_add_seq_using_seq_with_seq_method: .: (0.000237) test_consensus_iupac_gap_modes: .: (0.000471) test_consensus_iupac_missing_char: .: (0.000228) test_consensus_iupac_missing_char_option: .: (0.000213) test_consensus_iupac_no_gaps: .: (0.000169) test_consensus_iupac_of_ambiguous_bases: .: (0.000221) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.003005) test_consensus_opt_gap_mode: .: (0.000547) test_consensus_opt_missing_char: .: (0.000267) test_consensus_string_no_gaps: .: (0.000265) test_consensus_threshold_four_sequences: .: (0.000390) test_consensus_threshold_two_sequences: .: (0.000414) test_convert_match: .: (0.000297) test_convert_unmatch: .: (0.000245) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000199) test_convert_unmatch_different_match_char: .: (0.000241) test_convert_unmatch_multiple_sequences: .: (0.000265) test_default_gap_char: .: (0.000133) test_default_gap_regexp_matches_default_gap_char: .: (0.000158) test_default_missing_char: .: (0.000198) test_each_site_equal_length: .: (0.000225) test_each_site_unequal_length: .: (0.000264) test_equals: .: (0.000301) test_match_line_protein: .: (0.000535) test_normalizebang_extends_sequences_with_gaps: .: (0.000210) test_seq_length_is_max_seq_length: .: (0.000168) test_seq_length_when_one_sequence: .: (0.000204) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000166) test_seqclass_when_seqclass_set: .: (0.000152) test_seqclass_when_sequence_used: .: (0.000219) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000179) test_set_and_get_gap_char: .: (0.000177) test_store_cannot_override_key: .: (0.000154) test_store_with_default_keys_and_user_defined_keys: .: (0.000181) test_store_with_nil_key_uses_next_number_for_key: .: (0.000151) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000376) test_alignment_concat: .: (0.000206) test_alignment_length: .: (0.000203) test_alignment_lstrip!: .: (0.000230) test_alignment_lstrip_nil: .: (0.000213) test_alignment_normalize!: .: (0.000176) test_alignment_rstrip!: .: (0.000281) test_alignment_rstrip_nil: .: (0.000261) test_alignment_site: .: (0.000168) test_alignment_slice: .: (0.000161) test_alignment_strip!: .: (0.000297) test_alignment_strip_nil: .: (0.000213) test_alignment_subseq: .: (0.000279) test_alignment_window: .: (0.000192) test_collect_each_site: .: (0.000178) test_consensus_each_site_default: .: (0.000208) test_consensus_each_site_gap_mode_1: .: (0.000213) test_consensus_each_site_gap_mode_minus1: .: (0.000211) test_consensus_iupac: .: (0.000374) test_consensus_string_default: .: (0.000207) test_consensus_string_half: .: (0.000192) test_convert_match: .: (0.000172) test_convert_unmatch: .: (0.000218) test_each_seq: .: (0.000158) test_each_site: .: (0.000273) test_each_site_step: .: (0.000182) test_each_window: .: (0.000273) test_match_line: .: (0.000768) test_match_line_amino: .: (0.001058) test_match_line_nuc: .: (0.000248) test_private_alignment_site: .: (0.000162) test_remove_all_gaps!: .: (0.000191) test_seqclass: .: (0.000166) test_seqclass=: .: (0.000237) test_seqclass_default: .: (0.000130) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002895) test_determine_seq_method: .: (0.001621) test_entries: .: (0.000519) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000406) test_avoid_same_name_numbering: .: (0.000219) test_clustal_have_same_name_true: .: (0.000178) test_have_same_name_false: .: (0.000221) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000342) test_gap_char_default: .: (0.000223) test_gap_char_never_nil: .: (0.000152) test_gap_regexp: .: (0.000177) test_gap_regexp=: .: (0.000182) test_gap_regexp_never_nil: .: (0.000149) test_get_all_property_default: .: (0.000157) test_get_all_property_nodefault: .: (0.000172) test_is_gap_default_false: .: (0.000180) test_is_gap_default_true: .: (0.000220) test_is_gap_nodefault_false: .: (0.000162) test_is_gap_nodefault_true: .: (0.000153) test_missing_char=: .: (0.000229) test_missing_char_default: .: (0.000170) test_missing_char_never_nil: .: (0.000159) test_seqclass=: .: (0.000175) test_seqclass_default: .: (0.000169) test_seqclass_never_nil: .: (0.000228) test_set_all_property: .: (0.000211) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000629) test_consensus_string_50percent: .: (0.000170) test_consensus_string_50percent_nil: .: (0.000209) test_consensus_string_default: .: (0.000155) test_consensus_string_default_nil: .: (0.000144) test_has_gap_false: .: (0.000211) test_has_gap_true: .: (0.000142) test_match_line_amino_100percent: .: (0.000222) test_match_line_amino_missing: .: (0.000304) test_match_line_amino_strong: .: (0.000195) test_match_line_amino_weak: .: (0.000271) test_match_line_nuc_100percent: .: (0.000196) test_match_line_nuc_missing: .: (0.000229) test_remove_gaps!: .: (0.000172) test_remove_gaps_bang_not_removed: .: (0.000137) Bio::TestAtomFinder: test_atoms: .: (0.013266) test_each_atom: .: (0.000367) test_find_atom: .: (0.000297) Bio::TestBioFastaDefline: test_acc_version: .: (0.000567) test_accession: .: (0.000598) test_accessions: .: (0.000477) test_description: .: (0.000398) test_descriptions: .: (0.000392) test_entry_id: .: (0.000351) test_get: .: (0.000426) test_get_all_by_type: .: (0.000318) test_get_by_type: .: (0.000384) test_gi: .: (0.000329) test_id_strings: .: (0.000646) test_locus: .: (0.007157) test_method_missing: .: (0.000461) test_to_s: .: (0.000373) test_words: .: (0.001020) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000927) test_goid2term: .: (0.000461) test_parse_goids: .: (0.000449) Bio::TestBioGenBank: test_basecount: .: (0.000834) test_circular: .: (0.000429) test_classification: .: (0.000437) test_date: .: (0.000388) test_date_modified: .: (0.000813) test_division: .: (0.000384) test_each_cds_feature: .: (0.001019) test_each_cds_qualifiers: .: (0.000761) test_each_gene: .: (0.001008) test_entry_id: .: (0.000397) test_length: .: (0.000380) test_locus_circular: .: (0.000427) test_locus_class: .: (0.000386) test_locus_date: .: (0.000355) test_locus_division: .: (0.000404) test_locus_entry_id: .: (0.000359) test_locus_length: .: (0.000385) test_locus_natype: .: (0.000456) test_locus_strand: .: (0.000340) test_natype: .: (0.000329) test_seq: .: (0.000401) test_seq_len: .: (0.000421) test_strand: .: (0.000375) test_strandedness: .: (0.000370) test_to_biosequence: .: (0.002071) Bio::TestBioGenPept: test_circular: .: (0.000811) test_date: .: (0.000442) test_dbsource: .: (0.000269) test_division: .: (0.000271) test_entry_id: .: (0.000261) test_length: .: (0.000262) test_locus: .: (0.000285) test_seq: .: (0.000304) test_seq_len: .: (0.000300) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000734) test_aaseq: .: (0.000347) test_chromosome: .: (0.000304) test_codon_usage: .: (0.000415) test_cu_list: .: (0.000278) test_dblinks_as_hash: .: (0.000326) test_dblinks_as_strings: .: (0.000293) test_definition: .: (0.000322) test_division: .: (0.000500) test_eclinks: .: (0.000345) test_entry: .: (0.000268) test_entry_id: .: (0.000287) test_gbposition: .: (0.000291) test_gene: .: (0.000311) test_genes: .: (0.000288) test_keggclass: .: (0.000347) test_keggclasses: .: (0.000357) test_locations: .: (0.000603) test_motifs_as_hash: .: (0.000368) test_motifs_as_strings: .: (0.000275) test_name: .: (0.000280) test_names_as_array: .: (0.000295) test_new: .: (0.000292) test_ntlen: .: (0.000343) test_ntseq: .: (0.000363) test_organism: .: (0.000423) test_orthologs_as_hash: .: (0.000344) test_orthologs_as_strings: .: (0.000292) test_pathway: .: (0.000299) test_pathway_after_pathways_as_strings: .: (0.000337) test_pathway_before_pathways_as_strings: .: (0.000317) test_pathways_as_hash: .: (0.000309) test_pathways_as_strings: .: (0.000305) test_position: .: (0.000276) test_structure: .: (0.000378) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000980) test_comment: .: (0.000453) test_data_source: .: (0.000375) test_definition: .: (0.000409) test_disease: .: (0.000384) test_entry_id: .: (0.000406) test_lineage: .: (0.000459) test_nalen: .: (0.000389) test_name: .: (0.000388) test_new: .: (0.000383) test_num_gene: .: (0.000370) test_num_rna: .: (0.000375) test_original_databases: .: (0.000428) test_original_db: .: (0.000453) test_plasmids: .: (0.000382) test_references: .: (0.001970) test_statistics: .: (0.000436) test_taxid: .: (0.000462) test_taxonomy: .: (0.000485) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000549) test_comment: .: (0.000435) test_data_source: .: (0.000327) test_definition: .: (0.000301) test_disease: .: (0.000300) test_entry_id: .: (0.000359) test_lineage: .: (0.000327) test_nalen: .: (0.000297) test_name: .: (0.000297) test_new: .: (0.000358) test_num_gene: .: (0.000310) test_num_rna: .: (0.000266) test_original_databases: .: (0.000302) test_original_db: .: (0.000283) test_plasmids: .: (0.000415) test_references: .: (0.000434) test_statistics: .: (0.000289) test_taxid: .: (0.000402) test_taxonomy: .: (0.000336) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000516) test_compounds_as_strings: .: (0.000273) test_dblinks_as_hash: .: (0.000286) test_dblinks_as_strings: .: (0.000254) test_description: .: (0.000283) test_diseases_as_hash: .: (0.000249) test_diseases_as_strings: .: (0.000262) test_entry_id: .: (0.000279) test_enzymes_as_strings: .: (0.000397) test_genes_as_hash: .: (0.000233) test_genes_as_strings: .: (0.000244) test_keggclass: .: (0.000257) test_ko_pathway: .: (0.000246) test_modules_as_hash: .: (0.000283) test_modules_as_strings: .: (0.000246) test_name: .: (0.000257) test_new: .: (0.000281) test_organism: .: (0.000278) test_orthologs_as_hash: .: (0.000263) test_orthologs_as_strings: .: (0.000369) test_pathways_as_hash: .: (0.000318) test_pathways_as_strings: .: (0.000239) test_reactions_as_hash: .: (0.000263) test_reactions_as_strings: .: (0.000256) test_references: .: (0.000262) test_rel_pathways_as_hash: .: (0.000278) test_rel_pathways_as_strings: .: (0.000254) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000631) test_compounds_as_strings: .: (0.000614) test_dblinks_as_hash: .: (0.000287) test_dblinks_as_strings: .: (0.000314) test_description: .: (0.000286) test_diseases_as_hash: .: (0.000285) test_diseases_as_strings: .: (0.000264) test_entry_id: .: (0.000307) test_enzymes_as_strings: .: (0.000265) test_genes_as_hash: .: (0.000545) test_genes_as_strings: .: (0.000379) test_keggclass: .: (0.000301) test_ko_pathway: .: (0.000277) test_modules_as_hash: .: (0.000270) test_modules_as_strings: .: (0.000268) test_name: .: (0.000307) test_new: .: (0.000292) test_organism: .: (0.000310) test_orthologs_as_hash: .: (0.000279) test_orthologs_as_strings: .: (0.000366) test_pathways_as_hash: .: (0.000296) test_pathways_as_strings: .: (0.000310) test_reactions_as_hash: .: (0.000264) test_reactions_as_strings: .: (0.000264) test_references: .: (0.000256) test_rel_pathways_as_hash: .: (0.000312) test_rel_pathways_as_strings: .: (0.000272) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000462) test_compounds_as_strings: .: (0.000335) test_dblinks_as_hash: .: (0.000268) test_dblinks_as_strings: .: (0.000235) test_description: .: (0.000264) test_diseases_as_hash: .: (0.000255) test_diseases_as_strings: .: (0.000243) test_entry_id: .: (0.000294) test_enzymes_as_strings: .: (0.000246) test_genes_as_hash: .: (0.000266) test_genes_as_strings: .: (0.000277) test_keggclass: .: (0.000283) test_ko_pathway: .: (0.000265) test_modules_as_hash: .: (0.000413) test_modules_as_strings: .: (0.000267) test_name: .: (0.000262) test_new: .: (0.000253) test_organism: .: (0.000251) test_orthologs_as_hash: .: (0.000303) test_orthologs_as_strings: .: (0.000261) test_pathways_as_hash: .: (0.000262) test_pathways_as_strings: .: (0.000242) test_reactions_as_hash: .: (0.000254) test_reactions_as_strings: .: (0.000246) test_references: .: (0.000446) test_rel_pathways_as_hash: .: (0.000337) test_rel_pathways_as_strings: .: (0.000276) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000472) test_compounds_as_strings: .: (0.000331) test_dblinks_as_hash: .: (0.000308) test_dblinks_as_strings: .: (0.000295) test_description: .: (0.000410) test_diseases_as_hash: .: (0.000296) test_diseases_as_strings: .: (0.000275) test_entry_id: .: (0.000546) test_enzymes_as_strings: .: (0.000325) test_genes_as_hash: .: (0.000312) test_genes_as_strings: .: (0.000274) test_keggclass: .: (0.000286) test_ko_pathway: .: (0.000311) test_modules_as_hash: .: (0.000329) test_modules_as_strings: .: (0.000283) test_name: .: (0.000580) test_new: .: (0.000377) test_organism: .: (0.000321) test_orthologs_as_hash: .: (0.000299) test_orthologs_as_strings: .: (0.000280) test_pathways_as_hash: .: (0.000355) test_pathways_as_strings: .: (0.000298) test_reactions_as_hash: .: (0.000321) test_reactions_as_strings: .: (0.000307) test_references: .: (0.000807) test_rel_pathways_as_hash: .: (0.000365) test_rel_pathways_as_strings: .: (0.000298) Bio::TestBioKeggDRUG: test_activity: .: (0.000560) test_comment: .: (0.000312) test_dblinks_as_hash: .: (0.000384) test_dblinks_as_strings: .: (0.000390) test_entry_id: .: (0.000313) test_formula: .: (0.000285) test_kcf: .: (0.000304) test_mass: .: (0.000306) test_name: .: (0.000336) test_names: .: (0.000308) test_pathways_as_hash: .: (0.000323) test_pathways_as_strings: .: (0.000277) test_products: .: (0.000354) test_remark: .: (0.000314) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000538) test_composition: .: (0.000328) test_compounds: .: (0.004634) test_dblinks_as_hash: .: (0.000604) test_dblinks_as_strings: .: (0.000405) test_entry_id: .: (0.000371) test_enzymes: .: (0.000382) test_kcf: .: (0.000377) test_keggclass: .: (0.000370) test_mass: .: (0.000739) test_name: .: (0.000376) test_orthologs_as_hash: .: (0.000375) test_orthologs_as_strings: .: (0.000334) test_pathways_as_hash: .: (0.000318) test_pathways_as_strings: .: (0.000339) test_reactions: .: (0.000338) test_references: .: (0.000394) test_remark: .: (0.000650) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000430) test_composition: .: (0.000297) test_compounds: .: (0.000273) test_dblinks_as_hash: .: (0.000330) test_dblinks_as_strings: .: (0.000262) test_entry_id: .: (0.000265) test_enzymes: .: (0.000302) test_kcf: .: (0.000234) test_keggclass: .: (0.000526) test_mass: .: (0.000339) test_name: .: (0.000269) test_orthologs_as_hash: .: (0.000250) test_orthologs_as_strings: .: (0.000247) test_pathways_as_hash: .: (0.000268) test_pathways_as_strings: .: (0.000232) test_reactions: .: (0.000264) test_references: .: (0.000239) test_remark: .: (0.000264) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000892) test_compounds_as_strings: .: (0.000435) test_dblinks_as_hash: .: (0.000353) test_dblinks_as_strings: .: (0.000287) test_description: .: (0.000324) test_diseases_as_hash: .: (0.000312) test_diseases_as_strings: .: (0.000327) test_entry_id: .: (0.000712) test_enzymes_as_strings: .: (0.000301) test_genes_as_hash: .: (0.000325) test_genes_as_strings: .: (0.000348) test_keggclass: .: (0.000329) test_ko_pathway: .: (0.000364) test_modules_as_hash: .: (0.000363) test_modules_as_strings: .: (0.000359) test_name: .: (0.000344) test_new: .: (0.000668) test_organism: .: (0.000366) test_orthologs_as_hash: .: (0.000347) test_orthologs_as_strings: .: (0.000311) test_pathways_as_hash: .: (0.000321) test_pathways_as_strings: .: (0.000281) test_reactions_as_hash: .: (0.000530) test_reactions_as_strings: .: (0.000644) test_references: .: (0.000637) test_rel_pathways_as_hash: .: (0.000426) test_rel_pathways_as_strings: .: (0.000401) Bio::TestBioLITDB: test_author: .: (0.000685) test_entry_id: .: (0.000333) test_field: .: (0.000289) test_journal: .: (0.000256) test_keyword: .: (0.000315) test_reference: .: (0.000411) test_title: .: (0.000288) test_volume: .: (0.000265) Bio::TestBioNBRF: test_aalen: .: (0.000650) test_aaseq: .: (0.000311) test_entry: .: (0.000225) test_length: .: (0.000220) test_nalen: .: (0.000360) test_naseq: .: (0.000269) test_seq: .: (0.000224) test_seq_class: .: (0.000231) test_to_nbrf: .: (0.000260) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000377) test_to_newick_format_leaf: .: (0.000296) test_to_newick_format_leaf_NHX: .: (0.000259) Bio::TestBl2seqReport: test_db_len: .: (0.000933) test_db_num: .: (0.000451) test_new: .: (0.000378) test_undefed_methods: .: (0.000829) test_undefed_methods_for_iteration: .: (0.000969) Bio::TestBl2seqReportConstants: test_rs: .: (0.000348) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000454) test_hits: .: (0.000360) Bio::TestBlast: test_blast_reports_format0: .: (0.004887) test_blast_reports_format0_with_block: .: (0.001093) test_blast_reports_format7: .: (0.009719) test_blast_reports_format7_with_block: .: (0.012508) test_blast_reports_format7_with_parser: .: (0.057700) test_blast_reports_format7_with_parser_with_block: .: (0.015219) test_blast_reports_format8: .: (0.001079) test_blast_reports_format8_with_block: .: (0.000790) test_blast_reports_format8_with_parser: .: (0.000562) test_blast_reports_format8_with_parser_with_block: .: (0.000442) test_blast_reports_xml: .: (0.018252) test_blast_reports_xml_with_block: .: (0.017291) test_blastll: .: (0.000335) test_db: .: (0.000247) test_exec_genomenet: .: (0.000273) test_exec_local: .: (0.000232) test_exec_ncbi: .: (0.000219) test_filter: .: (0.000250) test_format: .: (0.001285) test_make_command_line: .: (0.000705) test_make_command_line_2: .: (0.006901) test_matrix: .: (0.000374) test_new: .: (0.000356) test_new_opt_string: .: (0.000484) test_option: .: (0.000256) test_option_set: .: (0.000308) test_option_set_m0: .: (0.000270) test_options: .: (0.000217) test_output: .: (0.000212) test_parse_result: .: (0.020102) test_parser: .: (0.000379) test_program: .: (0.000325) test_query: .: (0.000240) test_self_local: .: (0.000357) test_self_remote: .: (0.002039) test_server: .: (0.000315) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000535) test_delete: .: (0.000389) test_equal_equal: .: (0.000404) test_get: .: (0.000563) test_make_command_line_options: .: (0.000495) test_normalize!: .: (0.000333) test_parse: .: (0.000295) test_set: .: (0.000605) Bio::TestBlastReport: test_db: .: (0.017274) test_db_len: .: (0.017892) test_db_num: .: (0.017564) test_each_hit: .: (0.017727) test_each_iteration: .: (0.021710) test_eff_space: .: (0.019645) test_entrez_query: .: (0.015705) test_entropy: .: (0.013351) test_expect: .: (0.017256) test_filter: .: (0.019202) test_gap_extend: .: (0.017874) test_gap_open: .: (0.019331) test_hits: .: (0.013322) test_hsp_len: .: (0.015702) test_inclusion: .: (0.015668) test_iterations: .: (0.018285) test_kappa: .: (0.017575) test_lambda: .: (0.017351) test_matrix: .: (0.017814) test_message: .: (0.019643) test_parameters: .: (0.013728) test_pattern: .: (0.009193) test_program: .: (0.010575) test_query_def: .: (0.009270) test_query_id: .: (0.011237) test_query_len: .: (0.010631) test_reference: .: (0.009252) test_sc_match: .: (0.009316) test_sc_mismatch: .: (0.008982) test_statistics: .: (0.010576) test_version: .: (0.009703) Bio::TestBlastReportDefault: test_db: .: (0.000886) test_db_len: .: (0.000623) test_db_num: .: (0.000570) test_each_hit: .: (0.000525) test_each_iteration: .: (0.000457) test_eff_space: .: (0.000760) test_entropy: .: (0.000581) test_expect: .: (0.000561) test_gap_extend: .: (0.000489) test_gap_open: .: (0.000479) test_gapped_entropy: .: (0.000446) test_gapped_kappa: .: (0.000435) test_gapped_lambda: .: (0.000584) test_hits: .: (0.000454) test_iterations: .: (0.000410) test_kappa: .: (0.000440) test_lambda: .: (0.000424) test_matrix: .: (0.000504) test_message: .: (0.000388) test_pattern: .: (0.000400) test_program: .: (0.000404) test_query_def: .: (0.000587) test_query_len: .: (0.000447) test_reference: .: (0.000432) test_sc_match: .: (0.000500) test_sc_mismatch: .: (0.000494) test_version: .: (0.000423) Bio::TestBlastReportHit: test_Hit_accession: .: (0.008906) test_Hit_bit_score: .: (0.009116) test_Hit_definition: .: (0.011123) test_Hit_evalue: .: (0.009442) test_Hit_hit_id: .: (0.009537) test_Hit_hsps: .: (0.009144) test_Hit_identity: .: (0.009019) test_Hit_lap_at: .: (0.010626) test_Hit_len: .: (0.009364) test_Hit_midline: .: (0.009240) test_Hit_num: .: (0.008933) test_Hit_overlap: .: (0.010247) test_Hit_query_def: .: (0.010082) test_Hit_query_end: .: (0.009286) test_Hit_query_id: .: (0.009338) test_Hit_query_len: .: (0.009034) test_Hit_query_seq: .: (0.010587) test_Hit_query_start: .: (0.009501) test_Hit_taeget_def: .: (0.009272) test_Hit_target_end: .: (0.009150) test_Hit_target_id: .: (0.009266) test_Hit_target_len: .: (0.011281) test_Hit_target_seq: .: (0.009543) test_Hit_target_start: .: (0.009290) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000971) test_Hit_definition: .: (0.000398) test_Hit_evalue: .: (0.000358) test_Hit_hsps: .: (0.000340) test_Hit_identity: .: (0.000361) test_Hit_lap_at: .: (0.000438) test_Hit_len: .: (0.000398) test_Hit_midline: .: (0.000413) test_Hit_overlap: .: (0.000285) test_Hit_query_end: .: (0.000358) test_Hit_query_seq: .: (0.000710) test_Hit_query_start: .: (0.000628) test_Hit_taeget_def: .: (0.000641) test_Hit_target_end: .: (0.000618) test_Hit_target_id: .: (0.000485) test_Hit_target_len: .: (0.000499) test_Hit_target_seq: .: (0.000589) test_Hit_target_start: .: (0.000586) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.027450) test_Hit_bit_score: .: (0.026541) test_Hit_definition: .: (0.025579) test_Hit_evalue: .: (0.027064) test_Hit_hit_id: .: (0.026783) test_Hit_hsps: .: (0.024766) test_Hit_identity: .: (0.027264) test_Hit_lap_at: .: (0.027568) test_Hit_len: .: (0.024620) test_Hit_midline: .: (0.027386) test_Hit_num: .: (0.027965) test_Hit_overlap: .: (0.024865) test_Hit_query_def: .: (0.026579) test_Hit_query_end: .: (0.027658) test_Hit_query_id: .: (0.024450) test_Hit_query_len: .: (0.026707) test_Hit_query_seq: .: (0.027808) test_Hit_query_start: .: (0.026457) test_Hit_taeget_def: .: (0.025732) test_Hit_target_end: .: (0.027940) test_Hit_target_id: .: (0.027746) test_Hit_target_len: .: (0.025632) test_Hit_target_seq: .: (0.028239) test_Hit_target_start: .: (0.028414) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.025424) test_Hit_bit_score: .: (0.027564) test_Hit_definition: .: (0.027675) test_Hit_evalue: .: (0.024955) test_Hit_hit_id: .: (0.026826) test_Hit_hsps: .: (0.027770) test_Hit_identity: .: (0.026486) test_Hit_lap_at: .: (0.025972) test_Hit_len: .: (0.028085) test_Hit_midline: .: (0.027679) test_Hit_num: .: (0.025176) test_Hit_overlap: .: (0.027156) test_Hit_query_def: .: (0.027704) test_Hit_query_end: .: (0.024841) test_Hit_query_id: .: (0.026752) test_Hit_query_len: .: (0.027608) test_Hit_query_seq: .: (0.024668) test_Hit_query_start: .: (0.026370) test_Hit_taeget_def: .: (0.028053) test_Hit_target_end: .: (0.025652) test_Hit_target_id: .: (0.024943) test_Hit_target_len: .: (0.027178) test_Hit_target_seq: .: (0.026948) test_Hit_target_start: .: (0.024289) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.011472) test_Hit_bit_score: .: (0.009669) test_Hit_definition: .: (0.009277) test_Hit_evalue: .: (0.009050) test_Hit_hit_id: .: (0.008954) test_Hit_hsps: .: (0.010805) test_Hit_identity: .: (0.009271) test_Hit_lap_at: .: (0.009003) test_Hit_len: .: (0.008937) test_Hit_midline: .: (0.010643) test_Hit_num: .: (0.009510) test_Hit_overlap: .: (0.009158) test_Hit_query_def: .: (0.009094) test_Hit_query_end: .: (0.009014) test_Hit_query_id: .: (0.010623) test_Hit_query_len: .: (0.009351) test_Hit_query_seq: .: (0.008994) test_Hit_query_start: .: (0.009127) test_Hit_taeget_def: .: (0.010777) test_Hit_target_end: .: (0.009357) test_Hit_target_id: .: (0.009419) test_Hit_target_len: .: (0.008970) test_Hit_target_seq: .: (0.009052) test_Hit_target_start: .: (0.010607) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000663) test_Hit_bit_score: .: (0.000299) test_Hit_definition: .: (0.000293) test_Hit_evalue: .: (0.000266) test_Hit_hit_id: .: (0.000270) test_Hit_hsps: .: (0.000267) test_Hit_identity: .: (0.000256) test_Hit_lap_at: .: (0.000259) test_Hit_len: .: (0.000395) test_Hit_midline: .: (0.000299) test_Hit_num: .: (0.000232) test_Hit_overlap: .: (0.000232) test_Hit_query_def: .: (0.000256) test_Hit_query_end: .: (0.000233) test_Hit_query_id: .: (0.000227) test_Hit_query_len: .: (0.000215) test_Hit_query_seq: .: (0.000206) test_Hit_query_start: .: (0.000223) test_Hit_taeget_def: .: (0.000232) test_Hit_target_end: .: (0.000232) test_Hit_target_id: .: (0.000239) test_Hit_target_len: .: (0.000224) test_Hit_target_seq: .: (0.000424) test_Hit_target_start: .: (0.000301) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.009173) test_Hsp_bit_score: .: (0.008913) test_Hsp_density: .: (0.009120) test_Hsp_evalue: .: (0.011030) test_Hsp_gaps: .: (0.009423) test_Hsp_hit_frame: .: (0.009071) test_Hsp_hit_from: .: (0.009010) test_Hsp_hit_to: .: (0.009167) test_Hsp_hseq: .: (0.010829) test_Hsp_identity: .: (0.009099) test_Hsp_midline: .: (0.009191) test_Hsp_mismatch_count: .: (0.009997) test_Hsp_num: .: (0.010963) test_Hsp_pattern_from: .: (0.009331) test_Hsp_pattern_to: .: (0.009193) test_Hsp_percent_identity: .: (0.009439) test_Hsp_positive: .: (0.010314) test_Hsp_qseq: .: (0.010521) test_Hsp_query_frame: .: (0.009171) test_Hsp_query_from: .: (0.008931) test_Hsp_query_to: .: (0.009222) test_Hsp_score: .: (0.011119) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000828) test_Hsp_bit_score: .: (0.000323) test_Hsp_evalue: .: (0.000296) test_Hsp_gaps: .: (0.000325) test_Hsp_hit_frame: .: (0.000600) test_Hsp_hit_from: .: (0.000470) test_Hsp_hit_to: .: (0.000586) test_Hsp_hseq: .: (0.000449) test_Hsp_identity: .: (0.000296) test_Hsp_midline: .: (0.000384) test_Hsp_percent_identity: .: (0.000285) test_Hsp_positive: .: (0.000277) test_Hsp_qseq: .: (0.000544) test_Hsp_query_frame: .: (0.000605) test_Hsp_query_from: .: (0.000432) test_Hsp_query_to: .: (0.000410) test_Hsp_score: .: (0.000301) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.028579) test_Hsp_bit_score: .: (0.078724) test_Hsp_density: .: (0.028282) test_Hsp_evalue: .: (0.025023) test_Hsp_gaps: .: (0.027460) test_Hsp_hit_frame: .: (0.028125) test_Hsp_hit_from: .: (0.024986) test_Hsp_hit_to: .: (0.027393) test_Hsp_hseq: .: (0.045947) test_Hsp_identity: .: (0.025305) test_Hsp_midline: .: (0.027747) test_Hsp_mismatch_count: .: (0.027250) test_Hsp_num: .: (0.029015) test_Hsp_pattern_from: .: (0.026870) test_Hsp_pattern_to: .: (0.024881) test_Hsp_percent_identity: .: (0.026480) test_Hsp_positive: .: (0.026952) test_Hsp_qseq: .: (0.025420) test_Hsp_query_frame: .: (0.027285) test_Hsp_query_from: .: (0.025343) test_Hsp_query_to: .: (0.025092) test_Hsp_score: .: (0.026700) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.024437) test_Hsp_bit_score: .: (0.025676) test_Hsp_density: .: (0.028273) test_Hsp_evalue: .: (0.024531) test_Hsp_gaps: .: (0.026340) test_Hsp_hit_frame: .: (0.026226) test_Hsp_hit_from: .: (0.024693) test_Hsp_hit_to: .: (0.026502) test_Hsp_hseq: .: (0.025729) test_Hsp_identity: .: (0.024877) test_Hsp_midline: .: (0.027552) test_Hsp_mismatch_count: .: (0.024441) test_Hsp_num: .: (0.026149) test_Hsp_pattern_from: .: (0.026337) test_Hsp_pattern_to: .: (0.024248) test_Hsp_percent_identity: .: (0.026028) test_Hsp_positive: .: (0.026714) test_Hsp_qseq: .: (0.024433) test_Hsp_query_frame: .: (0.026197) test_Hsp_query_from: .: (0.025804) test_Hsp_query_to: .: (0.024894) test_Hsp_score: .: (0.026840) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.009438) test_Hsp_bit_score: .: (0.008776) test_Hsp_density: .: (0.009152) test_Hsp_evalue: .: (0.010333) test_Hsp_gaps: .: (0.008999) test_Hsp_hit_frame: .: (0.008786) test_Hsp_hit_from: .: (0.009182) test_Hsp_hit_to: .: (0.009327) test_Hsp_hseq: .: (0.010003) test_Hsp_identity: .: (0.008992) test_Hsp_midline: .: (0.008856) test_Hsp_mismatch_count: .: (0.009041) test_Hsp_num: .: (0.008865) test_Hsp_pattern_from: .: (0.010100) test_Hsp_pattern_to: .: (0.014290) test_Hsp_percent_identity: .: (0.008697) test_Hsp_positive: .: (0.008619) test_Hsp_qseq: .: (0.009250) test_Hsp_query_frame: .: (0.010282) test_Hsp_query_from: .: (0.008930) test_Hsp_query_to: .: (0.012011) test_Hsp_score: .: (0.008964) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000416) test_Hsp_bit_score: .: (0.000094) test_Hsp_density: .: (0.000080) test_Hsp_evalue: .: (0.000072) test_Hsp_gaps: .: (0.000075) test_Hsp_hit_frame: .: (0.000068) test_Hsp_hit_from: .: (0.000069) test_Hsp_hit_to: .: (0.000070) test_Hsp_hseq: .: (0.000068) test_Hsp_identity: .: (0.000066) test_Hsp_midline: .: (0.000068) test_Hsp_mismatch_count: .: (0.000067) test_Hsp_num: .: (0.000247) test_Hsp_pattern_from: .: (0.000130) test_Hsp_pattern_to: .: (0.000070) test_Hsp_percent_identity: .: (0.000064) test_Hsp_positive: .: (0.000069) test_Hsp_qseq: .: (0.000071) test_Hsp_query_frame: .: (0.000067) test_Hsp_query_from: .: (0.000087) test_Hsp_query_to: .: (0.000073) test_Hsp_score: .: (0.000066) Bio::TestBlastReportIteration: test_hits: .: (0.010239) test_message: .: (0.010746) test_num: .: (0.009006) test_statistics: .: (0.009233) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000931) test_message: .: (0.000493) test_num: .: (0.000481) Bio::TestBlastReportIterationMulti: test_each: .: (0.026867) test_hits: .: (0.024744) test_message: .: (0.026207) test_num: .: (0.027117) test_query_def: .: (0.024406) test_query_id: .: (0.026037) test_query_len: .: (0.027038) test_statistics: .: (0.023999) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.026594) test_hits: .: (0.035194) test_message: .: (0.028098) test_num: .: (0.025991) test_query_def: .: (0.025911) test_query_id: .: (0.024390) test_query_len: .: (0.026328) test_statistics: .: (0.025660) Bio::TestBlastReportIterationREXML: test_hits: .: (0.009711) test_message: .: (0.009086) test_num: .: (0.008883) test_statistics: .: (0.008759) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000539) test_message: .: (0.000260) test_num: .: (0.000394) test_statistics: .: (0.000285) Bio::TestBlastReportMulti: test_db: .: (0.027876) test_db_len: .: (0.027147) test_db_num: .: (0.024772) test_each_hit: .: (0.028179) test_each_iteration: .: (0.027243) test_eff_space: .: (0.025708) test_entropy: .: (0.026104) test_expect: .: (0.026811) test_filter: .: (0.028643) test_gap_extend: .: (0.030547) test_gap_open: .: (0.027032) test_hits: .: (0.024238) test_hsp_len: .: (0.027036) test_iterations: .: (0.027934) test_kappa: .: (0.024078) test_lambda: .: (0.027098) test_matrix: .: (0.026953) test_message: .: (0.023962) test_parameters: .: (0.026199) test_pattern: .: (0.027375) test_program: .: (0.024135) test_query_def: .: (0.025844) test_query_id: .: (0.027009) test_query_len: .: (0.024721) test_reference: .: (0.026063) test_reports: .: (0.026467) test_statistics: .: (0.023951) test_version: .: (0.026342) Bio::TestBlastReportMultiREXML: test_db: .: (0.027282) test_db_len: .: (0.025989) test_db_num: .: (0.027287) test_each_hit: .: (0.027123) test_each_iteration: .: (0.030691) test_eff_space: .: (0.024512) test_entropy: .: (0.027183) test_expect: .: (0.026512) test_filter: .: (0.024616) test_gap_extend: .: (0.026701) test_gap_open: .: (0.027241) test_hits: .: (0.024847) test_hsp_len: .: (0.026472) test_iterations: .: (0.026886) test_kappa: .: (0.026100) test_lambda: .: (0.024509) test_matrix: .: (0.027162) test_message: .: (0.026539) test_parameters: .: (0.026164) test_pattern: .: (0.026283) test_program: .: (0.026846) test_query_def: .: (0.025795) test_query_id: .: (0.024762) test_query_len: .: (0.026771) test_reference: .: (0.026641) test_reports: .: (0.024696) test_statistics: .: (0.026445) test_version: .: (0.026993) Bio::TestBlastReportREXML: test_db: .: (0.008868) test_db_len: .: (0.009263) test_db_num: .: (0.010542) test_each_hit: .: (0.008914) test_each_iteration: .: (0.008809) test_eff_space: .: (0.008863) test_entrez_query: .: (0.009718) test_entropy: .: (0.010434) test_expect: .: (0.008909) test_filter: .: (0.008710) test_gap_extend: .: (0.008878) test_gap_open: .: (0.010505) test_hits: .: (0.009180) test_hsp_len: .: (0.008942) test_inclusion: .: (0.008871) test_iterations: .: (0.010181) test_kappa: .: (0.009377) test_lambda: .: (0.008881) test_matrix: .: (0.008807) test_message: .: (0.008983) test_parameters: .: (0.010449) test_pattern: .: (0.008924) test_program: .: (0.008860) test_query_def: .: (0.008857) test_query_id: .: (0.010572) test_query_len: .: (0.009218) test_reference: .: (0.008768) test_sc_match: .: (0.008659) test_sc_mismatch: .: (0.010055) test_statistics: .: (0.009509) test_version: .: (0.008910) Bio::TestBlastReportTabular: test_db: .: (0.000771) test_db_len: .: (0.000273) test_db_num: .: (0.000238) test_each_hit: .: (0.000259) test_each_iteration: .: (0.000228) test_eff_space: .: (0.000219) test_entrez_query: .: (0.000239) test_entropy: .: (0.000195) test_expect: .: (0.000188) test_filter: .: (0.000204) test_gap_extend: .: (0.000220) test_gap_open: .: (0.000232) test_hits: .: (0.000213) test_hsp_len: .: (0.000210) test_inclusion: .: (0.000383) test_iterations: .: (0.000203) test_kappa: .: (0.000193) test_lambda: .: (0.000196) test_matrix: .: (0.000203) test_message: .: (0.000206) test_parameters: .: (0.000204) test_pattern: .: (0.000201) test_program: .: (0.000200) test_query_def: .: (0.000227) test_query_id: .: (0.000204) test_query_len: .: (0.000191) test_reference: .: (0.000205) test_sc_match: .: (0.000211) test_sc_mismatch: .: (0.000209) test_statistics: .: (0.000474) test_version: .: (0.000289) Bio::TestChain: test_aaseq: .: (0.000411) test_addLigand: .: (0.000159) test_addResidue: .: (0.000173) test_atom_seq: .: (0.000172) test_comp: .: (0.000184) test_each: .: (0.000143) test_each_heterogen: .: (0.000173) test_each_residue: .: (0.000152) test_get_heterogen_by_id: .: (0.000151) test_get_residue_by_id: .: (0.000143) test_inspect: .: (0.000194) test_rehash: .: (0.000150) test_rehash_heterogens: .: (0.000342) test_rehash_residues: .: (0.000146) test_square_brace: .: (0.000150) test_to_s: .: (0.000166) Bio::TestChainFinder: test_chains: .: (0.000324) test_each_chain: .: (0.000163) test_find_chain: .: (0.000219) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005679) test_header: .: (0.000711) test_match_line: .: (0.000560) test_sequence0: .: (0.000861) test_sequence1: .: (0.000644) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.006048) test_header: .: (0.000894) test_match_line: .: (0.000870) test_sequence0: .: (0.000737) test_sequence1: .: (0.000669) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.009669) test_header: .: (0.000921) test_match_line: .: (0.000673) test_sequence0: .: (0.000643) test_sequence1: .: (0.000753) Bio::TestCodonTable: test_Tables: .: (0.000318) test_accessor: .: (0.000155) test_definition: .: (0.000142) test_each: .: (0.000166) test_revtrans: .: (0.000205) test_self_accessor: .: (0.000154) test_self_copy: .: (0.000883) test_set_accessor: .: (0.105674) test_start: .: (0.000199) test_start_codon?: .: (0.000165) test_stop: .: (0.000145) test_stop_codon?: .: (0.000158) test_table: .: (0.000176) Bio::TestCodonTableConstants: test_Definitions: .: (0.000310) test_Starts: .: (0.000170) test_Tables: .: (0.000144) test_stops: .: (0.000161) Bio::TestColorScheme: test_buried: .: (0.001121) Bio::TestCommand: test_command_constants: .: (0.000261) test_escape_shell: .: (0.000210) test_escape_shell_unix: .: (0.000153) test_escape_shell_windows: .: (0.000154) test_make_cgi_params_by_array_of_array: .: (0.000321) test_make_cgi_params_by_array_of_hash: .: (0.000292) test_make_cgi_params_by_array_of_string: .: (0.000294) test_make_cgi_params_by_hash_in_string: .: (0.000386) test_make_cgi_params_by_hash_in_symbol: .: (0.000395) test_make_cgi_params_by_string: .: (0.000223) test_make_command_line: .: (0.000174) test_make_command_line_unix: .: (0.000154) test_make_command_line_windows: .: (0.000166) test_safe_command_line_array: .: (0.000171) test_safe_command_line_array_passthrough: .: (0.000269) Bio::TestContingencyTable: test_lite_example: .: (0.104869) Bio::TestDB: test_entry_id: .: (0.000374) test_exists: .: (0.000158) test_fetch: .: (0.000384) test_get: .: (0.000165) test_open: .: (0.000146) test_tags: .: (0.000144) Bio::TestDataType: test_const_like_method: .: (0.000550) test_pdb_achar: .: (0.000313) test_pdb_atom: .: (0.000250) test_pdb_character: .: (0.000243) test_pdb_date: .: (0.000254) test_pdb_idcode: .: (0.000237) test_pdb_integer: .: (0.000138) test_pdb_list: .: (0.000176) test_pdb_lstring: .: (0.000229) test_pdb_real: .: (0.000329) test_pdb_resudue_name: .: (0.000275) test_pdb_slist: .: (0.000153) test_pdb_string: .: (0.000251) test_pdb_stringrj: .: (0.000132) test_pdb_symop: .: (0.000248) test_specification_list: .: (0.000162) Bio::TestEMBL: test_ac: .: (0.000582) test_accession: .: (0.000416) test_cc: .: (0.000496) test_de: .: (0.000386) test_division: .: (0.000375) test_dr: .: (0.000325) test_dt: .: (0.000352) test_dt_created: .: (0.000345) test_dt_iterator: .: (0.000337) test_dt_updated: .: (0.000335) test_each_cds: .: (0.000528) test_each_gene: .: (0.000567) test_entry: .: (0.000420) test_fh: .: (0.000341) test_ft: .: (0.000598) test_ft_accessor: .: (0.000467) test_ft_iterator: .: (0.000462) test_id_line: .: (0.000352) test_id_line_data_class: .: (0.000473) test_id_line_division: .: (0.000350) test_id_line_entry_name: .: (0.000351) test_id_line_iterator: .: (0.000374) test_id_line_molecule_type: .: (0.000340) test_id_line_sequence_length: .: (0.000382) test_kw: .: (0.000346) test_molecule: .: (0.000357) test_oc: .: (0.000376) test_og: .: (0.000476) test_os: .: (0.000386) test_ref: .: (0.000450) test_references: .: (0.000713) test_seq: .: (0.000554) test_sequence_length: .: (0.000379) test_sq: .: (0.000373) test_sq_get: .: (0.000494) test_sv: .: (0.000402) test_version: .: (0.000393) Bio::TestEMBL89: test_ac: .: (0.000483) test_accession: .: (0.000441) test_cc: .: (0.000295) test_de: .: (0.000336) test_division: .: (0.000378) test_dr: .: (0.000357) test_dt: .: (0.000462) test_dt_created: .: (0.000345) test_dt_iterator: .: (0.000318) test_dt_updated: .: (0.000308) test_each_cds: .: (0.000574) test_each_gene: .: (0.000430) test_entry: .: (0.000380) test_fh: .: (0.000352) test_ft: .: (0.000441) test_ft_accessor: .: (0.000455) test_ft_iterator: .: (0.000431) test_id_line: .: (0.000360) test_id_line_data_class: .: (0.000378) test_id_line_division: .: (0.002830) test_id_line_entry_name: .: (0.000402) test_id_line_iterator: .: (0.000371) test_id_line_molecule_type: .: (0.000394) test_id_line_sequence_length: .: (0.000555) test_id_line_sequence_version: .: (0.000359) test_kw: .: (0.000367) test_molecule: .: (0.000373) test_oc: .: (0.000535) test_og: .: (0.000357) test_os: .: (0.000384) test_ref: .: (0.000437) test_references: .: (0.000684) test_seq: .: (0.000594) test_sequence_length: .: (0.000386) test_sq: .: (0.000434) test_sq_get: .: (0.000345) test_sv: .: (0.000384) test_version: .: (0.000409) Bio::TestEMBLAPI: test_ac: .: (0.000349) test_accessions: .: (0.000218) Bio::TestEMBLCommon: test_ac: .: (0.000256) test_accession: .: (0.000123) test_accessions: .: (0.000123) test_de: .: (0.000132) test_definition: .: (0.000132) test_description: .: (0.000138) test_dr: .: (0.000131) test_keywords: .: (0.000125) test_kw: .: (0.000128) test_oc: .: (0.000141) test_og: .: (0.000130) test_os: .: (0.000130) test_ref: .: (0.000130) test_references: .: (0.000147) Bio::TestEMBLDB: test_fetch: .: (0.000422) test_p_entry2hash: .: (0.000123) Bio::TestEMBLToBioSequence: test_classification: .: (0.002610) test_date_created: .: (0.000561) test_date_modified: .: (0.000454) test_definition: .: (0.000404) test_division: .: (0.000442) test_entry_id: .: (0.000370) test_entry_version: .: (0.000385) test_features: .: (0.000580) test_keywords: .: (0.000379) test_molecule_type: .: (0.000400) test_primary_accession: .: (0.000375) test_references: .: (0.000633) test_release_created: .: (0.000405) test_release_modified: .: (0.000381) test_secondary_accessions: .: (0.000384) test_sequence_version: .: (0.000407) test_species: .: (0.000400) test_topology: .: (0.000438) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002624) test_date_created: .: (0.002369) test_date_modified: .: (0.002600) test_definition: .: (0.002612) test_division: .: (0.002791) test_entry_id: .: (0.002786) test_entry_version: .: (0.002715) test_features: .: (0.002955) test_keywords: .: (0.002689) test_molecule_type: .: (0.002506) test_primary_accession: .: (0.002661) test_references: .: (0.002773) test_release_created: .: (0.005762) test_release_modified: .: (0.003039) test_secondary_accessions: .: (0.002785) test_sequence_version: .: (0.002589) test_species: .: (0.002575) test_topology: .: (0.002620) Bio::TestFasta: test_db: .: (0.000338) test_format: .: (0.000160) test_format_arg_integer: .: (0.000170) test_format_arg_str: .: (0.000158) test_ktup: .: (0.000143) test_matrix: .: (0.000136) test_option: .: (0.000191) test_options: .: (0.000310) test_output: .: (0.000153) test_program: .: (0.000141) test_server: .: (0.000130) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000306) test_accession: .: (0.000154) test_accessions: .: (0.000164) test_description: .: (0.000162) test_descriptions: .: (0.000162) test_entry_id: .: (0.000154) test_get_all_by_type: .: (0.000191) test_gi: .: (0.000160) test_id_strings: .: (0.000209) test_list_ids: .: (0.000150) test_locus: .: (0.000292) test_words: .: (0.000189) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000305) test_accession: .: (0.000166) test_accessions: .: (0.000177) test_description: .: (0.000152) test_descriptions: .: (0.000160) test_emb: .: (0.000174) test_entry_id: .: (0.000174) test_get_all_by_type: .: (0.000172) test_get_emb: .: (0.000171) test_gi: .: (0.000155) test_id_strings: .: (0.000386) test_list_ids: .: (0.000154) test_locus: .: (0.000163) test_words: .: (0.000196) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000287) test_accession: .: (0.000159) test_accessions: .: (0.000156) test_description: .: (0.000135) test_descriptions: .: (0.000168) test_entry_id: .: (0.000142) test_get_all_by_type: .: (0.000141) test_gi: .: (0.000139) test_id_strings: .: (0.000198) test_list_ids: .: (0.000277) test_locus: .: (0.000153) test_sp: .: (0.000170) test_words: .: (0.000185) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000315) test_accession: .: (0.000189) test_accessions: .: (0.000222) test_description: .: (0.000194) test_descriptions: .: (0.000181) test_entry_id: .: (0.000170) test_get_all_by_type: .: (0.000178) test_gi: .: (0.000219) test_id_strings: .: (0.000277) test_list_ids: .: (0.000180) test_locus: .: (0.000178) test_words: .: (0.000254) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000297) test_accession: .: (0.000168) test_accessions: .: (0.000157) test_description: .: (0.000155) test_descriptions: .: (0.000370) test_entry_id: .: (0.000174) test_get_all_by_type: .: (0.000163) test_gi: .: (0.000211) test_id_strings: .: (0.000244) test_list_ids: .: (0.000157) test_locus: .: (0.000167) test_words: .: (0.000231) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000292) test_accession: .: (0.000188) test_accessions: .: (0.000156) test_description: .: (0.000135) test_descriptions: .: (0.000138) test_entry_id: .: (0.000388) test_get_all_by_type: .: (0.000139) test_gi: .: (0.000143) test_id_strings: .: (0.000171) test_list_ids: .: (0.000130) test_locus: .: (0.000143) test_words: .: (0.000174) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000320) test_accession: .: (0.000206) test_accessions: .: (0.000167) test_description: .: (0.000148) test_descriptions: .: (0.000138) test_entry_id: .: (0.000175) test_get: .: (0.000174) test_get_all_by_type: .: (0.000408) test_id_strings: .: (0.000218) test_list_ids: .: (0.000145) test_locus: .: (0.000150) test_sp: .: (0.000166) test_words: .: (0.000230) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000334) test_accession: .: (0.000180) test_accessions: .: (0.000159) test_description: .: (0.000175) test_descriptions: .: (0.000153) test_entry_id: .: (0.000185) test_get: .: (0.000173) test_get_all_by_type: .: (0.000148) test_id_strings: .: (0.000528) test_list_ids: .: (0.000156) test_locus: .: (0.000153) test_tr: .: (0.000181) test_words: .: (0.000264) Bio::TestFastaFirstName: test_first_name1: .: (0.000297) test_first_name_multi_identifier: .: (0.000150) test_first_name_single_worded_defintion: .: (0.000140) test_no_definition: .: (0.000147) test_space_before_first_name: .: (0.000139) test_tabbed_defintion: .: (0.000141) Bio::TestFastaFormat: test_aalen: .: (0.000351) test_aaseq: .: (0.000170) test_acc_version: .: (0.000219) test_accession: .: (0.000311) test_accessions: .: (0.000223) test_data: .: (0.000164) test_definition: .: (0.000152) test_entry: .: (0.000156) test_entry_id: .: (0.000204) test_entry_overrun: .: (0.000152) test_first_name: .: (0.000173) test_gi: .: (0.000250) test_identifiers: .: (0.000207) test_length: .: (0.000170) test_query: .: (0.000182) test_seq: .: (0.000196) Bio::TestFastaFormatConst: test_delimiter: .: (0.000268) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000707) test_data: .: (0.000186) test_definition: .: (0.000150) test_entry: .: (0.000158) test_entry_id: .: (0.000227) test_first_name: .: (0.000165) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000341) test_naseq: .: (0.000157) test_naseq_class: .: (0.000184) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000358) Bio::TestFastaInitialize: test_new_1: .: (0.000761) test_option: .: (0.000149) test_option_backward_compatibility: .: (0.000190) Bio::TestFastaNumericFormat: test_arg: .: (0.000340) test_data: .: (0.000231) test_definition: .: (0.000152) test_each: .: (0.000193) test_entry: .: (0.000156) test_entry_id: .: (0.000190) test_length: .: (0.000182) test_to_biosequence: .: (0.000998) Bio::TestFastaQuery: test_query: .: (0.000218) test_self_local: .: (0.000102) test_self_parser: .: (0.000103) test_self_remote: .: (0.000117) Bio::TestFastacmd: test_database: .: (0.000258) test_fastacmd: .: (0.000124) test_methods: .: (0.000203) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000683) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000801) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000669) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000552) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000561) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000772) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000548) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000503) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000477) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000750) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000473) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000494) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000527) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000970) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.001169) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000700) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000549) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000600) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.008447) test_error_probabilities_as_sanger: .: (0.003947) test_error_probabilities_as_solexa: .: (0.003942) test_quality_scores_as_illumina: .: (0.000746) test_quality_scores_as_sanger: .: (0.000419) test_quality_scores_as_solexa: .: (0.000419) test_validate_format: .: (0.000556) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.001120) test_entry_id: .: (0.000836) test_error_probabilities: .: (0.130336) test_nalen: .: (0.001296) test_naseq: .: (0.000928) test_quality_scores: .: (0.001724) test_quality_string: .: (0.000800) test_roundtrip: .: (0.087891) test_seq: .: (0.001064) test_sequence_string: .: (0.000795) test_to_biosequence: .: (0.082709) test_to_biosequence_and_output: .: (0.003942) test_to_s: .: (0.000919) test_validate_format: .: (0.001060) test_validate_format_with_array: .: (0.000866) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000881) test_mask_20_with_empty_string: .: (0.000570) test_mask_20_with_longer_string: .: (0.000504) test_mask_20_with_x: .: (0.000460) test_mask_60: .: (0.000506) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.004579) test_error_probabilities_as_sanger: .: (0.004511) test_error_probabilities_as_solexa: .: (0.004451) test_quality_scores_as_illumina: .: (0.000676) test_quality_scores_as_sanger: .: (0.000378) test_quality_scores_as_solexa: .: (0.000481) test_validate_format: .: (0.000629) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.004849) test_error_probabilities_as_sanger: .: (0.003780) test_error_probabilities_as_solexa: .: (0.003956) test_quality_scores_as_illumina: .: (0.000989) test_quality_scores_as_sanger: .: (0.000579) test_quality_scores_as_solexa: .: (0.000363) test_validate_format: .: (0.000584) Bio::TestFeature: test_append: .: (0.000349) test_append_nil: .: (0.000153) test_assoc: .: (0.000167) test_each: .: (0.000137) test_feature: .: (0.000124) test_locations: .: (0.000217) test_new: .: (0.000132) test_position: .: (0.000128) test_qualifiers: .: (0.000136) Bio::TestFeatures: test_append: .: (0.000347) test_arg: .: (0.000161) test_each: .: (0.000144) test_features: .: (0.000154) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000909) test_aaindex2: .: (0.000308) test_blast: .: (0.000273) test_blastxml: .: (0.000913) test_embl: .: (0.000341) test_embl_oldrelease: .: (0.000307) test_fastaformat: .: (0.000417) test_fastanumericformat: .: (0.000194) test_fastq: .: (0.000242) test_genbank: .: (0.000255) test_genpept: .: (0.000275) test_hmmer: .: (0.000280) test_maxml_cluster: .: (0.002554) test_maxml_sequence: .: (0.000181) test_medline: .: (0.000205) test_prosite: .: (0.003519) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003043) test_transfac: .: (0.001653) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000453) test_auto_1arg_filename: .: (0.000576) test_auto_1arg_io: .: (0.000431) test_auto_1arg_io_with_block: .: (0.000794) test_auto_1arg_with_block: .: (0.000658) test_auto_2arg_filename_mode: .: (0.000398) test_auto_2arg_filename_mode_with_block: .: (0.000573) test_auto_3arg: .: (0.000486) test_auto_3arg_with_block: .: (0.000613) test_foreach: .: (0.000499) test_new_2arg_class: .: (0.000246) test_new_2arg_nil: .: (0.000339) test_open_0arg: .: (0.000185) test_open_1arg_class: .: (0.000177) test_open_1arg_filename: .: (0.000357) test_open_1arg_io: .: (0.000490) test_open_1arg_io_with_block: .: (0.000618) test_open_1arg_nil: .: (0.000176) test_open_1arg_with_block: .: (0.000553) test_open_2arg_autodetect: .: (0.000323) test_open_2arg_autodetect_io: .: (0.000543) test_open_2arg_autodetect_io_with_block: .: (0.000640) test_open_2arg_autodetect_with_block: .: (0.000575) test_open_2arg_class: .: (0.000232) test_open_2arg_class_io: .: (0.000230) test_open_2arg_class_io_with_block: .: (0.000602) test_open_2arg_class_with_block: .: (0.000485) test_open_2arg_filename_mode: .: (0.000399) test_open_2arg_filename_mode_with_block: .: (0.000605) test_open_3arg: .: (0.000550) test_open_3arg_with_block: .: (0.001293) test_open_4arg: .: (0.001198) test_to_a: .: (0.000563) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000529) test_close: .: (0.000210) test_dbclass: .: (0.000203) test_dbclass_eq: .: (0.000401) test_dbclass_nil: .: (0.000337) test_each: .: (0.000381) test_each_entry: .: (0.000490) test_ended_pos: .: (0.000333) test_entry_pos_flag: .: (0.000243) test_entry_raw: .: (0.000407) test_eof?: .: (0.000315) test_next_entry: .: (0.000555) test_path: .: (0.000235) test_pos: .: (0.000286) test_raw: .: (0.000344) test_rewind: .: (0.000324) test_start_pos: .: (0.000298) test_start_pos_ended_pos_not_recorded: .: (0.000301) test_to_io: .: (0.000247) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000440) test_simpleformat2: .: (0.000251) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000458) test_eof_false_after_prefetch: .: (0.000267) test_eof_false_first: .: (0.000157) test_eof_true: .: (0.000203) test_getc: .: (0.000162) test_getc_after_prefetch: .: (0.000168) test_gets: .: (0.000170) test_gets_equal_prefetch_gets: .: (0.000176) test_gets_paragraph_mode: .: (0.000222) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000304) test_gets_paragraph_mode_within_buffer: .: (0.000606) test_gets_rs: .: (0.000193) test_gets_rs_equal_prefetch_gets: .: (0.000211) test_gets_rs_within_buffer: .: (0.000493) test_pos: .: (0.000183) test_pos=: .: (0.000177) test_prefetch_buffer: .: (0.000173) test_prefetch_gets: .: (0.000197) test_prefetch_gets_with_arg: .: (0.000194) test_rewind: .: (0.000157) test_skip_spaces: .: (0.000195) test_to_io: .: (0.000225) test_ungetc: .: (0.000196) test_ungetc_after_prefetch: .: (0.000212) test_ungets: .: (0.000227) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000337) test_self_open_file: .: (0.000187) test_self_open_file_with_block: .: (0.000206) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000371) test_parse_file_open_arg_int_perm: .: (0.000140) test_parse_file_open_arg_int_perm_opt: .: (0.000141) test_parse_file_open_arg_integer: .: (0.000141) test_parse_file_open_arg_nil: .: (0.000130) test_parse_file_open_arg_opt: .: (0.000181) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000156) test_parse_file_open_arg_str: .: (0.000155) test_parse_file_open_arg_str_opt: .: (0.000184) test_parse_file_open_arg_str_perm: .: (0.000149) test_parse_file_open_arg_str_perm_opt: .: (0.000155) test_parse_file_open_arg_str_with_enc: .: (0.000150) test_parse_file_open_arg_str_with_ext_enc: .: (0.000153) test_parse_file_open_mode_integer: .: (0.000126) test_parse_file_open_mode_nil: .: (0.000169) test_parse_file_open_mode_str: .: (0.000162) test_parse_file_open_mode_str_with_enc: .: (0.000144) test_parse_file_open_mode_str_with_ext_enc: .: (0.000320) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000316) test_entry: .: (0.000185) test_entry_ended_pos: .: (0.000168) test_entry_pos_flag: .: (0.000173) test_entry_start_pos: .: (0.000153) test_get_entry: .: (0.000197) test_rewind: .: (0.000158) test_skip_leader: .: (0.000172) test_stream: .: (0.000139) test_stream_pos: .: (0.000165) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000284) test_delimiter_overrun: .: (0.000136) test_entry: .: (0.000187) test_entry_ended_pos: .: (0.000195) test_entry_ended_pos_default_nil: .: (0.000157) test_entry_start_pos: .: (0.000178) test_entry_start_pos_default_nil: .: (0.000180) test_get_entry: .: (0.000255) test_get_parsed_entry: .: (0.000247) test_header: .: (0.000132) test_skip_leader: .: (0.000183) test_skip_leader_without_header: .: (0.000213) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000369) test_entry_ended_pos: .: (0.000249) test_entry_start_pos: .: (0.000234) test_flag_to_fetch_header: .: (0.000224) test_get_entry: .: (0.000306) test_get_parsed_entry: .: (0.000284) test_rewind: .: (0.000266) test_skip_leader: .: (0.000176) Bio::TestGCGMsf: test_alignment: .: (0.001101) test_checksum: .: (0.000262) test_compcheck: .: (0.000242) test_date: .: (0.000243) test_description: .: (0.000364) test_entry_id: .: (0.000223) test_gap_length_weight: .: (0.000232) test_gap_weight: .: (0.000226) test_heading: .: (0.000249) test_length: .: (0.000231) test_seq_type: .: (0.000215) test_symbol_comparison_table: .: (0.003752) test_validate_checksum: .: (0.001373) Bio::TestGFF: test_record_class: .: (0.000659) test_records: .: (0.000662) Bio::TestGFF2: test_const_version: .: (0.000643) test_gff_version: .: (0.000456) test_metadata: .: (0.000659) test_metadata_size: .: (0.000410) test_records_size: .: (0.000372) test_to_s: .: (0.000853) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000377) test_attributes_case2: .: (0.000246) test_attributes_incompatible_backslash_semicolon: .: (0.000287) Bio::TestGFF2MetaData: test_data: .: (0.000276) test_directive: .: (0.000151) test_parse: .: (0.000163) Bio::TestGFF2Record: test_attribute: .: (0.000661) test_attribute_nonexistent: .: (0.000252) test_attributes: .: (0.000287) test_attributes_to_hash: .: (0.000280) test_comment_only?: .: (0.000244) test_delete_attribute: .: (0.000283) test_delete_attribute_multiple: .: (0.000431) test_delete_attribute_multiple2: .: (0.000304) test_delete_attribute_multiple_nil: .: (0.000268) test_delete_attribute_nil: .: (0.000308) test_delete_attribute_nonexistent: .: (0.000316) test_delete_attributes: .: (0.000480) test_delete_attributes_multiple: .: (0.000271) test_delete_attributes_nonexistent: .: (0.000301) test_end: .: (0.000391) test_eqeq: .: (0.000581) test_eqeq_false: .: (0.000670) test_feature: .: (0.000232) test_frame: .: (0.000235) test_get_attribute: .: (0.000356) test_get_attribute_nonexistent: .: (0.000257) test_get_attributes: .: (0.000459) test_get_attributes_nonexistent: .: (0.000239) test_replace_attributes: .: (0.000299) test_replace_attributes_multiple_multiple_over: .: (0.000295) test_replace_attributes_multiple_multiple_same: .: (0.000280) test_replace_attributes_multiple_multiple_two: .: (0.000474) test_replace_attributes_multiple_single: .: (0.000271) test_replace_attributes_nonexistent: .: (0.000296) test_replace_attributes_nonexistent_multiple: .: (0.000285) test_replace_attributes_single_multiple: .: (0.000350) test_score: .: (0.000406) test_self_parse: .: (0.000567) test_seqname: .: (0.000256) test_set_attribute: .: (0.000329) test_set_attribute_multiple: .: (0.000277) test_set_attribute_nonexistent: .: (0.000555) test_sort_attributes_by_tag!: .: (0.000376) test_sort_attributes_by_tag_bang_test2: .: (0.000354) test_sort_attributes_by_tag_bang_with_block: .: (0.000349) test_source: .: (0.000241) test_start: .: (0.000243) test_strand: .: (0.000597) test_to_s: .: (0.000437) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000305) test_comment_eq: .: (0.000110) test_comment_only?: .: (0.000172) test_comment_only_false: .: (0.000158) test_to_s: .: (0.000197) test_to_s_not_empty: .: (0.000304) Bio::TestGFF3: test_const_version: .: (0.001023) test_gff_version: .: (0.000550) test_records: .: (0.000921) test_sequence_regions: .: (0.000517) test_sequences: .: (0.000865) test_to_s: .: (0.001042) Bio::TestGFF3MetaData: test_data: .: (0.000372) test_directive: .: (0.000136) test_parse: .: (0.000174) Bio::TestGFF3Record: test_attributes: .: (0.000454) test_end: .: (0.000418) test_feature: .: (0.000272) test_frame: .: (0.000327) test_id: .: (0.000272) test_score: .: (0.000245) test_seqname: .: (0.000240) test_source: .: (0.000272) test_start: .: (0.000282) test_strand: .: (0.000552) test_to_s: .: (0.000419) test_to_s_attr_order_changed: .: (0.000550) Bio::TestGFF3RecordEscape: test_escape: .: (0.000354) test_escape_attribute: .: (0.000251) test_escape_seqid: .: (0.000247) test_unescape: .: (0.000213) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000469) test_eqeq: .: (0.000268) test_new_from_sequences_na: .: (0.000334) test_new_from_sequences_na_aa: .: (0.000366) test_new_from_sequences_na_aa_boundary_gap: .: (0.000410) test_new_from_sequences_na_aa_example: .: (0.000536) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000287) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000341) test_process_sequences_na: .: (0.000347) test_process_sequences_na_aa: .: (0.000279) test_process_sequences_na_aa_reverse_frameshift: .: (0.000271) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000527) test_process_sequences_na_aa_tooshort: .: (0.000484) test_process_sequences_na_tooshort: .: (0.000343) test_to_s: .: (0.000253) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000408) test_attributes_one: .: (0.000188) test_attributes_with_escaping: .: (0.000200) test_id_multiple: .: (0.000301) test_id_multiple2: .: (0.000520) test_id_replace: .: (0.000196) test_id_set: .: (0.000217) test_initialize_9: .: (0.000153) test_phase: .: (0.000213) test_score: .: (0.000224) test_to_s_void: .: (0.000236) Bio::TestGFF3RecordTarget: test_end: .: (0.000307) test_parse: .: (0.000279) test_start: .: (0.000153) test_strand: .: (0.000152) test_target_id: .: (0.000365) test_to_s: .: (0.000232) Bio::TestGFF3SequenceRegion: test_end: .: (0.000298) test_parse: .: (0.000249) test_seqid: .: (0.000245) test_start: .: (0.000151) test_to_s: .: (0.000233) Bio::TestGFFRecord: test_attributes: .: (0.000367) test_comment: .: (0.000184) test_end: .: (0.000177) test_feature: .: (0.000434) test_frame: .: (0.000184) test_score: .: (0.000171) test_seqname: .: (0.000173) test_source: .: (0.000226) test_start: .: (0.000186) test_strand: .: (0.000162) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000349) Bio::TestGeneAssociation: test_aspect: .: (0.000347) test_assigned_by: .: (0.000179) test_date: .: (0.000163) test_db: .: (0.000164) test_db_object_id: .: (0.000174) test_db_object_name: .: (0.000385) test_db_object_symbol: .: (0.000182) test_db_object_synonym: .: (0.000203) test_db_object_type: .: (0.000203) test_db_reference: .: (0.000172) test_evidence: .: (0.000167) test_goid: .: (0.000196) test_parser: .: (0.000581) test_qualifier: .: (0.000172) test_taxon: .: (0.000160) test_to_str: .: (0.000370) test_with: .: (0.000297) Bio::TestGenscanReport: test_date_run: .: (0.001014) test_gccontent: .: (0.000711) test_genscan_version: .: (0.000889) test_isochore: .: (0.000684) test_length: .: (0.000870) test_matrix: .: (0.000669) test_predictions_size: .: (0.000824) test_query_name: .: (0.000708) test_time: .: (0.000637) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.001035) test_donor_score: .: (0.000617) test_exon_type: .: (0.000601) test_exon_type_long: .: (0.005121) test_first: .: (0.000818) test_initiation_score: .: (0.001048) test_last: .: (0.000734) test_number: .: (0.000704) test_p_value: .: (0.000933) test_phase: .: (0.000687) test_range: .: (0.000855) test_score: .: (0.000675) test_strand: .: (0.000793) test_t_score: .: (0.000637) test_termination_score: .: (0.000627) Bio::TestGenscanReportGene: test_aaseq: .: (0.001030) test_naseq: .: (0.000723) test_number: .: (0.000750) test_polyA: .: (0.000674) test_promoter: .: (0.000785) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000910) test_reports_ary_contents: .: (0.000612) Bio::TestHMMERReportConstants: test_rs: .: (0.000265) Bio::TestHMMERReportHit: test_accession: .: (0.000903) test_append_hsp: .: (0.000613) test_bit_score: .: (0.000614) test_definition: .: (0.000739) test_description: .: (0.000606) test_each: .: (0.000647) test_each_hsp: .: (0.000655) test_entry_id: .: (0.000864) test_evalue: .: (0.000622) test_hit: .: (0.000584) test_hit_id: .: (0.000795) test_hsps: .: (0.000680) test_num: .: (0.000627) test_score: .: (0.000612) test_target_def: .: (0.000789) test_target_id: .: (0.000680) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000838) test_each: .: (0.000629) test_each_hit: .: (0.000821) test_histogram: .: (0.000679) test_hits: .: (0.000596) test_hsps: .: (0.000586) test_parameter: .: (0.000814) test_program: .: (0.000708) test_query_info: .: (0.000679) test_statistical_detail: .: (0.000846) test_total_seq_searched: .: (0.000670) test_whole_seq_top_hits: .: (0.000607) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000968) test_histogram: .: (0.000969) test_statistical_detail: .: (0.000799) test_total_seq_searched: .: (0.000653) test_whole_seq_top_hit: .: (0.000939) Bio::TestHMMERReportHsp: test_accession: .: (0.000849) test_bit_score: .: (0.000655) test_csline: .: (0.000627) test_domain: .: (0.000824) test_evalue: .: (0.000652) test_flatseq: .: (0.000673) test_hmm_f: .: (0.000860) test_hmm_t: .: (0.000749) test_hmmseq: .: (0.000675) test_hsp: .: (0.000667) test_midline: .: (0.000899) test_query_frame: .: (0.000743) test_query_from: .: (0.000609) test_query_seq: .: (0.000607) test_query_to: .: (0.000927) test_rfline: .: (0.000752) test_score: .: (0.000645) test_seq_f: .: (0.000898) test_seq_ft: .: (0.000753) test_seq_t: .: (0.000628) test_set_alignment: .: (0.000586) test_targat_to: .: (0.000917) test_target_frame: .: (0.000674) test_target_from: .: (0.000704) test_target_seq: .: (0.000614) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000813) test_find_hetatm: .: (0.000267) test_hetatms: .: (0.000344) Bio::TestHeterogen: test_addAtom: .: (0.000397) test_each: .: (0.000488) test_each_hetatm: .: (0.000237) test_get_residue_id_from_atom: .: (0.000205) test_het_atom: .: (0.000179) test_iCode: .: (0.000175) test_inspect: .: (0.000336) test_resSeq: .: (0.004947) test_sort: .: (0.000305) test_square_bracket: .: (0.005999) test_to_s: .: (0.000390) test_update_resudue_id: .: (0.000339) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.003649) test_find_heterogen: .: (0.000264) test_heterogens: .: (0.000228) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.005601) test_match_description: .: (0.005166) test_match_evalue: .: (0.000293) test_match_ipr_description: .: (0.000235) test_match_ipr_id: .: (0.005249) test_match_match_end: .: (0.000274) test_match_match_start: .: (0.005702) test_match_method: .: (0.000256) test_matches_size: .: (0.003620) test_query_id: .: (0.000252) test_query_length: .: (0.003325) Bio::TestIprscanRawReport: test_entry_id: .: (0.011053) test_match_accession: .: (0.002183) test_match_crc64: .: (0.001877) test_match_date: .: (0.002004) test_match_description: .: (0.001969) test_match_evalue: .: (0.002114) test_match_go_terms: .: (0.002170) test_match_ipr_description: .: (0.002096) test_match_ipr_id: .: (0.002151) test_match_match_end: .: (0.002320) test_match_match_start: .: (0.002177) test_match_method: .: (0.002189) test_match_query_id: .: (0.002264) test_match_query_length: .: (0.003694) test_match_status: .: (0.002311) test_obj: .: (0.001945) test_query_id: .: (0.001885) test_query_length: .: (0.001910) test_self_reports_in_raw: .: (0.003450) Bio::TestIprscanReport: test_output_raw: .: (0.000939) test_to_raw: .: (0.000542) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000672) test_match_accession: .: (0.000485) test_match_date: .: (0.000632) test_match_description: .: (0.000510) test_match_evalue: .: (0.000472) test_match_go_terms: .: (0.000451) test_match_ipr_description: .: (0.000745) test_match_ipr_id: .: (0.000510) test_match_match_end: .: (0.000455) test_match_match_start: .: (0.000428) test_match_method: .: (0.000691) test_match_status: .: (0.000441) test_matches_size: .: (0.000437) test_query_id: .: (0.000428) test_query_length: .: (0.000595) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000704) test_to_hash_match?: .: (0.000581) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.001242) Bio::TestKeggCompound: test_comment: .: (0.000616) test_dblinks_as_hash: .: (0.000415) test_dblinks_as_strings: .: (0.000366) test_entry_id: .: (0.000536) test_enzymes: .: (0.000626) test_formula: .: (0.000367) test_kcf: .: (0.000303) test_mass: .: (0.000358) test_name: .: (0.000330) test_names: .: (0.000362) test_pathways_as_hash: .: (0.000501) test_pathways_as_strings: .: (0.000395) test_reactions: .: (0.000616) test_remark: .: (0.000570) test_rpairs: .: (0.000407) Bio::TestKeggEnzyme: test_all_reac: .: (0.000786) test_classes: .: (0.000553) test_cofactors: .: (0.000520) test_comment: .: (0.000532) test_dblinks_as_hash: .: (0.000574) test_dblinks_as_strings: .: (0.000710) test_diseases: .: (0.000439) test_entry: .: (0.000545) test_entry_id: .: (0.000460) test_genes: .: (0.012624) test_genes_as_hash: .: (0.010615) test_genes_as_strings: .: (0.003791) test_inhibitors: .: (0.000606) test_iubmb_reactions: .: (0.000620) test_kegg_reactions: .: (0.000559) test_motifs: .: (0.000782) test_name: .: (0.000661) test_names: .: (0.000594) test_obsolete?: .: (0.000520) test_orthologs_as_hash: .: (0.000516) test_orthologs_as_strings: .: (0.000482) test_pathways_as_hash: .: (0.000939) test_pathways_as_strings: .: (0.000692) test_products: .: (0.000594) test_reaction: .: (0.000598) test_structures: .: (0.000717) test_substrates: .: (0.000726) test_sysname: .: (0.000515) Bio::TestKeggGenesDblinks: test_data: .: (0.000422) test_dblinks_0: .: (0.000201) test_dblinks_1: .: (0.000178) test_dblinks_2: .: (0.000192) Bio::TestKeggGenesStructure: test_data: .: (0.000366) test_ids: .: (0.000226) test_ids_in_array: .: (0.000197) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.009729) test_graphics__size: .: (0.006583) test_id: .: (0.006371) test_link: .: (0.007409) test_name: .: (0.059647) test_reaction: .: (0.006129) test_type: .: (0.006182) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.005991) test_graphics__size: .: (0.005589) test_id: .: (0.005791) test_link: .: (0.005849) test_name: .: (0.006417) test_reaction: .: (0.006752) test_type: .: (0.005704) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.005943) test_category: .: (0.005412) test_entry_id: .: (0.005311) test_fgcolor=: .: (0.005420) test_height=: .: (0.005714) test_label=: .: (0.006838) test_shape=: .: (0.005951) test_width=: .: (0.005587) test_x=: .: (0.005579) test_y=: .: (0.005665) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.005521) test_graphics__size: .: (0.005384) test_id: .: (0.006559) test_link: .: (0.005846) test_name: .: (0.005541) test_reaction: .: (0.005539) test_type: .: (0.005513) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000474) test_graphics=: .: (0.000331) test_id=: .: (0.000185) test_link=: .: (0.000176) test_name=: .: (0.000170) test_reaction=: .: (0.000166) test_type=: .: (0.000168) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000358) test_category=: .: (0.000212) test_entry_id=: .: (0.000171) test_fgcolor=: .: (0.000171) test_height=: .: (0.000163) test_label=: .: (0.000450) test_pathway=: .: (0.000155) test_shape=: .: (0.000200) test_width=: .: (0.000187) test_x=: .: (0.000172) test_y=: .: (0.000162) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.005701) test_coords: .: (0.005548) test_fgcolor: .: (0.006751) test_height: .: (0.005612) test_name: .: (0.005666) test_type: .: (0.005656) test_width: .: (0.005385) test_x: .: (0.005397) test_y: .: (0.005357) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.006697) test_coords: .: (0.006045) test_fgcolor: .: (0.005478) test_height: .: (0.005619) test_name: .: (0.005304) test_type: .: (0.005307) test_width: .: (0.005329) test_x: .: (0.005648) test_y: .: (0.006621) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000344) test_coords=: .: (0.000183) test_fgcolor=: .: (0.000179) test_height=: .: (0.000171) test_name=: .: (0.000381) test_type=: .: (0.000173) test_width=: .: (0.000228) test_x=: .: (0.000171) test_y=: .: (0.000168) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.005529) test_entries__size: .: (0.005479) test_image: .: (0.005704) test_link: .: (0.005330) test_name: .: (0.005399) test_number: .: (0.005596) test_org: .: (0.006788) test_reactions=: .: (0.005546) test_reactions__size: .: (0.005546) test_relations=: .: (0.005496) test_relations__size: .: (0.005369) test_title: .: (0.005313) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.011962) test_name: .: (0.010758) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000352) test_initialize_0: .: (0.000165) test_initialize_1: .: (0.000167) test_initialize_2: .: (0.000168) test_name=: .: (0.000195) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.005537) test_name: .: (0.005514) test_products: .: (0.005300) test_substrates: .: (0.005508) test_type: .: (0.006853) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000386) test_name=: .: (0.000188) test_products=: .: (0.000185) test_substraces=: .: (0.000198) test_type=: .: (0.000191) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000584) test_entry_id=: .: (0.000198) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.005663) test_entry2: .: (0.005373) test_name: .: (0.005703) test_type: .: (0.005366) test_value: .: (0.005455) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000336) test_node1=: .: (0.000192) test_node2=: .: (0.000378) test_rel=: .: (0.000198) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000323) test_entry2=: .: (0.000179) test_name=: .: (0.000182) test_type=: .: (0.000186) test_value=: .: (0.000249) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.012468) test_name: .: (0.010609) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000362) test_initialize_0: .: (0.000175) test_initialize_1: .: (0.000163) test_initialize_2: .: (0.000155) test_name=: .: (0.000173) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000481) test_initialize_0: .: (0.000150) test_initialize_1: .: (0.000152) test_initialize_2: .: (0.000154) test_name=: .: (0.000175) Bio::TestKeggModule: test_compounds: .: (0.000582) test_compounds_as_hash: .: (0.000355) test_compounds_as_strings: .: (0.000303) test_definition: .: (0.000301) test_entry_id: .: (0.000394) test_keggclass: .: (0.000304) test_name: .: (0.000283) test_new: .: (0.000267) test_orthologs: .: (0.000340) test_orthologs_as_array: .: (0.000374) test_orthologs_as_hash: .: (0.000312) test_orthologs_as_strings: .: (0.000294) test_pathways: .: (0.000406) test_pathways_as_hash: .: (0.000300) test_pathways_as_strings: .: (0.000246) test_reactions: .: (0.000349) test_reactions_as_hash: .: (0.000327) test_reactions_as_strings: .: (0.000303) Bio::TestKeggOrthology: test_dblinks: .: (0.000648) test_dblinks_as_hash: .: (0.000692) test_dblinks_as_strings: .: (0.000436) test_definition: .: (0.000476) test_entry_id: .: (0.000434) test_genes_as_hash: .: (0.008190) test_genes_as_strings: .: (0.003149) test_keggclass: .: (0.000594) test_keggclasses: .: (0.000547) test_modules: .: (0.000566) test_modules_as_hash: .: (0.000439) test_modules_as_strings: .: (0.000435) test_name: .: (0.002635) test_names: .: (0.000503) test_pathways_as_strings: .: (0.000496) test_pathways_in_keggclass: .: (0.000622) test_references: .: (0.000692) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000504) test_compounds_as_strings: .: (0.000511) test_dblinks_as_hash: .: (0.000369) test_dblinks_as_strings: .: (0.000309) test_description: .: (0.000335) test_diseases_as_hash: .: (0.000273) test_diseases_as_strings: .: (0.000276) test_entry_id: .: (0.000299) test_enzymes_as_strings: .: (0.000274) test_genes_as_hash: .: (0.000265) test_genes_as_strings: .: (0.000264) test_keggclass: .: (0.000507) test_ko_pathway: .: (0.000368) test_modules_as_hash: .: (0.000352) test_modules_as_strings: .: (0.000329) test_name: .: (0.000299) test_organism: .: (0.000290) test_orthologs_as_hash: .: (0.000279) test_orthologs_as_strings: .: (0.000268) test_pathways_as_hash: .: (0.000305) test_pathways_as_strings: .: (0.000525) test_reactions_as_hash: .: (0.000276) test_reactions_as_strings: .: (0.000302) test_references: .: (0.000298) test_rel_pathways_as_hash: .: (0.000315) test_rel_pathways_as_strings: .: (0.000281) Bio::TestKeggReaction: test_definition: .: (0.000506) test_entry_id: .: (0.000308) test_enzymes: .: (0.000631) test_equation: .: (0.000333) test_name: .: (0.000353) test_orthologs_as_hash: .: (0.000356) test_orthologs_as_strings: .: (0.000341) test_pathways_as_hash: .: (0.000355) test_pathways_as_strings: .: (0.000332) test_rpairs_as_hash: .: (0.000327) test_rpairs_as_strings: .: (0.000550) test_rpairs_as_tokens: .: (0.000380) Bio::TestLasergene: test_methods: .: (0.004756) Bio::TestLocations: test_complement: .: (0.000429) test_hat: .: (0.000225) test_normal: .: (0.000217) test_replace_single_base: .: (0.000212) test_should_not_modify_argument: .: (0.000212) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002545) test_locations_to_s: .: (0.001285) Bio::TestMEDLINE: test_authors: .: (0.000687) test_authors_with_last_name_all_caps: .: (0.000162) test_authors_with_suffix: .: (0.000167) Bio::TestMEDLINE_20146148: test_ab: .: (0.000591) test_ad: .: (0.000694) test_au: .: (0.000506) test_authors: .: (0.000413) test_doi: .: (0.000386) test_dp: .: (0.000613) test_ip: .: (0.000468) test_mh: .: (0.000450) test_pages: .: (0.000404) test_pg: .: (0.000852) test_pii: .: (0.000472) test_pmid: .: (0.000403) test_pt: .: (0.000437) test_reference: .: (0.001008) test_self_new: .: (0.000411) test_so: .: (0.000401) test_ta: .: (0.000360) test_ti: .: (0.000550) test_ui: .: (0.000461) test_vi: .: (0.000369) test_year: .: (0.000374) Bio::TestMapSimple: test_attributes: .: (0.000373) Bio::TestMapping: test_add_mapping_as_map: .: (0.000681) test_add_mapping_as_marker: .: (0.000259) test_contains_marker?: .: (0.000218) test_mapped_to?: .: (0.000197) test_mapping_location_comparison: .: (0.000368) test_mappings_as_map_each: .: (0.000213) test_mappings_as_marker_each: .: (0.000251) test_mappings_on: .: (0.000258) test_multiple_mappings_between_same_marker_and_map: .: (0.000326) test_positions_on: .: (0.000512) test_raise_error_kind_of: .: (0.000485) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000468) test_check_options_with_invalid_opts: .: (0.000332) test_check_options_with_valid_opts: .: (0.000258) test_command_to_be_run: .: (0.000248) test_config_defaults: .: (0.000219) test_minimal_config: .: (0.000219) test_more_config: .: (0.000190) test_run: .: (0.000157) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000798) test_report_has_motifs: .: (0.000331) Bio::TestModel: test_addChain: .: (0.000307) test_comp: .: (0.000182) test_each: .: (0.000191) test_each_chain: .: (0.000153) test_inspect: .: (0.000156) test_rehash: .: (0.000139) test_square_brace: .: (0.000149) test_to_s: .: (0.000153) Bio::TestModelFinder: test_find_model: .: (0.000537) Bio::TestMotif: test_creation_and_attributes: .: (0.000356) test_length: .: (0.000151) Bio::TestMyGraph: test_cliquishness: .: (0.000545) Bio::TestNA: test_accessor: .: (0.000274) test_na: .: (0.000153) test_name: .: (0.000136) test_names: .: (0.000154) test_to_re: .: (0.000276) test_weight: .: (0.000156) test_weight_rna: .: (0.000161) Bio::TestNAConstants: test_NAMES: .: (0.000314) test_NAMES_1_to_name: .: (0.000154) test_WEIGHT: .: (0.000140) Bio::TestNATranslate: test_translate: .: (0.000417) test_translate_1: .: (0.000226) test_translate_2: .: (0.000159) test_translate_3: .: (0.000148) test_translate_4: .: (0.000247) test_translate_5: .: (0.000171) test_translate_6: .: (0.000176) Bio::TestNCBIDB: test_fetch: .: (0.000342) test_p_entry2hash: .: (0.000129) test_p_subtag2array: .: (0.000463) test_p_toptag2array: .: (0.000215) Bio::TestNewick: test_reparse: .: (0.001084) test_reparse_before_lazy_parsing: .: (0.000469) test_string_tree: .: (0.001065) Bio::TestNewick2: test_string_tree: .: (0.000726) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000314) test_parse_newick_leaf: .: (0.000260) test_parse_newick_tokenize: .: (0.000414) Bio::TestNexus: test_nexus: .: (0.012706) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000698) test_uncapitalized_letter_Q32725_9POAL: .: (0.000259) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000360) test_load_parameters: .: (0.000216) test_parameters: .: (0.000164) test_set_default_parameters: .: (0.000187) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000704) test_expected_parameters_set_in_control_file: .: (0.000632) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000609) test_new_with_parameters: .: (0.000296) test_new_with_two_argument: .: (0.000205) test_new_without_argument: .: (0.000189) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001507) test_rates_hundred_and_fiftieth_position: .: (0.001290) test_rates_last_position: .: (0.001234) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.005762) test_tree: .: (0.005440) test_tree_length: .: (0.006226) test_tree_log_likelihood: .: (0.005451) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000588) test_parameters_should_be_loaded_from_control: .: (0.000355) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001473) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000431) test_dN_dS: .: (0.000266) test_kappa: .: (0.000280) test_lnL: .: (0.000250) test_m3_classes: .: (0.000385) test_m3_lnL: .: (0.000267) test_m3_to_s: .: (0.000245) test_m3_tree: .: (0.000562) test_omega: .: (0.000232) test_to_s: .: (0.000404) test_tree: .: (0.000534) test_tree_length: .: (0.000238) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000641) test_p: .: (0.000403) test_position: .: (0.000584) test_probability: .: (0.000412) test_w: .: (0.000382) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000939) test_graph_omega: .: (0.000583) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000381) test_footer: .: (0.000228) test_header: .: (0.000212) test_initialize: .: (0.000235) test_models: .: (0.000263) test_nb_sites: .: (0.000911) test_num_codons: .: (0.000259) test_num_sequences: .: (0.000278) test_significant: .: (0.000302) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000429) test_nb_sites: .: (0.000359) test_significant: .: (0.000280) test_sites: .: (0.001342) Bio::TestPDB: test_accession: .: (0.001597) test_addModel: .: (0.000831) test_authors: .: (0.001076) test_bracket: .: (0.000783) test_classification: .: (0.000943) test_dbref: .: (0.000860) test_definition: .: (0.000968) test_each: .: (0.000762) test_each_model: .: (0.000930) test_entry_id: .: (0.000730) test_helix: .: (0.001159) test_inspect: .: (0.000778) test_jrnl: .: (0.000764) test_keywords: .: (0.001033) test_record: .: (0.000782) test_remark: .: (0.001249) test_seqres: .: (0.000996) test_sheet: .: (0.001578) test_ssbond: .: (0.000778) test_to_s: .: (0.014313) test_turn: .: (0.015242) test_version: .: (0.012814) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000436) test_U12: .: (0.005447) test_U13: .: (0.000246) test_U22: .: (0.000215) test_U23: .: (0.000223) test_U33: .: (0.004853) test_altLoc: .: (0.000266) test_chainID: .: (0.000326) test_charge: .: (0.000219) test_element: .: (0.000232) test_iCode: .: (0.000220) test_name: .: (0.000225) test_resName: .: (0.000234) test_resSeq: .: (0.000253) test_segID: .: (0.000222) test_serial: .: (0.000205) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000362) test_anisou: .: (0.000195) test_chainID: .: (0.000169) test_charge: .: (0.000154) test_comparable: .: (0.000505) test_do_parse: .: (0.000164) test_element: .: (0.000154) test_iCode: .: (0.000182) test_name: .: (0.000155) test_occupancy: .: (0.000233) test_original_data: .: (0.000174) test_record_name: .: (0.000166) test_resName: .: (0.000161) test_resSeq: .: (0.000164) test_residue: .: (0.000166) test_segID: .: (0.000175) test_serial: .: (0.000166) test_sigatm: .: (0.000161) test_tempFactor: .: (0.000491) test_ter: .: (0.000181) test_to_a: .: (0.000190) test_to_s: .: (0.000233) test_x: .: (0.000212) test_xyz: .: (0.000215) test_y: .: (0.000349) test_z: .: (0.000191) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000342) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000317) test_idcode: .: (0.000159) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000689) test_chainID2: .: (0.000197) test_icode1: .: (0.000167) test_icode2: .: (0.000186) test_measure: .: (0.000205) test_modNum: .: (0.000192) test_pep1: .: (0.000174) test_pep2: .: (0.000176) test_seqNum1: .: (0.000193) test_seqNum2: .: (0.000183) test_serNum: .: (0.000217) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000347) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000293) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000560) test_alpha: .: (0.000166) test_b: .: (0.000161) test_beta: .: (0.000169) test_c: .: (0.000164) test_gamma: .: (0.000172) test_sGroup: .: (0.000222) test_z: .: (0.000160) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000375) test_database: .: (0.000227) test_dbAccession: .: (0.000204) test_dbIdCode: .: (0.000211) test_dbseqBegin: .: (0.000443) test_dbseqEnd: .: (0.000198) test_idCode: .: (0.000182) test_idbnsBeg: .: (0.000224) test_insertBegin: .: (0.000214) test_insertEnd: .: (0.000190) test_seqBegin: .: (0.000184) test_seqEnd: .: (0.000233) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000342) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000285) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000286) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000280) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000299) test_depDate: .: (0.000177) test_idCode: .: (0.000166) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000336) test_hetID: .: (0.000184) test_iCode: .: (0.000178) test_numHetAtoms: .: (0.000204) test_seqNum: .: (0.000214) test_text: .: (0.000215) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000310) test_anisou: .: (0.000377) test_chainID: .: (0.000156) test_charge: .: (0.000138) test_comparable: .: (0.000180) test_do_parse: .: (0.000163) test_element: .: (0.000156) test_iCode: .: (0.000143) test_name: .: (0.000152) test_occupancy: .: (0.000213) test_original_data: .: (0.000166) test_record_name: .: (0.000187) test_resName: .: (0.000156) test_resSeq: .: (0.000158) test_residue: .: (0.000150) test_segID: .: (0.000178) test_serial: .: (0.000150) test_sigatm: .: (0.000411) test_tempFactor: .: (0.000221) test_ter: .: (0.000159) test_to_a: .: (0.000159) test_to_s: .: (0.000214) test_x: .: (0.000202) test_xyz: .: (0.000204) test_y: .: (0.000195) test_z: .: (0.000184) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000427) test_ChainH: .: (0.000209) test_ICode1: .: (0.000491) test_altLoc1: .: (0.000204) test_altLoc2: .: (0.000200) test_altLocH: .: (0.000199) test_chainID2: .: (0.000195) test_iCode2: .: (0.000239) test_iCodeH: .: (0.000226) test_name1: .: (0.000218) test_name2: .: (0.000230) test_nameH: .: (0.000226) test_resName1: .: (0.000227) test_resName2: .: (0.000395) test_resSeq1: .: (0.000211) test_resSeq2: .: (0.000291) test_resSeqH: .: (0.000227) test_sym1: .: (0.000235) test_sym2: .: (0.000207) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000381) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000334) test_altLoc2: .: (0.000172) test_chainID1: .: (0.000184) test_chainID2: .: (0.000180) test_iCode1: .: (0.000389) test_iCode2: .: (0.000197) test_name1: .: (0.000193) test_name2: .: (0.000194) test_resName1: .: (0.000199) test_resName2: .: (0.000194) test_resSeq1: .: (0.000199) test_resSeq2: .: (0.000191) test_sym1: .: (0.000187) test_sym2: .: (0.000205) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000352) test_numCoord: .: (0.000165) test_numHelix: .: (0.000175) test_numHet: .: (0.000243) test_numRemark: .: (0.000154) test_numSeq: .: (0.000145) test_numSheet: .: (0.000172) test_numSite: .: (0.000152) test_numTer: .: (0.000146) test_numTurn: .: (0.000152) test_numXform: .: (0.000160) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000291) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000304) test_comment: .: (0.000167) test_iCode: .: (0.000195) test_idCode: .: (0.000168) test_resName: .: (0.000176) test_seqNum: .: (0.000164) test_stdRes: .: (0.000408) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000326) test_Mn2: .: (0.000157) test_Mn3: .: (0.000155) test_Vn: .: (0.000149) test_iGiven: .: (0.000161) test_serial: .: (0.000146) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000304) test_Mn2: .: (0.000152) test_Mn3: .: (0.000151) test_Vn: .: (0.000171) test_iGiven: .: (0.000154) test_serial: .: (0.000149) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000301) test_Mn2: .: (0.000423) test_Mn3: .: (0.000160) test_Vn: .: (0.000161) test_iGiven: .: (0.000160) test_serial: .: (0.000199) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000336) test_rIdCode: .: (0.000182) test_repDate: .: (0.000176) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000337) test_On2: .: (0.000174) test_On3: .: (0.000171) test_Tn: .: (0.000149) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000363) test_modId: .: (0.000186) test_modNum: .: (0.000397) test_modType: .: (0.000237) test_record: .: (0.000180) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000293) test_text: .: (0.000154) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000289) test_Sn2: .: (0.000152) test_Sn3: .: (0.000140) test_Un: .: (0.000141) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000277) test_Sn2: .: (0.000144) test_Sn3: .: (0.000179) test_Un: .: (0.000154) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000327) test_Sn2: .: (0.000410) test_Sn3: .: (0.000196) test_Un: .: (0.000165) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000374) test_conflict: .: (0.000178) test_database: .: (0.000185) test_dbIdCode: .: (0.000213) test_dbRes: .: (0.000173) test_dbSeq: .: (0.000189) test_iCode: .: (0.000211) test_idCode: .: (0.000186) test_resName: .: (0.000179) test_seqNum: .: (0.000172) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000320) test_numRes: .: (0.000190) test_resName: .: (0.000182) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000393) test_curChainId: .: (0.000206) test_curICode: .: (0.000198) test_curResName: .: (0.000211) test_curResSeq: .: (0.000189) test_endChainID: .: (0.000191) test_endICode: .: (0.000188) test_endResName: .: (0.000376) test_endSeqNum: .: (0.000233) test_initChainID: .: (0.000209) test_initICode: .: (0.000193) test_initResName: .: (0.000234) test_initSeqNum: .: (0.000193) test_numStrands: .: (0.000193) test_prevAtom: .: (0.000192) test_prevChainId: .: (0.000191) test_prevICode: .: (0.000201) test_prevResName: .: (0.000189) test_prevResSeq: .: (0.000464) test_sense: .: (0.000253) test_sheetID: .: (0.000237) test_strand: .: (0.000223) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000387) test_chainID: .: (0.000233) test_charge: .: (0.000217) test_element: .: (0.000206) test_iCode: .: (0.000226) test_name: .: (0.000220) test_resName: .: (0.000210) test_resSeq: .: (0.000454) test_segID: .: (0.000228) test_serial: .: (0.000214) test_sigOcc: .: (0.000190) test_sigTemp: .: (0.000192) test_sigX: .: (0.000178) test_sigY: .: (0.000253) test_sigZ: .: (0.000185) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000351) test_SigmaU12: .: (0.000184) test_SigmaU13: .: (0.000213) test_SigmaU22: .: (0.000173) test_SigmaU23: .: (0.000167) test_SigmaU33: .: (0.000174) test_altLoc: .: (0.000434) test_chainID: .: (0.000208) test_charge: .: (0.000189) test_element: .: (0.000215) test_iCode: .: (0.000214) test_name: .: (0.000196) test_resName: .: (0.000182) test_resSeq: .: (0.000239) test_segID: .: (0.000178) test_serial: .: (0.000177) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000377) test_chainID2: .: (0.000183) test_chainID3: .: (0.000191) test_chainID4: .: (0.000192) test_iCode1: .: (0.000231) test_iCode2: .: (0.000189) test_iCode3: .: (0.000183) test_iCode4: .: (0.000186) test_numRes: .: (0.000211) test_resName1: .: (0.000191) test_resName2: .: (0.000188) test_resName3: .: (0.000186) test_resName4: .: (0.000180) test_seq1: .: (0.000182) test_seq2: .: (0.000193) test_seq3: .: (0.000434) test_seq4: .: (0.000192) test_seqNum: .: (0.000181) test_siteID: .: (0.000188) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000370) test_altLoc2: .: (0.000172) test_atom1: .: (0.000163) test_atom2: .: (0.000188) test_chainID1: .: (0.000168) test_chainID2: .: (0.000172) test_iCode1: .: (0.000165) test_iCode2: .: (0.000163) test_resName1: .: (0.000164) test_resName2: .: (0.000434) test_resSeq1: .: (0.000183) test_resSeq2: .: (0.000201) test_sym1: .: (0.000227) test_sym2: .: (0.000191) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000386) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000325) test_sIdCode: .: (0.000172) test_sprsdeDate: .: (0.000172) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000356) test_iCode: .: (0.000174) test_resName: .: (0.000201) test_resSeq: .: (0.000476) test_serial: .: (0.000206) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000323) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000313) test_t1: .: (0.000163) test_t2: .: (0.000160) test_t3: .: (0.000160) test_text: .: (0.000171) Bio::TestPROSITE: test_ac: .: (0.001488) test_cc: .: (0.001263) test_de: .: (0.001365) test_division: .: (0.001142) test_dr: .: (0.016522) test_dt: .: (0.001410) test_false_neg: .: (0.001342) test_false_pos: .: (0.001323) test_false_positive_sequences: .: (0.001310) test_list_falsenegative: .: (0.012175) test_list_falsepositive: .: (0.069054) test_list_potentialhit: .: (0.013093) test_list_truepositive: .: (0.013733) test_list_unknown: .: (0.015922) test_list_xref: .: (0.013541) test_ma: .: (0.001485) test_max_repeat: .: (0.001655) test_name: .: (0.001524) test_nr: .: (0.001628) test_pa: .: (0.001605) test_pa2re: .: (0.001526) test_partial: .: (0.001349) test_pdb_xref: .: (0.001279) test_pdoc_xref: .: (0.001243) test_positive: .: (0.001302) test_positive_hits: .: (0.001335) test_positive_sequences: .: (0.001338) test_release: .: (0.001319) test_ru: .: (0.001265) test_self_pa2re: .: (0.001273) test_site: .: (0.001289) test_skip_flag: .: (0.001332) test_swissprot_release_number: .: (0.001374) test_swissprot_release_sequences: .: (0.001394) test_taxon_range: .: (0.001335) test_total: .: (0.001362) test_total_hits: .: (0.001405) test_total_sequences: .: (0.001305) test_unknown: .: (0.001285) test_unknown_hits: .: (0.001269) test_unknown_sequences: .: (0.001268) Bio::TestPROSITEConst: test_delimiter: .: (0.000383) test_tagsize: .: (0.000153) Bio::TestPTS1: test_function_set: .: (0.000367) test_function_set_number_1: .: (0.000167) test_function_set_number_2: .: (0.000177) test_function_set_number_3: .: (0.000230) test_function_show: .: (0.000142) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000338) Bio::TestPTS1New: test_fungi: .: (0.000277) test_general: .: (0.000193) test_metazoa: .: (0.000148) Bio::TestQualifier: test_qualifier: .: (0.000261) test_value: .: (0.000146) Bio::TestREBASE: test_methods: .: (0.000916) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001092) test_bit_score: .: (0.000806) test_evalue: .: (0.000680) test_gaps: .: (0.000650) test_hit_from: .: (0.000745) test_hit_to: .: (0.000671) test_hseq: .: (0.000624) test_identity: .: (0.000635) test_midline: .: (0.000641) test_percent_identity: .: (0.000628) test_positive: .: (0.000602) test_qseq: .: (0.000666) test_query_from: .: (0.000649) test_query_to: .: (0.000637) test_score: .: (0.000611) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000745) test_hits_size: .: (0.001102) test_iterations_size: .: (0.001057) test_program: .: (0.000615) test_query_def: .: (0.001113) test_query_len: .: (0.001061) test_version: .: (0.000601) test_version_date: .: (0.000624) test_version_number: .: (0.000587) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000802) test_definition: .: (0.000649) test_evalue: .: (0.000635) test_hsps_size: .: (0.000591) test_identity: .: (0.000668) test_lap_at: .: (0.000680) test_len: .: (0.000640) test_midline: .: (0.000677) test_overlap: .: (0.000646) test_query_end: .: (0.000703) test_query_seq: .: (0.000655) test_query_start: .: (0.000667) test_target_def: .: (0.000627) test_target_end: .: (0.000679) test_target_len: .: (0.000644) test_target_seq: .: (0.000682) test_target_start: .: (0.000640) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000629) test_get_entry: .: (0.000509) test_rewind: .: (0.000196) test_skip_leader: .: (0.000278) Bio::TestReference: test_abstract: .: (0.000297) test_affiliations: .: (0.000143) test_authors: .: (0.000235) test_format_bibitem: .: (0.000223) test_format_bibtex: .: (0.000332) test_format_bibtex_with_arguments: .: (0.000319) test_format_cell: .: (0.000172) test_format_current: .: (0.000216) test_format_endnote: .: (0.000252) test_format_general: .: (0.000190) test_format_genome_biol: .: (0.000235) test_format_genome_res: .: (0.000192) test_format_nar: .: (0.000264) test_format_nature: .: (0.000215) test_format_rd: .: (0.000226) test_format_science: .: (0.000256) test_format_trends: .: (0.000235) test_issue: .: (0.000164) test_journal: .: (0.000150) test_mesh: .: (0.000226) test_pages: .: (0.000140) test_pubmed: .: (0.000133) test_pubmed_url: .: (0.000172) test_url: .: (0.000140) test_volume: .: (0.000143) test_year: .: (0.000157) Bio::TestReference_noURL: test_format_endnote: .: (0.000405) test_url: .: (0.000165) Bio::TestReferences: test_append: .: (0.000407) test_each: .: (0.000193) Bio::TestRelation: test_comparison_operator: .: (0.000310) test_uniq: .: (0.000262) Bio::TestResidue: test_addAtom: .: (0.000441) test_each: .: (0.000323) test_each_atom: .: (0.000251) test_get_residue_id_from_atom: .: (0.000261) test_het_atom: .: (0.000259) test_iCode: .: (0.000202) test_inspect: .: (0.000266) test_resSeq: .: (0.000188) test_sort: .: (0.000246) test_square_bracket: .: (0.000313) test_to_s: .: (0.000293) test_update_resudue_id: .: (0.000234) Bio::TestResidueFinder: test_each_residue: .: (0.000432) test_find_residue: .: (0.000187) test_residues: .: (0.000236) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.080756) test_cut_from_bio_sequence_na: .: (0.025080) test_cut_without_permutations: .: (0.015299) test_view_ranges: .: (0.014728) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001069) test_cuts_after_remove_incomplete_cuts: .: (0.000564) test_strands_for_display: .: (0.001870) test_strands_for_display_current: .: (0.000628) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000638) test_fragments_for_display_1: .: (0.000665) test_fragments_for_display_10: .: (0.000887) test_fragments_for_display_2: .: (0.000654) test_fragments_for_display_3: .: (0.000924) test_fragments_for_display_4: .: (0.000724) test_fragments_for_display_5: .: (0.000687) test_fragments_for_display_6: .: (0.000539) test_fragments_for_display_7: .: (0.000535) test_fragments_for_display_8: .: (0.000513) test_fragments_for_display_9: .: (0.000684) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000409) test_obj_3: .: (0.000256) test_obj_7: .: (0.000218) test_obj_z: .: (0.000239) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000510) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000392) test_bracket_eq: .: (0.000221) test_concat: .: (0.000177) test_delete: .: (0.000209) test_dup: .: (0.000206) test_each: .: (0.000182) test_eqeq: .: (0.000165) test_eqeq_false: .: (0.000144) test_eqeq_other: .: (0.000139) test_eqeq_self: .: (0.000146) test_include?: .: (0.000157) test_internal_data: .: (0.000269) test_internal_data_eq: .: (0.000213) test_length: .: (0.000149) test_ltlt: .: (0.000161) test_ltlt_larger: .: (0.000173) test_ltlt_middle: .: (0.000202) test_plus: .: (0.000204) test_plus_error: .: (0.000276) test_push: .: (0.000181) test_reverse_each: .: (0.000194) test_self_bracket: .: (0.000149) test_self_new: .: (0.000200) test_size: .: (0.000139) test_sort!: .: (0.000127) test_to_a: .: (0.000141) test_uniq!: .: (0.000156) test_unshift: .: (0.000231) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003334) test_complement: .: (0.002837) test_complement_with_cut_symbols: .: (0.003056) test_cut_locations: .: (0.006049) test_cut_locations_in_enzyme_notation: .: (0.003398) test_primary: .: (0.003174) test_primary_with_cut_symbols: .: (0.003198) test_to_re: .: (0.003094) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.001199) test_align_with_cuts: .: (0.000872) test_argument_error: .: (0.001145) test_ds: .: (0.000934) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000523) test_complement: .: (0.000250) test_contents: .: (0.000241) test_primary: .: (0.000230) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000558) test_complement: .: (0.000236) test_contents: .: (0.000225) test_primary: .: (0.000208) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000331) test_contents: .: (0.000173) test_primary: .: (0.000194) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000335) test_complement_to_array_index: .: (0.000354) test_complement_to_array_index_class: .: (0.000237) test_contents: .: (0.000179) test_primary: .: (0.000184) test_primary_to_array_index: .: (0.000245) test_primary_to_array_index_class: .: (0.000260) test_to_array_index: .: (0.000385) test_to_array_index_class: .: (0.000380) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000571) test_rebase: .: (0.000191) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000849) test_creation_with_no_cuts: .: (0.000567) test_cut_locations: .: (0.000396) test_cut_locations_in_enzyme_notation: .: (0.000425) test_orientation: .: (0.000382) test_pattern: .: (0.000562) test_pattern_palindromic?: .: (0.000467) test_stripped: .: (0.000387) test_to_re: .: (0.000525) test_with_cut_symbols: .: (0.000400) test_with_spaces: .: (0.000511) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000890) test_creation_with_no_cuts: .: (0.000451) test_cut_locations: .: (0.000414) test_cut_locations_in_enzyme_notation: .: (0.000551) test_orientation: .: (0.000413) test_pattern: .: (0.000435) test_pattern_palindromic?: .: (0.000620) test_stripped: .: (0.000424) test_to_re: .: (0.000407) test_with_cut_symbols: .: (0.000480) test_with_spaces: .: (0.000600) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000525) test_initialize_with_pattern: .: (0.000377) test_max: .: (0.000214) test_min: .: (0.000196) test_to_array_index: .: (0.000213) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000340) test_bracket_eq: .: (0.000353) test_concat: .: (0.000165) test_delete: .: (0.000141) test_dup: .: (0.000194) test_each: .: (0.000182) test_eqeq: .: (0.000151) test_eqeq_false: .: (0.000139) test_eqeq_other: .: (0.000132) test_eqeq_self: .: (0.000126) test_include?: .: (0.000169) test_internal_data_hash: .: (0.000142) test_internal_data_hash_eq: .: (0.000185) test_length: .: (0.000139) test_ltlt: .: (0.000150) test_ltlt_noeffect: .: (0.000142) test_plus: .: (0.000175) test_plus_error: .: (0.000215) test_private_push_element: .: (0.000166) test_private_push_element_intermediate: .: (0.000143) test_private_push_element_last: .: (0.000150) test_private_push_element_noeffect: .: (0.000152) test_private_sorted_keys: .: (0.000141) test_private_unshift_element: .: (0.000182) test_private_unshift_element_first: .: (0.000162) test_private_unshift_element_intermediate: .: (0.000138) test_private_unshift_element_noeffect: .: (0.000165) test_push: .: (0.000157) test_reverse_each: .: (0.000180) test_self_bracket: .: (0.000149) test_self_new: .: (0.000205) test_size: .: (0.000174) test_sort!: .: (0.000133) test_to_a: .: (0.000142) test_uniq!: .: (0.000137) test_unshift: .: (0.000174) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000331) test_left_padding: .: (0.000164) test_right_padding: .: (0.000179) test_strip_padding: .: (0.000197) Bio::TestSOFT: test_dataset: .: (0.004971) test_series: .: (0.005000) Bio::TestSOSUIReport: test_entry_id: .: (0.000413) test_prediction: .: (0.000224) test_tmh: .: (0.000219) test_tmhs: .: (0.000246) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000271) test_rs: .: (0.000158) Bio::TestSOSUITMH: test_grade: .: (0.000332) test_range: .: (0.000216) test_sequence: .: (0.000205) Bio::TestSampleGraph: test_bellman_ford: .: (0.000529) test_bfs_shortest_path: .: (0.000259) test_breadth_first_search: .: (0.000205) test_depth_first_search: .: (0.000301) test_dijkstra: .: (0.000268) test_dump_list: .: (0.000258) test_dump_matrix: .: (0.000367) test_extract_subgraph_by_label: .: (0.000355) test_extract_subgraph_by_list: .: (0.000248) test_extract_subgraph_retains_disconnected_nodes: .: (0.000203) test_small_world_aka_node_degree_histogram: .: (0.000202) test_to_matrix: .: (0.000404) test_to_matrix_fixed_index: .: (0.000294) test_undirected_cliquishness: .: (0.000333) Bio::TestScf_version_2: test_complement: .: (0.007338) test_seq: .: (0.011487) test_to_biosequence: .: (0.007366) Bio::TestScf_version_3: test_complement: .: (0.021331) test_seq: .: (0.021011) test_to_biosequence: .: (0.020613) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000353) test_AA_new_sequence_all_legal_symbols: .: (0.000176) test_AA_new_sequence_removes_whitespace: .: (0.000182) test_AA_new_sequence_upcases_symbols: .: (0.000164) test_DNA_new_blank_sequence: .: (0.000163) test_DNA_new_sequence_downcases_symbols: .: (0.000164) test_DNA_new_sequence_removes_whitespace: .: (0.000170) test_NA_randomize_with_counts: .: (0.000878) test_NA_randomize_with_counts_and_block: .: (0.000769) test_RNA_new_sequence: .: (0.000174) test_ambiguous_dna_sequence_complement: .: (0.000186) test_ambiguous_rna_sequence_complement: .: (0.000164) test_amino_acid_codes: .: (0.000223) test_amino_acid_molecular_weight: .: (0.000293) test_amino_acid_names: .: (0.000237) test_amino_acid_randomize_can_be_chained: .: (0.001114) test_amino_acid_randomize_has_same_composition: .: (0.000740) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000531) test_dna_composition: .: (0.000196) test_dna_gc_percent: .: (0.000394) test_dna_molecular_weight: .: (0.000241) test_dna_pikachu: .: (0.000149) test_dna_sequence_complement: .: (0.000147) test_dna_sequence_translate: .: (0.000551) test_dna_to_re: .: (0.000226) test_element_reference_operator_with_one_argument: .: (0.000145) test_element_reference_operator_with_two_arguments: .: (0.000151) test_invalid_nucleic_acid_illegal_bases: .: (0.000198) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000219) test_nucleic_acid_names: .: (0.000178) test_randomize_dna_can_be_chained: .: (0.000531) test_randomize_dna_retains_composition: .: (0.000276) test_randomize_dna_with_block: .: (0.000306) test_rna_composition: .: (0.000219) test_rna_gc_percent: .: (0.000204) test_rna_molecular_weight: .: (0.000410) test_rna_pikachu: .: (0.000168) test_rna_sequence_complement: .: (0.000152) test_rna_sequence_translate: .: (0.000407) test_rna_to_re: .: (0.000232) test_total: .: (0.000165) test_two_consecutive_dna_randomizations_not_equal: .: (0.000260) test_valid_dna_sequence_illegal_bases: .: (0.000143) Bio::TestSequenceAA: test_codes: .: (0.000329) test_molecular_weight: .: (0.000229) test_names: .: (0.000162) test_to_re: .: (0.000368) test_to_s: .: (0.000142) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000358) Bio::TestSequenceAANew: test_new: .: (0.000188) test_new_n: .: (0.000111) test_new_r: .: (0.000126) test_new_t: .: (0.000132) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000348) test_concat: .: (0.000187) test_push: .: (0.000162) test_seq: .: (0.000164) test_splicing: .: (0.000278) test_sum: .: (0.000165) test_to_s: .: (0.000161) test_to_str: .: (0.000157) test_total: .: (0.000156) test_window_search: .: (0.000260) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000303) test_normalize_A: .: (0.000151) test_normalize_a: .: (0.000135) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000992) test_randomize_with_block: .: (0.002661) test_randomize_with_hash: .: (0.000988) test_randomize_with_hash_block: .: (0.003157) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.001515) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.001227) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000422) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000182) test_subseq_returns_subsequence: .: (0.000155) test_to_s_returns_self_as_string: .: (0.000168) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000300) test_window_search_with_width_3_step_two_with_residual: .: (0.000145) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000310) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000364) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000342) test_na_self_randomize: .: (0.000231) Bio::TestSequenceDBLink: test_database: .: (0.000259) test_id: .: (0.000149) test_secondary_ids: .: (0.000176) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000328) test_parse_uniprot_DR_line: .: (0.000187) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.001121) test_output_width_35: .: (0.000357) test_output_width_nil: .: (0.000595) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000556) test_output_after_adding_sequence: .: (0.000381) test_output_after_truncating_sequence: .: (0.000270) test_output_from_error_probabilities: .: (0.010871) test_output_width45: .: (0.006374) test_output_with_converting_score_phred2solexa: .: (0.008062) test_output_with_converting_score_solexa2phred: .: (0.000484) test_output_with_default_score: .: (0.004475) Bio::TestSequenceMasker: test_mask: .: (0.000419) test_mask_with_enumerator: .: (0.005275) test_mask_with_enumerator_empty_mask_char: .: (0.000294) test_mask_with_enumerator_excess: .: (0.000487) test_mask_with_enumerator_longer_mask_char: .: (0.000215) test_mask_with_enumerator_shorter: .: (0.000243) test_mask_with_error_probability: .: (0.000314) test_mask_with_quality_score: .: (0.000212) Bio::TestSequenceNA: test_at_content: .: (0.005171) test_at_skew: .: (0.000382) test_codon_usage: .: (0.000221) test_complement: .: (0.000290) test_dna: .: (0.000196) test_dna!: .: (0.000168) test_forward_complement: .: (0.000280) test_gc_content: .: (0.005208) test_gc_percent: .: (0.003429) test_gc_skew: .: (0.004092) test_iliegal_bases: .: (0.000226) test_molecular_weight: .: (0.000316) test_names: .: (0.000273) test_reverse_complement: .: (0.000228) test_rna: .: (0.000176) test_rna!: .: (0.000166) test_splicing: .: (0.000276) test_to_re: .: (0.000248) test_to_s: .: (0.000160) Bio::TestSequenceNACommon: test_composition: .: (0.000391) test_concat: .: (0.000172) test_push: .: (0.000178) test_seq: .: (0.000170) test_splicing: .: (0.000475) test_sum: .: (0.000167) test_to_s: .: (0.000154) test_to_str: .: (0.000141) test_total: .: (0.000182) test_window_search: .: (0.000282) Bio::TestSequenceNANew: test_new: .: (0.000276) test_new_n: .: (0.000146) test_new_r: .: (0.000147) test_new_t: .: (0.000202) Bio::TestSequenceNATranslation: test_translate: .: (0.000502) test_translate_0: .: (0.000845) test_translate_1: .: (0.000293) test_translate_2: .: (0.000259) test_translate_3: .: (0.000255) test_translate_4: .: (0.000269) test_translate_5: .: (0.000308) test_translate_6: .: (0.000267) test_translate_7: .: (0.000611) test_translate_given_codon_table: .: (0.028929) test_translate_n1: .: (0.000630) test_translate_n2: .: (0.000505) test_translate_n3: .: (0.000503) test_translate_unknown_o: .: (0.000331) test_translate_unknown_x: .: (0.000324) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000316) test_convert_scores_from_phred_to_solexa: .: (0.000657) test_convert_scores_from_solexa_to_phred: .: (0.000238) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000331) test_convert_scores_from_phred: .: (0.000165) test_convert_scores_from_phred_to_solexa: .: (0.000402) test_convert_scores_from_solexa: .: (0.000230) test_convert_scores_from_solexa_to_phred: .: (0.000222) test_convert_scores_to_phred: .: (0.000160) test_convert_scores_to_solexa: .: (0.000715) test_p2q: .: (0.000217) test_phred_p2q: .: (0.000276) test_phred_q2p: .: (0.003323) test_q2p: .: (0.003106) test_quality_score_type: .: (0.000165) test_self_convert_scores_to_solexa: .: (0.000402) test_self_p2q: .: (0.000210) test_self_q2p: .: (0.003152) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000332) test_convert_scores_from_phred: .: (0.000383) test_convert_scores_from_phred_to_solexa: .: (0.000613) test_convert_scores_from_solexa: .: (0.000150) test_convert_scores_from_solexa_to_phred: .: (0.000216) test_convert_scores_to_phred: .: (0.000197) test_convert_scores_to_solexa: .: (0.000148) test_p2q: .: (0.000263) test_q2p: .: (0.004087) test_quality_score_type: .: (0.000188) test_self_convert_scores_to_phred: .: (0.000268) test_self_p2q: .: (0.000264) test_self_q2p: .: (0.004307) test_solexa_p2q: .: (0.000451) test_solexa_q2p: .: (0.003758) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000456) test_center: .: (0.000188) test_chomp: .: (0.000242) test_chop: .: (0.000193) test_delete: .: (0.000176) test_delete_prefix: .: (0.000219) test_delete_suffix: .: (0.000186) test_downcase: .: (0.000179) test_each_char: .: (0.000374) test_each_char_enum: .: (0.000224) test_each_grapheme_cluster: .: (0.000612) test_each_grapheme_cluster_enum: .: (0.000208) test_each_line: .: (0.000206) test_each_line_enum: .: (0.000183) test_gsub: .: (0.000176) test_gsub_with_block: .: (0.000462) test_ljust: .: (0.000256) test_lstrip: .: (0.000187) test_multiply: .: (0.000172) test_next: .: (0.000162) test_reverse: .: (0.000162) test_rjust: .: (0.000164) test_rstrip: .: (0.000155) test_slice: .: (0.000180) test_slice2: .: (0.000174) test_split: .: (0.000200) test_squeeze: .: (0.000154) test_strip: .: (0.001964) test_sub: .: (0.000179) test_sub_with_block: .: (0.000368) test_succ: .: (0.000231) test_swapcase: .: (0.000182) test_tr: .: (0.000177) test_tr_s: .: (0.000211) test_upcase: .: (0.000174) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000379) test_partition_nomatch: .: (0.000202) test_partition_sep_TSeq: .: (0.000188) test_partition_sep_regexp: .: (0.000486) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000379) test_rpartition_nomatch: .: (0.000198) test_rpartition_sep_TSeq: .: (0.000188) test_rpartition_sep_regexp: .: (0.000267) Bio::TestShRNA: test_blocK_it: .: (0.016014) test_blocK_it_: .: (0.016260) test_blocK_it_BLOCK_IT: .: (0.018809) test_blocK_it_BLOCK_iT: .: (0.015474) test_blocK_it_piGene: .: (0.015160) test_bottom_strand: .: (0.016526) test_bottom_strand_class: .: (0.015309) test_bottom_strand_nil: .: (0.015175) test_design: .: (0.016504) test_design_BLOCK_IT: .: (0.015694) test_report: .: (0.016349) test_report_before_design: .: (0.015750) test_top_strand: .: (0.015286) test_top_strand_class: .: (0.017041) test_top_strand_nil: .: (0.015217) Bio::TestShRNANew: test_new: .: (0.000518) Bio::TestSiRNA: test_antisense_size: .: (0.000313) test_design: .: (0.015265) test_design_reynolds: .: (0.020254) test_design_uitei: .: (0.015147) test_max_gc_percent: .: (0.000195) test_min_gc_percent: .: (0.000165) test_reynolds: .: (0.020756) test_reynolds?: .: (0.000439) test_uitei: .: (0.015092) test_uitei?: .: (0.000107) Bio::TestSiRNANew: test_new: .: (0.000397) Bio::TestSiRNAPair: test_antisense: .: (0.015787) test_gc_percent: .: (0.016988) test_report: .: (0.015064) test_rule: .: (0.015077) test_sense: .: (0.016455) test_start: .: (0.014676) test_stop: .: (0.016724) test_target: .: (0.015163) Bio::TestSiRNAPairNew: test_new: .: (0.000519) Bio::TestSim4Report: test_all_hits: .: (0.000595) test_each: .: (0.000425) test_each_hit: .: (0.000316) test_hits: .: (0.000323) test_num_hits: .: (0.000299) test_query_def: .: (0.000291) test_query_id: .: (0.000278) test_query_len: .: (0.000283) test_seq1: .: (0.000330) Bio::TestSim4Report2: test_all_hits: .: (0.000471) test_each: .: (0.000434) test_each_hit: .: (0.000331) test_hits: .: (0.000312) test_num_hits: .: (0.000291) test_query_def: .: (0.000298) test_query_id: .: (0.000275) test_query_len: .: (0.000245) test_seq1: .: (0.000296) Bio::TestSim4Report4: test_all_hits: .: (0.000471) test_each: .: (0.000300) test_each_hit: .: (0.000437) test_hits: .: (0.000309) test_num_hits: .: (0.000302) test_query_def: .: (0.000262) test_query_id: .: (0.000266) test_query_len: .: (0.000267) test_seq1: .: (0.000322) Bio::TestSim4ReportHit: test_align: .: (0.000499) test_complement?: .: (0.000282) test_definition: .: (0.000261) test_each: .: (0.000569) test_exons: .: (0.000414) test_hit_id: .: (0.000266) test_hsps: .: (0.000376) test_introns: .: (0.000382) test_len: .: (0.000263) test_query_def: .: (0.000259) test_query_id: .: (0.000273) test_query_len: .: (0.000295) test_segmentpairs: .: (0.000433) test_seq1: .: (0.000289) test_seq2: .: (0.000279) test_target_def: .: (0.000239) test_target_id: .: (0.000252) test_target_len: .: (0.000233) Bio::TestSim4ReportHit2: test_align: .: (0.000518) test_complement?: .: (0.000243) test_definition: .: (0.000358) test_each: .: (0.000443) test_exons: .: (0.000411) test_hit_id: .: (0.000280) test_hsps: .: (0.000391) test_introns: .: (0.000378) test_len: .: (0.000291) test_query_def: .: (0.000262) test_query_id: .: (0.000386) test_query_len: .: (0.000306) test_segmentpairs: .: (0.000422) test_seq1: .: (0.000317) test_seq2: .: (0.000285) test_target_def: .: (0.000253) test_target_id: .: (0.000309) test_target_len: .: (0.000267) Bio::TestSim4ReportHit4: test_align: .: (0.000588) test_complement?: .: (0.000262) test_definition: .: (0.000289) test_each: .: (0.000496) test_exons: .: (0.000438) test_hit_id: .: (0.000293) test_hsps: .: (0.000417) test_introns: .: (0.000548) test_len: .: (0.000301) test_query_def: .: (0.000272) test_query_id: .: (0.000260) test_query_len: .: (0.000242) test_segmentpairs: .: (0.000460) test_seq1: .: (0.000301) test_seq2: .: (0.000280) test_target_def: .: (0.000236) test_target_id: .: (0.000399) test_target_len: .: (0.000232) Bio::TestSim4ReportSegment: test_from: .: (0.000278) test_self_new: .: (0.000170) test_seq: .: (0.000145) test_to: .: (0.000140) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000489) test_direction: .: (0.000315) test_hit_from: .: (0.000289) test_hit_to: .: (0.000449) test_hseq: .: (0.000339) test_midline: .: (0.000311) test_percent_identity: .: (0.000308) test_qseq: .: (0.000341) test_query_from: .: (0.000318) test_query_to: .: (0.000328) test_seq1: .: (0.000480) test_seq2: .: (0.000411) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000480) test_direction: .: (0.000329) test_hit_from: .: (0.000323) test_hit_to: .: (0.000325) test_hseq: .: (0.000474) test_midline: .: (0.000371) test_percent_identity: .: (0.000362) test_qseq: .: (0.000326) test_query_from: .: (0.000322) test_query_to: .: (0.000322) test_seq1: .: (0.000348) test_seq2: .: (0.000481) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000524) test_direction: .: (0.000412) test_hit_from: .: (0.000376) test_hit_to: .: (0.000458) test_hseq: .: (0.000402) test_midline: .: (0.000344) test_percent_identity: .: (0.000373) test_qseq: .: (0.000351) test_query_from: .: (0.000568) test_query_to: .: (0.000431) test_seq1: .: (0.000403) test_seq2: .: (0.000401) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000719) test_direction: .: (0.000476) test_hit_from: .: (0.000356) test_hit_to: .: (0.000341) test_hseq: .: (0.000339) test_midline: .: (0.000594) test_percent_identity: .: (0.000478) test_qseq: .: (0.000359) test_query_from: .: (0.000423) test_query_to: .: (0.000343) test_seq1: .: (0.000670) test_seq2: .: (0.000504) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000539) test_direction: .: (0.000400) test_hit_from: .: (0.000407) test_hit_to: .: (0.000527) test_hseq: .: (0.000498) test_midline: .: (0.000357) test_percent_identity: .: (0.000401) test_qseq: .: (0.000384) test_query_from: .: (0.000555) test_query_to: .: (0.000480) test_seq1: .: (0.000466) test_seq2: .: (0.000443) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000631) test_direction: .: (0.000345) test_hit_from: .: (0.000337) test_hit_to: .: (0.000339) test_hseq: .: (0.000318) test_midline: .: (0.000339) test_percent_identity: .: (0.000321) test_qseq: .: (0.000423) test_query_from: .: (0.000312) test_query_to: .: (0.000302) test_seq1: .: (0.000355) test_seq2: .: (0.000357) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000471) test_direction: .: (0.000399) test_hit_from: .: (0.000334) test_hit_to: .: (0.000318) test_hseq: .: (0.000304) test_midline: .: (0.000297) test_percent_identity: .: (0.000302) test_qseq: .: (0.000341) test_query_from: .: (0.000398) test_query_to: .: (0.000373) test_seq1: .: (0.000340) test_seq2: .: (0.000332) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000303) test_entry_id: .: (0.000148) test_filename: .: (0.000150) test_len: .: (0.000149) test_self_new: .: (0.000201) test_self_parse: .: (0.000182) Bio::TestTMHMMReport: test_entry_id: .: (0.000578) test_exp_aas_in_tmhs: .: (0.000288) test_exp_first_60aa: .: (0.000318) test_helix: .: (0.000338) test_predicted_tmhs: .: (0.000385) test_query_len: .: (0.000281) test_tmhs: .: (0.000322) test_to_s: .: (0.000400) test_total_prob_of_N_in: .: (0.000451) Bio::TestTMHMMReport_reports: test_reports: .: (0.000311) Bio::TestTMHMMTMH: test_entry_id: .: (0.000475) test_pos: .: (0.000320) test_range: .: (0.000301) test_status: .: (0.000472) test_version: .: (0.000307) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000443) test_cutoff: .: (0.000265) test_entry_id: .: (0.000250) test_length: .: (0.000247) test_loc: .: (0.003418) test_name: .: (0.000281) test_networks: .: (0.000269) test_prediction: .: (0.000290) test_query_len: .: (0.000287) test_query_sequences: .: (0.000254) test_rc: .: (0.000268) test_version: .: (0.000264) Bio::TestTargetPReportConst: test_delimiter: .: (0.000279) test_rs: .: (0.000140) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000390) test_togows_access_wait: .: (2.004880) Bio::TestTogoWSREST: test_debug: .: (0.000667) test_debug_default: .: (0.000286) test_internal_http: .: (0.000407) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000317) test_entry: .: (0.000144) test_entry_database_list: .: (0.000138) test_new: .: (0.000330) test_new_with_uri_object: .: (0.000675) test_new_with_uri_string: .: (0.000287) test_retrieve: .: (0.000129) test_search: .: (0.000149) test_search_database_list: .: (0.000137) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000509) test_prepare_return_value: .: (0.000310) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000446) Bio::TestTree: test_get_edge_distance: .: (0.000615) test_get_edge_distance_string: .: (0.000237) test_get_node_name: .: (0.000157) test_initialize: .: (0.000160) test_options: .: (0.000144) test_root: .: (0.000149) test_root=: .: (0.000390) Bio::TestTree2: test_add_edge: .: (0.006042) test_add_node: .: (0.000414) test_adjacency_matrix: .: (0.000356) test_adjacency_matrix_with_block: .: (0.000317) test_adjacent_nodes: .: (0.000448) test_adjacent_nodes_nonexistent: .: (0.000230) test_ancestors: .: (0.000257) test_children: .: (0.000229) test_clear: .: (0.000235) test_clear_node: .: (0.000258) test_clear_node_nonexistent: .: (0.000350) test_collect_edge!: .: (0.000363) test_collect_node!: .: (0.000318) test_concat: .: (0.000560) test_descendents: .: (0.000249) test_distance_matrix: .: (0.000479) test_each_edge: .: (0.000261) test_each_node: .: (0.000268) test_each_out_edge: .: (0.000229) test_each_out_edge_chimpanzee: .: (0.000209) test_each_out_edge_human: .: (0.000251) test_each_out_edge_mammals: .: (0.006699) test_each_out_edge_nonexistent: .: (0.000325) test_each_out_edge_primates: .: (0.000310) test_each_out_edge_rat: .: (0.000238) test_each_out_edge_rodents: .: (0.000244) test_edges: .: (0.000209) test_get_edge: .: (0.000320) test_get_edge_indirect: .: (0.000325) test_get_edge_merged: .: (0.000219) test_get_edge_nonexistent: .: (0.000189) test_get_node_bootstrap: .: (0.000495) test_get_node_bootstrap_string=: .: (0.000211) test_get_node_by_name: .: (0.000259) test_get_node_by_name_noexistent: .: (0.000174) test_include?: .: (0.000214) test_include_nonexistent: .: (0.000206) test_insert_node: .: (0.000285) test_leaves: .: (0.000231) test_leaves_noargs: .: (0.000349) test_lowest_common_ancestor: .: (0.000218) test_nodes: .: (0.000241) test_number_of_edges: .: (0.000214) test_number_of_nodes: .: (0.000207) test_out_degree: .: (0.000267) test_out_degree_nonexistent: .: (0.000223) test_out_edges: .: (0.000245) test_out_edges_mammals: .: (0.000269) test_out_edges_nonexistent: .: (0.000222) test_out_edges_primates: .: (0.000424) test_out_edges_rodents: .: (0.004560) test_parent: .: (0.000371) test_path: .: (0.000290) test_remove_edge: .: (0.000244) test_remove_edge_if: .: (0.000251) test_remove_edge_if_nothing_removed: .: (0.000251) test_remove_edge_nonexistent: .: (0.000567) test_remove_node: .: (0.000273) test_remove_node_if: .: (0.000381) test_remove_node_if_false: .: (0.000232) test_remove_node_nonexistent: .: (0.000337) test_remove_nonsense_nodes: .: (0.000279) test_subtree: .: (0.000284) test_subtree_with_all_paths: .: (0.000356) test_total_distance: .: (0.000227) Bio::TestTreeEdge: test_distance: .: (0.000297) test_distance=: .: (0.004778) test_distance_string: .: (0.000200) test_distance_string=: .: (0.000138) test_initialize: .: (0.000315) test_inspect: .: (0.000114) test_to_s: .: (0.000099) Bio::TestTreeNode: test_bootstrap: .: (0.000242) test_bootstrap=: .: (0.000141) test_bootstrap_string: .: (0.000100) test_bootstrap_string=: .: (0.000160) test_initialize: .: (0.000144) test_inspect: .: (0.000140) test_name: .: (0.000107) test_to_s: .: (0.000099) Bio::TestUniProt: test_gene_name: .: (0.008301) Bio::TestUniProtKB: test_ac: .: (0.003208) test_accession: .: (0.008180) test_cc: .: (0.011853) test_cc_alternative_products: .: (0.004651) test_cc_database: .: (0.011054) test_cc_mass_spectrometry: .: (0.005047) test_de: .: (0.003000) test_dr: .: (0.017279) test_dr_with_key: .: (0.059520) test_dr_with_key_empty: .: (0.005656) test_dt: .: (0.003617) test_dt_annotation: .: (0.003801) test_dt_created: .: (0.008690) test_dt_sequence: .: (0.003037) test_entry: .: (0.008407) test_ft: .: (0.014262) test_gene_name: .: (0.005291) test_gene_names: .: (0.003183) test_gn: .: (0.004365) test_gn_old_parser: .: (0.003328) test_gn_uniprot_parser: .: (0.003282) test_id_line: .: (0.005188) test_id_line_data_class: .: (0.005363) test_id_line_entry_name: .: (0.003473) test_id_line_molecule_type: .: (0.003604) test_id_line_sequence_length: .: (0.004409) test_kw: .: (0.003432) test_molecule: .: (0.004886) test_oc: .: (0.005991) test_og_1: .: (0.003697) test_og_2: .: (0.004489) test_og_3: .: (0.003442) test_og_4: .: (0.003143) test_og_5: .: (0.003370) test_og_6: .: (0.003048) test_os: .: (0.004020) test_os_access: .: (0.003371) test_os_access2: .: (0.003272) test_ox: .: (0.003245) test_protein_name: .: (0.003373) test_ref: .: (0.007277) test_seq: .: (0.003582) test_sequence_length: .: (0.003330) test_sq: .: (0.003507) test_sq_crc64: .: (0.003128) test_sq_len: .: (0.003233) test_sq_mw: .: (0.003242) test_synonyms: .: (0.003031) Bio::TestUniProtKB_CC: test_allergen: .: (0.000417) test_alternative_products_access_as_hash: .: (0.000582) test_alternative_products_ai: .: (0.000351) test_alternative_products_apu: .: (0.000446) test_alternative_products_as: .: (0.000322) test_alternative_products_rf: .: (0.000154) test_biophysicochemical_properties: .: (0.000419) test_biotechnology: .: (0.000396) test_catalytic_activity: .: (0.000256) test_caution: .: (0.000320) test_cofactor: .: (0.000262) test_developmental_stage: .: (0.000293) test_disease: .: (0.001857) test_domain: .: (0.000410) test_enzyme_regulation: .: (0.000279) test_function: .: (0.000270) test_induction: .: (0.000232) test_interaction: .: (0.000410) test_mass_spectrometry: .: (0.000333) test_miscellaneous: .: (0.000505) test_pathway: .: (0.000271) test_pharmaceutical: .: (0.000293) test_polymorphism: .: (0.000441) test_ptm: .: (0.000255) test_rna_editing: .: (0.000292) test_similarity: .: (0.000241) test_subcellular_location: .: (0.000265) test_subunit: .: (0.000215) test_tissue_specificity: .: (0.000489) test_toxic_dose: .: (0.000222) test_web_resource: .: (0.000323) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000561) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000510) test_protein_name: .: (0.000491) test_synonyms: .: (0.000362) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000395) test_entry: .: (0.000170) test_entry_id: .: (0.000153) test_entry_name: .: (0.000159) test_id_line: .: (0.000166) test_molecule: .: (0.000156) test_sequence_length: .: (0.000161) Bio::TestUniProtKB_P03589: test_ac: .: (0.000652) test_accession: .: (0.000466) test_cc: .: (0.000837) test_cc_alternative_products: .: (0.000650) test_cc_database: .: (0.000644) test_cc_mass_spectrometry: .: (0.000755) test_de: .: (0.000452) test_dr: .: (0.000723) test_dr_with_key: .: (0.000639) test_dr_with_key_empty: .: (0.000793) test_dt: .: (0.000416) test_dt_annotation: .: (0.000391) test_dt_created: .: (0.000431) test_dt_sequence: .: (0.000396) test_entry: .: (0.000532) test_ft: .: (0.000915) test_gene_name: .: (0.000512) test_gene_names: .: (0.000692) test_gn: .: (0.000480) test_gn_old_parser: .: (0.000591) test_gn_uniprot_parser: .: (0.000754) test_id_line: .: (0.000487) test_id_line_data_class: .: (0.000448) test_id_line_entry_name: .: (0.000794) test_id_line_sequence_length: .: (0.000566) test_kw: .: (0.000537) test_oc: .: (0.000836) test_oh: .: (0.000876) test_os: .: (0.000489) test_os_access: .: (0.000673) test_os_access2: .: (0.000461) test_ox: .: (0.000469) test_protein_name: .: (0.000762) test_protein_name_after_calling_de: .: (0.000485) test_ref: .: (0.000632) test_seq: .: (0.000872) test_sequence_length: .: (0.000495) test_sq: .: (0.000583) test_sq_crc64: .: (0.000431) test_sq_len: .: (0.000443) test_sq_mw: .: (0.000650) test_synonyms: .: (0.000486) Bio::TestUniProtKB_P28907: test_ac: .: (0.001394) test_accession: .: (0.001557) test_cc: .: (0.001709) test_cc_alternative_products: .: (0.001997) test_cc_database: .: (0.001704) test_cc_mass_spectrometry: .: (0.001712) test_de: .: (0.001688) test_dr: .: (0.003200) test_dr_with_key: .: (0.003224) test_dr_with_key_empty: .: (0.003069) test_dt: .: (0.001428) test_dt_annotation: .: (0.001608) test_dt_created: .: (0.001290) test_dt_sequence: .: (0.001376) test_entry: .: (0.001285) test_ft: .: (0.002600) test_gene_name: .: (0.001312) test_gene_names: .: (0.001318) test_gn: .: (0.001298) test_gn_old_parser: .: (0.003960) test_gn_uniprot_parser: .: (0.001674) test_id_line: .: (0.001633) test_id_line_data_class: .: (0.001390) test_id_line_entry_name: .: (0.001448) test_id_line_sequence_length: .: (0.001319) test_kw: .: (0.001387) test_oc: .: (0.001524) test_os: .: (0.001420) test_os_access: .: (0.001312) test_os_access2: .: (0.001383) test_ox: .: (0.001572) test_protein_name: .: (0.001415) test_protein_name_after_calling_de: .: (0.001369) test_ref: .: (0.002051) test_seq: .: (0.001443) test_sequence_length: .: (0.001543) test_sq: .: (0.001518) test_sq_crc64: .: (0.001541) test_sq_len: .: (0.001536) test_sq_mw: .: (0.001282) test_synonyms: .: (0.001494) test_synonyms_after_calling_de: .: (0.001830) Bio::TestUniProtKB_P49144: test_ac: .: (0.000916) test_accession: .: (0.000743) test_cc: .: (0.001502) test_cc_alternative_products: .: (0.001095) test_cc_database: .: (0.001238) test_cc_mass_spectrometry: .: (0.001267) test_de: .: (0.000644) test_dr: .: (0.001188) test_dr_with_key: .: (0.001162) test_dr_with_key_empty: .: (0.001337) test_dt: .: (0.000977) test_dt_annotation: .: (0.000660) test_dt_created: .: (0.000882) test_dt_sequence: .: (0.000688) test_entry: .: (0.000910) test_ft: .: (0.001768) test_gene_name: .: (0.000749) test_gene_names: .: (0.000716) test_gn: .: (0.000822) test_gn_old_parser: .: (0.000705) test_gn_uniprot_parser: .: (0.000907) test_id_line: .: (0.000648) test_id_line_data_class: .: (0.000847) test_id_line_entry_name: .: (0.000596) test_id_line_sequence_length: .: (0.000884) test_kw: .: (0.000707) test_oc: .: (0.000794) test_os: .: (0.000730) test_os_access: .: (0.000632) test_os_access2: .: (0.000745) test_ox: .: (0.002461) test_protein_name: .: (0.000812) test_protein_name_after_calling_de: .: (0.000956) test_ref: .: (0.000949) test_seq: .: (0.000714) test_sequence_length: .: (0.000814) test_sq: .: (0.000624) test_sq_crc64: .: (0.000810) test_sq_len: .: (0.000882) test_sq_mw: .: (0.000659) test_synonyms: .: (0.000898) test_synonyms_after_calling_de: .: (0.000836) Bio::TestUniProtKB_Ref: test_RA: .: (0.000676) test_RC: .: (0.000317) test_RG: .: (0.000285) test_RL: .: (0.000276) test_RN: .: (0.000477) test_RP: .: (0.000284) test_RT: .: (0.000289) test_RX: .: (0.000288) test_ref: .: (0.000276) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000543) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000573) test_alternative_products_with_ft: .: (0.000642) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000550) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000362) test_RL_lines: .: (0.000182) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000514) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000320) test_RG_line: .: (0.000352) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000617) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000456) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000300) test_RL_line: .: (0.000264) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000901) test_RP_line: .: (0.000295) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000264) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000353) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000250) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000229) test_CC_interaction_isoform: .: (0.000223) test_CC_interaction_no_gene_name: .: (0.000206) test_CC_interaction_self_association: .: (0.000504) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000327) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000451) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000500) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000434) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000677) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000318) test_DT_line: .: (0.000193) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.003250) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000743) test_CC_web_resource: .: (0.000131) test_FT_VER_SEQ: .: (0.000245) test_OH_line_exception: .: (0.000305) test_OH_lines: .: (0.000330) Bio::TestUtils: test_centreOfGravity: .: (0.000688) test_dihedral_angle: .: (0.000459) test_distance: .: (0.000378) test_geometricCentre: .: (0.000509) test_rad2deg: .: (0.000225) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000341) test_dijkstra_on_weighted_graph: .: (0.000174) Finished in 13.67340816 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 288.22 tests/s, 1579.78 assertions/s /usr/bin/ruby3.3 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.3 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.3.0:/var/lib/gems/3.3.0:/usr/local/lib/ruby/gems/3.3.0:/usr/lib/ruby/gems/3.3.0:/usr/lib/aarch64-linux-gnu/ruby/gems/3.3.0:/usr/share/rubygems-integration/3.3.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.3.0 ruby3.3 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.3 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000581) test_dbs: .: (0.000297) test_go_ids: .: (0.000229) test_go_terms: .: (0.000261) test_parser: .: (0.000441) test_set_date: .: (0.000268) test_set_desc: .: (0.000227) test_to_str: .: (0.000248) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000633) test_mktmpdir_without_block: .: (0.000531) test_remove_entry_secure: .: (0.000410) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.026098) test_call_command_fork: .: (0.000162) test_call_command_open3: .: (0.056547) test_call_command_popen: .: (0.023921) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.027805) test_call_command_fork: .: (0.000154) test_call_command_open3: .: (0.042107) test_call_command_popen: .: (0.008855) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.024076) test_call_command_fork: .: (0.000221) test_call_command_open3: .: (0.043398) test_call_command_popen: .: (0.020766) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.001610) test_call_command_fork_chdir: .: (0.000352) test_call_command_popen_chdir: .: (0.016477) test_query_command_chdir: .: (0.012860) test_query_command_fork_chdir: .: (0.000424) test_query_command_popen_chdir: .: (0.011663) Bio::FuncTestCommandQuery: test_query_command: .: (0.059823) test_query_command_fork: .: (0.001140) test_query_command_open3: .: (0.017816) test_query_command_popen: .: (0.002773) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000787) test_initialize: .: (0.000309) test_path: .: (0.000207) test_path_after_close: .: (0.000354) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.017109) test_output_fasta: .: (0.006071) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000379) test_accession: .: (0.000184) test_accessions: .: (0.000791) test_comment: .: (0.000181) test_common_name: .: (0.000182) test_definition: .: (0.000180) test_features: .: (0.000317) test_gi: .: (0.000180) test_keywords: .: (0.000148) test_locus: .: (0.000102) test_nid: .: (0.000156) test_organism: .: (0.000162) test_origin: .: (0.000136) test_references: .: (0.000470) test_segment: .: (0.000151) test_source: .: (0.000220) test_taxonomy: .: (0.000148) test_version: .: (0.000153) test_versions: .: (0.000144) Bio::TestAA: test_13: .: (0.000221) test_1n: .: (0.000100) test_name2one: .: (0.000138) test_name2three: .: (0.000101) test_one2name: .: (0.000098) test_one2three: .: (0.000086) test_three2name: .: (0.000090) test_three2one: .: (0.000108) test_to_1_1: .: (0.000080) test_to_1_3: .: (0.000096) test_to_1_name: .: (0.000092) test_to_3_1: .: (0.000099) test_to_3_3: .: (0.000090) test_to_3_name: .: (0.000111) test_to_re: .: (0.000142) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000199) Bio::TestAAindex: test_api: .: (0.000139) test_auto_aax1: .: (0.000265) test_auto_aax2: .: (0.000212) Bio::TestAAindex1: test_author: .: (0.000327) test_comment: .: (0.000237) test_correlation_coefficient: .: (0.000343) test_dblinks: .: (0.000203) test_definition: .: (0.000193) test_entry_id: .: (0.000182) test_index: .: (0.000245) test_journal: .: (0.000210) test_title: .: (0.000212) Bio::TestAAindex2: test_access_A_R: .: (0.000676) test_access_R_A: .: (0.000482) test_author: .: (0.000212) test_cols: .: (0.000189) test_comment: .: (0.000193) test_dblinks: .: (0.000207) test_definition: .: (0.000216) test_entry_id: .: (0.000187) test_journal: .: (0.000202) test_matrix: .: (0.000499) test_matrix_1_2: .: (0.000498) test_matrix_2_2: .: (0.000696) test_matrix_A_R: .: (0.009355) test_matrix_R_A: .: (0.000549) test_matrix_determinant: .: (0.001436) test_matrix_rank: .: (0.001801) test_matrix_transpose: .: (0.000624) test_rows: .: (0.000209) test_title: .: (0.000200) Bio::TestAAindexConstant: test_delimiter: .: (0.000222) test_tagsize: .: (0.000092) Bio::TestAbif: test_complement: .: (0.005804) test_seq: .: (0.005593) test_to_biosequence: .: (0.006149) Bio::TestActsLikeMap: test_mixin: .: (0.000292) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000270) Bio::TestActsLikeMarker: test_mixin: .: (0.000189) Bio::TestAlignment: test_add_seq_no_key: .: (0.000279) test_add_seq_using_seq_with_aaseq_method: .: (0.000161) test_add_seq_using_seq_with_definition_method: .: (0.000119) test_add_seq_using_seq_with_entry_id_method: .: (0.000128) test_add_seq_using_seq_with_naseq_method: .: (0.000134) test_add_seq_using_seq_with_seq_method: .: (0.000133) test_consensus_iupac_gap_modes: .: (0.000413) test_consensus_iupac_missing_char: .: (0.000182) test_consensus_iupac_missing_char_option: .: (0.000186) test_consensus_iupac_no_gaps: .: (0.000219) test_consensus_iupac_of_ambiguous_bases: .: (0.000268) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002848) test_consensus_opt_gap_mode: .: (0.000410) test_consensus_opt_missing_char: .: (0.000259) test_consensus_string_no_gaps: .: (0.000195) test_consensus_threshold_four_sequences: .: (0.000228) test_consensus_threshold_two_sequences: .: (0.000242) test_convert_match: .: (0.000261) test_convert_unmatch: .: (0.000138) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000141) test_convert_unmatch_different_match_char: .: (0.000146) test_convert_unmatch_multiple_sequences: .: (0.000178) test_default_gap_char: .: (0.000093) test_default_gap_regexp_matches_default_gap_char: .: (0.000160) test_default_missing_char: .: (0.000096) test_each_site_equal_length: .: (0.000195) test_each_site_unequal_length: .: (0.000143) test_equals: .: (0.000181) test_match_line_protein: .: (0.000366) test_normalizebang_extends_sequences_with_gaps: .: (0.000147) test_seq_length_is_max_seq_length: .: (0.000111) test_seq_length_when_one_sequence: .: (0.000193) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000117) test_seqclass_when_seqclass_set: .: (0.000117) test_seqclass_when_sequence_used: .: (0.000119) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000118) test_set_and_get_gap_char: .: (0.000118) test_store_cannot_override_key: .: (0.000115) test_store_with_default_keys_and_user_defined_keys: .: (0.000139) test_store_with_nil_key_uses_next_number_for_key: .: (0.000517) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000287) test_alignment_concat: .: (0.000149) test_alignment_length: .: (0.000100) test_alignment_lstrip!: .: (0.000269) test_alignment_lstrip_nil: .: (0.000131) test_alignment_normalize!: .: (0.000098) test_alignment_rstrip!: .: (0.000164) test_alignment_rstrip_nil: .: (0.000103) test_alignment_site: .: (0.000108) test_alignment_slice: .: (0.000109) test_alignment_strip!: .: (0.000184) test_alignment_strip_nil: .: (0.000129) test_alignment_subseq: .: (0.000138) test_alignment_window: .: (0.000115) test_collect_each_site: .: (0.000144) test_consensus_each_site_default: .: (0.000149) test_consensus_each_site_gap_mode_1: .: (0.000139) test_consensus_each_site_gap_mode_minus1: .: (0.000155) test_consensus_iupac: .: (0.000270) test_consensus_string_default: .: (0.000139) test_consensus_string_half: .: (0.000266) test_convert_match: .: (0.000276) test_convert_unmatch: .: (0.000121) test_each_seq: .: (0.000116) test_each_site: .: (0.000175) test_each_site_step: .: (0.000135) test_each_window: .: (0.000166) test_match_line: .: (0.001182) test_match_line_amino: .: (0.001453) test_match_line_nuc: .: (0.000214) test_private_alignment_site: .: (0.000118) test_remove_all_gaps!: .: (0.000126) test_seqclass: .: (0.000493) test_seqclass=: .: (0.000153) test_seqclass_default: .: (0.000102) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002654) test_determine_seq_method: .: (0.008511) test_entries: .: (0.000866) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000378) test_avoid_same_name_numbering: .: (0.001553) test_clustal_have_same_name_true: .: (0.000155) test_have_same_name_false: .: (0.000122) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.001764) test_gap_char_default: .: (0.000164) test_gap_char_never_nil: .: (0.001346) test_gap_regexp: .: (0.000131) test_gap_regexp=: .: (0.000103) test_gap_regexp_never_nil: .: (0.000094) test_get_all_property_default: .: (0.001641) test_get_all_property_nodefault: .: (0.000155) test_is_gap_default_false: .: (0.000108) test_is_gap_default_true: .: (0.001574) test_is_gap_nodefault_false: .: (0.001514) test_is_gap_nodefault_true: .: (0.000118) test_missing_char=: .: (0.000096) test_missing_char_default: .: (0.003084) test_missing_char_never_nil: .: (0.000139) test_seqclass=: .: (0.001645) test_seqclass_default: .: (0.000135) test_seqclass_never_nil: .: (0.000097) test_set_all_property: .: (0.000109) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001635) test_consensus_string_50percent: .: (0.000172) test_consensus_string_50percent_nil: .: (0.000115) test_consensus_string_default: .: (0.000966) test_consensus_string_default_nil: .: (0.002527) test_has_gap_false: .: (0.001643) test_has_gap_true: .: (0.001382) test_match_line_amino_100percent: .: (0.002048) test_match_line_amino_missing: .: (0.002173) test_match_line_amino_strong: .: (0.000237) test_match_line_amino_weak: .: (0.000156) test_match_line_nuc_100percent: .: (0.000149) test_match_line_nuc_missing: .: (0.000335) test_remove_gaps!: .: (0.000114) test_remove_gaps_bang_not_removed: .: (0.000099) Bio::TestAtomFinder: test_atoms: .: (0.013928) test_each_atom: .: (0.000207) test_find_atom: .: (0.000149) Bio::TestBioFastaDefline: test_acc_version: .: (0.000737) test_accession: .: (0.000383) test_accessions: .: (0.000324) test_description: .: (0.000248) test_descriptions: .: (0.000245) test_entry_id: .: (0.000216) test_get: .: (0.000257) test_get_all_by_type: .: (0.000217) test_get_by_type: .: (0.000233) test_gi: .: (0.000226) test_id_strings: .: (0.000468) test_locus: .: (0.000221) test_method_missing: .: (0.000258) test_to_s: .: (0.000260) test_words: .: (0.000580) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000768) test_goid2term: .: (0.000339) test_parse_goids: .: (0.000326) Bio::TestBioGenBank: test_basecount: .: (0.000381) test_circular: .: (0.000248) test_classification: .: (0.000315) test_date: .: (0.000248) test_date_modified: .: (0.000579) test_division: .: (0.000222) test_each_cds_feature: .: (0.000581) test_each_cds_qualifiers: .: (0.000569) test_each_gene: .: (0.000541) test_entry_id: .: (0.000215) test_length: .: (0.000220) test_locus_circular: .: (0.000283) test_locus_class: .: (0.005473) test_locus_date: .: (0.000302) test_locus_division: .: (0.000285) test_locus_entry_id: .: (0.000299) test_locus_length: .: (0.000264) test_locus_natype: .: (0.000265) test_locus_strand: .: (0.000273) test_natype: .: (0.000248) test_seq: .: (0.000299) test_seq_len: .: (0.000388) test_strand: .: (0.000242) test_strandedness: .: (0.000320) test_to_biosequence: .: (0.001555) Bio::TestBioGenPept: test_circular: .: (0.000383) test_date: .: (0.000188) test_dbsource: .: (0.000185) test_division: .: (0.000468) test_entry_id: .: (0.000266) test_length: .: (0.000178) test_locus: .: (0.000193) test_seq: .: (0.000224) test_seq_len: .: (0.000200) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000427) test_aaseq: .: (0.000265) test_chromosome: .: (0.000227) test_codon_usage: .: (0.000345) test_cu_list: .: (0.000428) test_dblinks_as_hash: .: (0.000266) test_dblinks_as_strings: .: (0.000198) test_definition: .: (0.000226) test_division: .: (0.000208) test_eclinks: .: (0.000225) test_entry: .: (0.000199) test_entry_id: .: (0.000178) test_gbposition: .: (0.000229) test_gene: .: (0.000488) test_genes: .: (0.000229) test_keggclass: .: (0.000232) test_keggclasses: .: (0.000233) test_locations: .: (0.000358) test_motifs_as_hash: .: (0.000282) test_motifs_as_strings: .: (0.000203) test_name: .: (0.000205) test_names_as_array: .: (0.000228) test_new: .: (0.000237) test_ntlen: .: (0.000330) test_ntseq: .: (0.000327) test_organism: .: (0.000467) test_orthologs_as_hash: .: (0.000266) test_orthologs_as_strings: .: (0.000207) test_pathway: .: (0.000225) test_pathway_after_pathways_as_strings: .: (0.000258) test_pathway_before_pathways_as_strings: .: (0.000253) test_pathways_as_hash: .: (0.000230) test_pathways_as_strings: .: (0.000330) test_position: .: (0.000212) test_structure: .: (0.000212) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000948) test_comment: .: (0.000359) test_data_source: .: (0.000292) test_definition: .: (0.000293) test_disease: .: (0.000275) test_entry_id: .: (0.000285) test_lineage: .: (0.000334) test_nalen: .: (0.000296) test_name: .: (0.000317) test_new: .: (0.000322) test_num_gene: .: (0.000306) test_num_rna: .: (0.000286) test_original_databases: .: (0.000280) test_original_db: .: (0.000312) test_plasmids: .: (0.000284) test_references: .: (0.001610) test_statistics: .: (0.000324) test_taxid: .: (0.000341) test_taxonomy: .: (0.000337) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000442) test_comment: .: (0.000252) test_data_source: .: (0.000225) test_definition: .: (0.000227) test_disease: .: (0.000222) test_entry_id: .: (0.000224) test_lineage: .: (0.000266) test_nalen: .: (0.000250) test_name: .: (0.000204) test_new: .: (0.000210) test_num_gene: .: (0.000228) test_num_rna: .: (0.000279) test_original_databases: .: (0.000210) test_original_db: .: (0.000196) test_plasmids: .: (0.000279) test_references: .: (0.000420) test_statistics: .: (0.000221) test_taxid: .: (0.000220) test_taxonomy: .: (0.006335) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000458) test_compounds_as_strings: .: (0.000210) test_dblinks_as_hash: .: (0.000192) test_dblinks_as_strings: .: (0.000175) test_description: .: (0.000230) test_diseases_as_hash: .: (0.000243) test_diseases_as_strings: .: (0.000178) test_entry_id: .: (0.000230) test_enzymes_as_strings: .: (0.000239) test_genes_as_hash: .: (0.000196) test_genes_as_strings: .: (0.000186) test_keggclass: .: (0.000222) test_ko_pathway: .: (0.000386) test_modules_as_hash: .: (0.000210) test_modules_as_strings: .: (0.000186) test_name: .: (0.000213) test_new: .: (0.000240) test_organism: .: (0.000221) test_orthologs_as_hash: .: (0.000183) test_orthologs_as_strings: .: (0.000204) test_pathways_as_hash: .: (0.000233) test_pathways_as_strings: .: (0.000196) test_reactions_as_hash: .: (0.000209) test_reactions_as_strings: .: (0.000193) test_references: .: (0.000198) test_rel_pathways_as_hash: .: (0.000236) test_rel_pathways_as_strings: .: (0.000197) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000498) test_compounds_as_strings: .: (0.000264) test_dblinks_as_hash: .: (0.000220) test_dblinks_as_strings: .: (0.000194) test_description: .: (0.000256) test_diseases_as_hash: .: (0.000223) test_diseases_as_strings: .: (0.000199) test_entry_id: .: (0.000228) test_enzymes_as_strings: .: (0.000203) test_genes_as_hash: .: (0.000260) test_genes_as_strings: .: (0.000233) test_keggclass: .: (0.000230) test_ko_pathway: .: (0.000231) test_modules_as_hash: .: (0.000221) test_modules_as_strings: .: (0.000525) test_name: .: (0.000230) test_new: .: (0.000238) test_organism: .: (0.000219) test_orthologs_as_hash: .: (0.000190) test_orthologs_as_strings: .: (0.000178) test_pathways_as_hash: .: (0.000190) test_pathways_as_strings: .: (0.000194) test_reactions_as_hash: .: (0.000184) test_reactions_as_strings: .: (0.000181) test_references: .: (0.000180) test_rel_pathways_as_hash: .: (0.000220) test_rel_pathways_as_strings: .: (0.000211) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000375) test_compounds_as_strings: .: (0.000376) test_dblinks_as_hash: .: (0.000216) test_dblinks_as_strings: .: (0.000183) test_description: .: (0.000212) test_diseases_as_hash: .: (0.000180) test_diseases_as_strings: .: (0.000174) test_entry_id: .: (0.000209) test_enzymes_as_strings: .: (0.000175) test_genes_as_hash: .: (0.000189) test_genes_as_strings: .: (0.000178) test_keggclass: .: (0.000519) test_ko_pathway: .: (0.000244) test_modules_as_hash: .: (0.000189) test_modules_as_strings: .: (0.000187) test_name: .: (0.000214) test_new: .: (0.000234) test_organism: .: (0.000192) test_orthologs_as_hash: .: (0.000219) test_orthologs_as_strings: .: (0.000189) test_pathways_as_hash: .: (0.000257) test_pathways_as_strings: .: (0.000256) test_reactions_as_hash: .: (0.000247) test_reactions_as_strings: .: (0.000231) test_references: .: (0.000209) test_rel_pathways_as_hash: .: (0.000243) test_rel_pathways_as_strings: .: (0.000209) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000550) test_compounds_as_strings: .: (0.000231) test_dblinks_as_hash: .: (0.000253) test_dblinks_as_strings: .: (0.000243) test_description: .: (0.000357) test_diseases_as_hash: .: (0.000260) test_diseases_as_strings: .: (0.000242) test_entry_id: .: (0.000295) test_enzymes_as_strings: .: (0.000233) test_genes_as_hash: .: (0.000223) test_genes_as_strings: .: (0.000261) test_keggclass: .: (0.000249) test_ko_pathway: .: (0.000284) test_modules_as_hash: .: (0.000315) test_modules_as_strings: .: (0.000254) test_name: .: (0.000255) test_new: .: (0.000249) test_organism: .: (0.000288) test_orthologs_as_hash: .: (0.000242) test_orthologs_as_strings: .: (0.000219) test_pathways_as_hash: .: (0.000277) test_pathways_as_strings: .: (0.000242) test_reactions_as_hash: .: (0.000267) test_reactions_as_strings: .: (0.000258) test_references: .: (0.000609) test_rel_pathways_as_hash: .: (0.000314) test_rel_pathways_as_strings: .: (0.000257) Bio::TestBioKeggDRUG: test_activity: .: (0.000484) test_comment: .: (0.000337) test_dblinks_as_hash: .: (0.000358) test_dblinks_as_strings: .: (0.000316) test_entry_id: .: (0.000312) test_formula: .: (0.000291) test_kcf: .: (0.000275) test_mass: .: (0.000304) test_name: .: (0.000305) test_names: .: (0.000307) test_pathways_as_hash: .: (0.000324) test_pathways_as_strings: .: (0.000275) test_products: .: (0.000283) test_remark: .: (0.000279) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000401) test_composition: .: (0.006762) test_compounds: .: (0.000654) test_dblinks_as_hash: .: (0.001193) test_dblinks_as_strings: .: (0.000376) test_entry_id: .: (0.000332) test_enzymes: .: (0.000323) test_kcf: .: (0.000280) test_keggclass: .: (0.000276) test_mass: .: (0.000261) test_name: .: (0.000283) test_orthologs_as_hash: .: (0.000375) test_orthologs_as_strings: .: (0.000724) test_pathways_as_hash: .: (0.000343) test_pathways_as_strings: .: (0.000280) test_reactions: .: (0.000303) test_references: .: (0.000337) test_remark: .: (0.000263) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000449) test_composition: .: (0.000304) test_compounds: .: (0.000293) test_dblinks_as_hash: .: (0.000303) test_dblinks_as_strings: .: (0.000590) test_entry_id: .: (0.000305) test_enzymes: .: (0.000277) test_kcf: .: (0.000252) test_keggclass: .: (0.000274) test_mass: .: (0.000296) test_name: .: (0.000283) test_orthologs_as_hash: .: (0.000304) test_orthologs_as_strings: .: (0.000272) test_pathways_as_hash: .: (0.000573) test_pathways_as_strings: .: (0.000241) test_reactions: .: (0.000250) test_references: .: (0.000217) test_remark: .: (0.000268) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000527) test_compounds_as_strings: .: (0.000357) test_dblinks_as_hash: .: (0.000267) test_dblinks_as_strings: .: (0.000254) test_description: .: (0.000290) test_diseases_as_hash: .: (0.000282) test_diseases_as_strings: .: (0.000262) test_entry_id: .: (0.000297) test_enzymes_as_strings: .: (0.000294) test_genes_as_hash: .: (0.000259) test_genes_as_strings: .: (0.000244) test_keggclass: .: (0.000317) test_ko_pathway: .: (0.000284) test_modules_as_hash: .: (0.000344) test_modules_as_strings: .: (0.000324) test_name: .: (0.000293) test_new: .: (0.000274) test_organism: .: (0.000288) test_orthologs_as_hash: .: (0.000554) test_orthologs_as_strings: .: (0.000298) test_pathways_as_hash: .: (0.000300) test_pathways_as_strings: .: (0.000282) test_reactions_as_hash: .: (0.000433) test_reactions_as_strings: .: (0.000359) test_references: .: (0.000539) test_rel_pathways_as_hash: .: (0.000445) test_rel_pathways_as_strings: .: (0.000336) Bio::TestBioLITDB: test_author: .: (0.000465) test_entry_id: .: (0.000270) test_field: .: (0.000252) test_journal: .: (0.000249) test_keyword: .: (0.000298) test_reference: .: (0.000444) test_title: .: (0.000330) test_volume: .: (0.000262) Bio::TestBioNBRF: test_aalen: .: (0.000443) test_aaseq: .: (0.000257) test_entry: .: (0.000229) test_length: .: (0.000228) test_nalen: .: (0.000313) test_naseq: .: (0.000283) test_seq: .: (0.000242) test_seq_class: .: (0.000242) test_to_nbrf: .: (0.000277) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000356) test_to_newick_format_leaf: .: (0.000269) test_to_newick_format_leaf_NHX: .: (0.000230) Bio::TestBl2seqReport: test_db_len: .: (0.000713) test_db_num: .: (0.000462) test_new: .: (0.000324) test_undefed_methods: .: (0.000817) test_undefed_methods_for_iteration: .: (0.000755) Bio::TestBl2seqReportConstants: test_rs: .: (0.000255) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.006784) test_hits: .: (0.000422) Bio::TestBlast: test_blast_reports_format0: .: (0.005117) test_blast_reports_format0_with_block: .: (0.001091) test_blast_reports_format7: .: (0.016292) test_blast_reports_format7_with_block: .: (0.040740) test_blast_reports_format7_with_parser: .: (0.007533) test_blast_reports_format7_with_parser_with_block: .: (0.007142) test_blast_reports_format8: .: (0.000944) test_blast_reports_format8_with_block: .: (0.000722) test_blast_reports_format8_with_parser: .: (0.000494) test_blast_reports_format8_with_parser_with_block: .: (0.000382) test_blast_reports_xml: .: (0.011451) test_blast_reports_xml_with_block: .: (0.007197) test_blastll: .: (0.000306) test_db: .: (0.000245) test_exec_genomenet: .: (0.000196) test_exec_local: .: (0.000192) test_exec_ncbi: .: (0.000198) test_filter: .: (0.000226) test_format: .: (0.000220) test_make_command_line: .: (0.000443) test_make_command_line_2: .: (0.000404) test_matrix: .: (0.000227) test_new: .: (0.000534) test_new_opt_string: .: (0.000311) test_option: .: (0.000254) test_option_set: .: (0.000317) test_option_set_m0: .: (0.000290) test_options: .: (0.000221) test_output: .: (0.000213) test_parse_result: .: (0.006477) test_parser: .: (0.000284) test_program: .: (0.000221) test_query: .: (0.000192) test_self_local: .: (0.000288) test_self_remote: .: (0.001558) test_server: .: (0.000262) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000405) test_delete: .: (0.000322) test_equal_equal: .: (0.000362) test_get: .: (0.000364) test_make_command_line_options: .: (0.000341) test_normalize!: .: (0.000354) test_parse: .: (0.000240) test_set: .: (0.000353) Bio::TestBlastReport: test_db: .: (0.011230) test_db_len: .: (0.007005) test_db_num: .: (0.006710) test_each_hit: .: (0.006618) test_each_iteration: .: (0.010716) test_eff_space: .: (0.006853) test_entrez_query: .: (0.006587) test_entropy: .: (0.009764) test_expect: .: (0.006869) test_filter: .: (0.006617) test_gap_extend: .: (0.006272) test_gap_open: .: (0.009658) test_hits: .: (0.006920) test_hsp_len: .: (0.006611) test_inclusion: .: (0.008847) test_iterations: .: (0.007131) test_kappa: .: (0.006593) test_lambda: .: (0.006334) test_matrix: .: (0.009110) test_message: .: (0.007067) test_parameters: .: (0.006654) test_pattern: .: (0.008578) test_program: .: (0.006976) test_query_def: .: (0.006635) test_query_id: .: (0.006325) test_query_len: .: (0.009465) test_reference: .: (0.006672) test_sc_match: .: (0.006438) test_sc_mismatch: .: (0.008593) test_statistics: .: (0.006867) test_version: .: (0.006631) Bio::TestBlastReportDefault: test_db: .: (0.000683) test_db_len: .: (0.000535) test_db_num: .: (0.000476) test_each_hit: .: (0.000700) test_each_iteration: .: (0.000454) test_eff_space: .: (0.000541) test_entropy: .: (0.000492) test_expect: .: (0.000514) test_gap_extend: .: (0.000494) test_gap_open: .: (0.000511) test_gapped_entropy: .: (0.000480) test_gapped_kappa: .: (0.000452) test_gapped_lambda: .: (0.000440) test_hits: .: (0.000456) test_iterations: .: (0.000417) test_kappa: .: (0.000470) test_lambda: .: (0.000468) test_matrix: .: (0.000558) test_message: .: (0.000443) test_pattern: .: (0.000437) test_program: .: (0.000464) test_query_def: .: (0.000479) test_query_len: .: (0.000450) test_reference: .: (0.000462) test_sc_match: .: (0.000472) test_sc_mismatch: .: (0.000469) test_version: .: (0.000410) Bio::TestBlastReportHit: test_Hit_accession: .: (0.009669) test_Hit_bit_score: .: (0.007121) test_Hit_definition: .: (0.006855) test_Hit_evalue: .: (0.008734) test_Hit_hit_id: .: (0.007951) test_Hit_hsps: .: (0.006965) test_Hit_identity: .: (0.006369) test_Hit_lap_at: .: (0.009519) test_Hit_len: .: (0.007117) test_Hit_midline: .: (0.006743) test_Hit_num: .: (0.009089) test_Hit_overlap: .: (0.007254) test_Hit_query_def: .: (0.007090) test_Hit_query_end: .: (0.008788) test_Hit_query_id: .: (0.007792) test_Hit_query_len: .: (0.006955) test_Hit_query_seq: .: (0.006207) test_Hit_query_start: .: (0.009083) test_Hit_taeget_def: .: (0.007379) test_Hit_target_end: .: (0.006745) test_Hit_target_id: .: (0.009005) test_Hit_target_len: .: (0.006945) test_Hit_target_seq: .: (0.006695) test_Hit_target_start: .: (0.008480) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000880) test_Hit_definition: .: (0.000529) test_Hit_evalue: .: (0.000506) test_Hit_hsps: .: (0.001344) test_Hit_identity: .: (0.000539) test_Hit_lap_at: .: (0.000679) test_Hit_len: .: (0.000508) test_Hit_midline: .: (0.000582) test_Hit_overlap: .: (0.000746) test_Hit_query_end: .: (0.000567) test_Hit_query_seq: .: (0.000603) test_Hit_query_start: .: (0.000542) test_Hit_taeget_def: .: (0.000465) test_Hit_target_end: .: (0.000532) test_Hit_target_id: .: (0.000692) test_Hit_target_len: .: (0.000458) test_Hit_target_seq: .: (0.000591) test_Hit_target_start: .: (0.000542) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.020215) test_Hit_bit_score: .: (0.018994) test_Hit_definition: .: (0.021281) test_Hit_evalue: .: (0.020591) test_Hit_hit_id: .: (0.020402) test_Hit_hsps: .: (0.020431) test_Hit_identity: .: (0.020335) test_Hit_lap_at: .: (0.020005) test_Hit_len: .: (0.020055) test_Hit_midline: .: (0.020094) test_Hit_num: .: (0.020061) test_Hit_overlap: .: (0.020143) test_Hit_query_def: .: (0.019929) test_Hit_query_end: .: (0.020179) test_Hit_query_id: .: (0.020190) test_Hit_query_len: .: (0.020446) test_Hit_query_seq: .: (0.020042) test_Hit_query_start: .: (0.020136) test_Hit_taeget_def: .: (0.020117) test_Hit_target_end: .: (0.020020) test_Hit_target_id: .: (0.020189) test_Hit_target_len: .: (0.020106) test_Hit_target_seq: .: (0.020305) test_Hit_target_start: .: (0.020137) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.020315) test_Hit_bit_score: .: (0.019998) test_Hit_definition: .: (0.020497) test_Hit_evalue: .: (0.020499) test_Hit_hit_id: .: (0.020140) test_Hit_hsps: .: (0.020118) test_Hit_identity: .: (0.020058) test_Hit_lap_at: .: (0.020367) test_Hit_len: .: (0.019977) test_Hit_midline: .: (0.020503) test_Hit_num: .: (0.020168) test_Hit_overlap: .: (0.019819) test_Hit_query_def: .: (0.019593) test_Hit_query_end: .: (0.019896) test_Hit_query_id: .: (0.019873) test_Hit_query_len: .: (0.020346) test_Hit_query_seq: .: (0.019967) test_Hit_query_start: .: (0.020297) test_Hit_taeget_def: .: (0.020067) test_Hit_target_end: .: (0.020247) test_Hit_target_id: .: (0.019968) test_Hit_target_len: .: (0.020363) test_Hit_target_seq: .: (0.019876) test_Hit_target_start: .: (0.020067) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.008928) test_Hit_bit_score: .: (0.006766) test_Hit_definition: .: (0.006773) test_Hit_evalue: .: (0.008821) test_Hit_hit_id: .: (0.006840) test_Hit_hsps: .: (0.006541) test_Hit_identity: .: (0.008907) test_Hit_lap_at: .: (0.006918) test_Hit_len: .: (0.006581) test_Hit_midline: .: (0.008706) test_Hit_num: .: (0.006762) test_Hit_overlap: .: (0.006821) test_Hit_query_def: .: (0.008764) test_Hit_query_end: .: (0.006901) test_Hit_query_id: .: (0.006663) test_Hit_query_len: .: (0.009030) test_Hit_query_seq: .: (0.006900) test_Hit_query_start: .: (0.006767) test_Hit_taeget_def: .: (0.008736) test_Hit_target_end: .: (0.007019) test_Hit_target_id: .: (0.006793) test_Hit_target_len: .: (0.008751) test_Hit_target_seq: .: (0.006785) test_Hit_target_start: .: (0.007937) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000560) test_Hit_bit_score: .: (0.000141) test_Hit_definition: .: (0.000093) test_Hit_evalue: .: (0.000085) test_Hit_hit_id: .: (0.000081) test_Hit_hsps: .: (0.000074) test_Hit_identity: .: (0.000110) test_Hit_lap_at: .: (0.000108) test_Hit_len: .: (0.000077) test_Hit_midline: .: (0.000072) test_Hit_num: .: (0.000075) test_Hit_overlap: .: (0.000075) test_Hit_query_def: .: (0.000082) test_Hit_query_end: .: (0.000071) test_Hit_query_id: .: (0.000073) test_Hit_query_len: .: (0.000069) test_Hit_query_seq: .: (0.000067) test_Hit_query_start: .: (0.000072) test_Hit_taeget_def: .: (0.000069) test_Hit_target_end: .: (0.000068) test_Hit_target_id: .: (0.000066) test_Hit_target_len: .: (0.000067) test_Hit_target_seq: .: (0.000072) test_Hit_target_start: .: (0.000074) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.009216) test_Hsp_bit_score: .: (0.006916) test_Hsp_density: .: (0.006895) test_Hsp_evalue: .: (0.009113) test_Hsp_gaps: .: (0.006768) test_Hsp_hit_frame: .: (0.006476) test_Hsp_hit_from: .: (0.008882) test_Hsp_hit_to: .: (0.006833) test_Hsp_hseq: .: (0.006732) test_Hsp_identity: .: (0.008871) test_Hsp_midline: .: (0.006933) test_Hsp_mismatch_count: .: (0.006474) test_Hsp_num: .: (0.009283) test_Hsp_pattern_from: .: (0.006727) test_Hsp_pattern_to: .: (0.006747) test_Hsp_percent_identity: .: (0.008480) test_Hsp_positive: .: (0.007043) test_Hsp_qseq: .: (0.006680) test_Hsp_query_frame: .: (0.008935) test_Hsp_query_from: .: (0.006701) test_Hsp_query_to: .: (0.006670) test_Hsp_score: .: (0.009212) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000894) test_Hsp_bit_score: .: (0.000528) test_Hsp_evalue: .: (0.000515) test_Hsp_gaps: .: (0.000501) test_Hsp_hit_frame: .: (0.000486) test_Hsp_hit_from: .: (0.000541) test_Hsp_hit_to: .: (0.000580) test_Hsp_hseq: .: (0.000732) test_Hsp_identity: .: (0.000469) test_Hsp_midline: .: (0.000548) test_Hsp_percent_identity: .: (0.000461) test_Hsp_positive: .: (0.000454) test_Hsp_qseq: .: (0.000563) test_Hsp_query_frame: .: (0.000646) test_Hsp_query_from: .: (0.000573) test_Hsp_query_to: .: (0.000532) test_Hsp_score: .: (0.000451) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.020653) test_Hsp_bit_score: .: (0.020507) test_Hsp_density: .: (0.020139) test_Hsp_evalue: .: (0.020177) test_Hsp_gaps: .: (0.020110) test_Hsp_hit_frame: .: (0.019846) test_Hsp_hit_from: .: (0.020086) test_Hsp_hit_to: .: (0.019765) test_Hsp_hseq: .: (0.020106) test_Hsp_identity: .: (0.020037) test_Hsp_midline: .: (0.020191) test_Hsp_mismatch_count: .: (0.020266) test_Hsp_num: .: (0.019991) test_Hsp_pattern_from: .: (0.020365) test_Hsp_pattern_to: .: (0.020433) test_Hsp_percent_identity: .: (0.019955) test_Hsp_positive: .: (0.020196) test_Hsp_qseq: .: (0.019980) test_Hsp_query_frame: .: (0.020160) test_Hsp_query_from: .: (0.019897) test_Hsp_query_to: .: (0.020126) test_Hsp_score: .: (0.019978) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.020417) test_Hsp_bit_score: .: (0.020072) test_Hsp_density: .: (0.020402) test_Hsp_evalue: .: (0.020341) test_Hsp_gaps: .: (0.019849) test_Hsp_hit_frame: .: (0.019959) test_Hsp_hit_from: .: (0.020207) test_Hsp_hit_to: .: (0.019882) test_Hsp_hseq: .: (0.019994) test_Hsp_identity: .: (0.019980) test_Hsp_midline: .: (0.020208) test_Hsp_mismatch_count: .: (0.020201) test_Hsp_num: .: (0.020065) test_Hsp_pattern_from: .: (0.020091) test_Hsp_pattern_to: .: (0.021706) test_Hsp_percent_identity: .: (0.038745) test_Hsp_positive: .: (0.037035) test_Hsp_qseq: .: (0.037067) test_Hsp_query_frame: .: (0.036953) test_Hsp_query_from: .: (0.039560) test_Hsp_query_to: .: (0.032865) test_Hsp_score: .: (0.042443) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.015139) test_Hsp_bit_score: .: (0.011541) test_Hsp_density: .: (0.011560) test_Hsp_evalue: .: (0.017956) test_Hsp_gaps: .: (0.017377) test_Hsp_hit_frame: .: (0.011575) test_Hsp_hit_from: .: (0.013459) test_Hsp_hit_to: .: (0.013851) test_Hsp_hseq: .: (0.015570) test_Hsp_identity: .: (0.013389) test_Hsp_midline: .: (0.015202) test_Hsp_mismatch_count: .: (0.011102) test_Hsp_num: .: (0.017199) test_Hsp_pattern_from: .: (0.011233) test_Hsp_pattern_to: .: (0.015122) test_Hsp_percent_identity: .: (0.013286) test_Hsp_positive: .: (0.015112) test_Hsp_qseq: .: (0.011240) test_Hsp_query_frame: .: (0.016996) test_Hsp_query_from: .: (0.011333) test_Hsp_query_to: .: (0.015201) test_Hsp_score: .: (0.017978) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000709) test_Hsp_bit_score: .: (0.000332) test_Hsp_density: .: (0.000325) test_Hsp_evalue: .: (0.000314) test_Hsp_gaps: .: (0.000300) test_Hsp_hit_frame: .: (0.000303) test_Hsp_hit_from: .: (0.000317) test_Hsp_hit_to: .: (0.000299) test_Hsp_hseq: .: (0.000293) test_Hsp_identity: .: (0.000285) test_Hsp_midline: .: (0.000283) test_Hsp_mismatch_count: .: (0.000301) test_Hsp_num: .: (0.000331) test_Hsp_pattern_from: .: (0.000296) test_Hsp_pattern_to: .: (0.000310) test_Hsp_percent_identity: .: (0.000291) test_Hsp_positive: .: (0.000295) test_Hsp_qseq: .: (0.000286) test_Hsp_query_frame: .: (0.000290) test_Hsp_query_from: .: (0.000446) test_Hsp_query_to: .: (0.000410) test_Hsp_score: .: (0.000298) Bio::TestBlastReportIteration: test_hits: .: (0.013388) test_message: .: (0.009908) test_num: .: (0.008208) test_statistics: .: (0.010940) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000758) test_message: .: (0.000668) test_num: .: (0.000603) Bio::TestBlastReportIterationMulti: test_each: .: (0.021818) test_hits: .: (0.021438) test_message: .: (0.022291) test_num: .: (0.021291) test_query_def: .: (0.022457) test_query_id: .: (0.022231) test_query_len: .: (0.022462) test_statistics: .: (0.037846) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.043433) test_hits: .: (0.039543) test_message: .: (0.039579) test_num: .: (0.033492) test_query_def: .: (0.041794) test_query_id: .: (0.039593) test_query_len: .: (0.039562) test_statistics: .: (0.023914) Bio::TestBlastReportIterationREXML: test_hits: .: (0.007837) test_message: .: (0.008239) test_num: .: (0.010833) test_statistics: .: (0.007039) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000617) test_message: .: (0.000314) test_num: .: (0.000297) test_statistics: .: (0.000292) Bio::TestBlastReportMulti: test_db: .: (0.040485) test_db_len: .: (0.032807) test_db_num: .: (0.043088) test_each_hit: .: (0.039079) test_each_iteration: .: (0.037834) test_eff_space: .: (0.037430) test_entropy: .: (0.041255) test_expect: .: (0.038260) test_filter: .: (0.039555) test_gap_extend: .: (0.038799) test_gap_open: .: (0.037500) test_hits: .: (0.037821) test_hsp_len: .: (0.039247) test_iterations: .: (0.042424) test_kappa: .: (0.023522) test_lambda: .: (0.026712) test_matrix: .: (0.029786) test_message: .: (0.029301) test_parameters: .: (0.037528) test_pattern: .: (0.048038) test_program: .: (0.040460) test_query_def: .: (0.037271) test_query_id: .: (0.044321) test_query_len: .: (0.054544) test_reference: .: (0.099338) test_reports: .: (0.037315) test_statistics: .: (0.041633) test_version: .: (0.037458) Bio::TestBlastReportMultiREXML: test_db: .: (0.037405) test_db_len: .: (0.037100) test_db_num: .: (0.037411) test_each_hit: .: (0.020531) test_each_iteration: .: (0.021101) test_eff_space: .: (0.020438) test_entropy: .: (0.022040) test_expect: .: (0.020332) test_filter: .: (0.021379) test_gap_extend: .: (0.021444) test_gap_open: .: (0.021257) test_hits: .: (0.020626) test_hsp_len: .: (0.020248) test_iterations: .: (0.021506) test_kappa: .: (0.021026) test_lambda: .: (0.020384) test_matrix: .: (0.020105) test_message: .: (0.019881) test_parameters: .: (0.021569) test_pattern: .: (0.021149) test_program: .: (0.019850) test_query_def: .: (0.019716) test_query_id: .: (0.021973) test_query_len: .: (0.021347) test_reference: .: (0.020199) test_reports: .: (0.019925) test_statistics: .: (0.022059) test_version: .: (0.020884) Bio::TestBlastReportREXML: test_db: .: (0.006708) test_db_len: .: (0.009426) test_db_num: .: (0.007314) test_each_hit: .: (0.008963) test_each_iteration: .: (0.007020) test_eff_space: .: (0.008030) test_entrez_query: .: (0.008143) test_entropy: .: (0.006809) test_expect: .: (0.008792) test_filter: .: (0.007285) test_gap_extend: .: (0.008088) test_gap_open: .: (0.007904) test_hits: .: (0.006841) test_hsp_len: .: (0.008859) test_inclusion: .: (0.007300) test_iterations: .: (0.008117) test_kappa: .: (0.007651) test_lambda: .: (0.006822) test_matrix: .: (0.008771) test_message: .: (0.007227) test_parameters: .: (0.008889) test_pattern: .: (0.007172) test_program: .: (0.006634) test_query_def: .: (0.009005) test_query_id: .: (0.007122) test_query_len: .: (0.008644) test_reference: .: (0.006910) test_sc_match: .: (0.007954) test_sc_mismatch: .: (0.007794) test_statistics: .: (0.007109) test_version: .: (0.008754) Bio::TestBlastReportTabular: test_db: .: (0.000705) test_db_len: .: (0.000311) test_db_num: .: (0.000289) test_each_hit: .: (0.000299) test_each_iteration: .: (0.000309) test_eff_space: .: (0.000323) test_entrez_query: .: (0.000324) test_entropy: .: (0.000293) test_expect: .: (0.000295) test_filter: .: (0.000288) test_gap_extend: .: (0.000295) test_gap_open: .: (0.000312) test_hits: .: (0.000295) test_hsp_len: .: (0.000314) test_inclusion: .: (0.000293) test_iterations: .: (0.000291) test_kappa: .: (0.000327) test_lambda: .: (0.000293) test_matrix: .: (0.000286) test_message: .: (0.000299) test_parameters: .: (0.000287) test_pattern: .: (0.000403) test_program: .: (0.000291) test_query_def: .: (0.000295) test_query_id: .: (0.000344) test_query_len: .: (0.000290) test_reference: .: (0.000316) test_sc_match: .: (0.000208) test_sc_mismatch: .: (0.000210) test_statistics: .: (0.000223) test_version: .: (0.000186) Bio::TestChain: test_aaseq: .: (0.000404) test_addLigand: .: (0.000150) test_addResidue: .: (0.000149) test_atom_seq: .: (0.000162) test_comp: .: (0.000177) test_each: .: (0.000148) test_each_heterogen: .: (0.000161) test_each_residue: .: (0.000157) test_get_heterogen_by_id: .: (0.000234) test_get_residue_by_id: .: (0.000155) test_inspect: .: (0.000210) test_rehash: .: (0.000145) test_rehash_heterogens: .: (0.000137) test_rehash_residues: .: (0.000135) test_square_brace: .: (0.000147) test_to_s: .: (0.000174) Bio::TestChainFinder: test_chains: .: (0.000318) test_each_chain: .: (0.000160) test_find_chain: .: (0.000153) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005515) test_header: .: (0.000717) test_match_line: .: (0.000653) test_sequence0: .: (0.000702) test_sequence1: .: (0.000667) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.005266) test_header: .: (0.000871) test_match_line: .: (0.000776) test_sequence0: .: (0.000782) test_sequence1: .: (0.003033) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.007462) test_header: .: (0.000752) test_match_line: .: (0.000906) test_sequence0: .: (0.000774) test_sequence1: .: (0.000851) Bio::TestCodonTable: test_Tables: .: (0.000389) test_accessor: .: (0.000231) test_definition: .: (0.000225) test_each: .: (0.000223) test_revtrans: .: (0.000283) test_self_accessor: .: (0.000215) test_self_copy: .: (0.000669) test_set_accessor: .: (0.048159) test_start: .: (0.000089) test_start_codon?: .: (0.000060) test_stop: .: (0.000047) test_stop_codon?: .: (0.000044) test_table: .: (0.000042) Bio::TestCodonTableConstants: test_Definitions: .: (0.000171) test_Starts: .: (0.000050) test_Tables: .: (0.000037) test_stops: .: (0.000046) Bio::TestColorScheme: test_buried: .: (0.001076) Bio::TestCommand: test_command_constants: .: (0.000170) test_escape_shell: .: (0.000095) test_escape_shell_unix: .: (0.000055) test_escape_shell_windows: .: (0.000074) test_make_cgi_params_by_array_of_array: .: (0.000220) test_make_cgi_params_by_array_of_hash: .: (0.000317) test_make_cgi_params_by_array_of_string: .: (0.000076) test_make_cgi_params_by_hash_in_string: .: (0.000245) test_make_cgi_params_by_hash_in_symbol: .: (0.000230) test_make_cgi_params_by_string: .: (0.000119) test_make_command_line: .: (0.000069) test_make_command_line_unix: .: (0.000050) test_make_command_line_windows: .: (0.000058) test_safe_command_line_array: .: (0.000063) test_safe_command_line_array_passthrough: .: (0.000055) Bio::TestContingencyTable: test_lite_example: .: (0.071373) Bio::TestDB: test_entry_id: .: (0.000227) test_exists: .: (0.000047) test_fetch: .: (0.000095) test_get: .: (0.000042) test_open: .: (0.000038) test_tags: .: (0.000040) Bio::TestDataType: test_const_like_method: .: (0.000375) test_pdb_achar: .: (0.000443) test_pdb_atom: .: (0.000179) test_pdb_character: .: (0.000107) test_pdb_date: .: (0.000114) test_pdb_idcode: .: (0.000101) test_pdb_integer: .: (0.000049) test_pdb_list: .: (0.000066) test_pdb_lstring: .: (0.000115) test_pdb_real: .: (0.000087) test_pdb_resudue_name: .: (0.000112) test_pdb_slist: .: (0.000048) test_pdb_string: .: (0.000106) test_pdb_stringrj: .: (0.000045) test_pdb_symop: .: (0.000096) test_specification_list: .: (0.000205) Bio::TestEMBL: test_ac: .: (0.000398) test_accession: .: (0.000176) test_cc: .: (0.000145) test_de: .: (0.000178) test_division: .: (0.000189) test_dr: .: (0.000148) test_dt: .: (0.000165) test_dt_created: .: (0.000316) test_dt_iterator: .: (0.000257) test_dt_updated: .: (0.000177) test_each_cds: .: (0.000362) test_each_gene: .: (0.000277) test_entry: .: (0.000217) test_fh: .: (0.000163) test_ft: .: (0.000391) test_ft_accessor: .: (0.000263) test_ft_iterator: .: (0.000257) test_id_line: .: (0.000198) test_id_line_data_class: .: (0.000431) test_id_line_division: .: (0.000230) test_id_line_entry_name: .: (0.000167) test_id_line_iterator: .: (0.000498) test_id_line_molecule_type: .: (0.000223) test_id_line_sequence_length: .: (0.000189) test_kw: .: (0.000229) test_molecule: .: (0.000198) test_oc: .: (0.000217) test_og: .: (0.000155) test_os: .: (0.000187) test_ref: .: (0.000234) test_references: .: (0.000350) test_seq: .: (0.000345) test_sequence_length: .: (0.000188) test_sq: .: (0.000179) test_sq_get: .: (0.000159) test_sv: .: (0.000156) test_version: .: (0.000152) Bio::TestEMBL89: test_ac: .: (0.000658) test_accession: .: (0.000190) test_cc: .: (0.000149) test_de: .: (0.000176) test_division: .: (0.000187) test_dr: .: (0.000142) test_dt: .: (0.000158) test_dt_created: .: (0.000141) test_dt_iterator: .: (0.000134) test_dt_updated: .: (0.000143) test_each_cds: .: (0.000274) test_each_gene: .: (0.000235) test_entry: .: (0.000199) test_fh: .: (0.000156) test_ft: .: (0.000254) test_ft_accessor: .: (0.004368) test_ft_iterator: .: (0.001012) test_id_line: .: (0.000298) test_id_line_data_class: .: (0.000234) test_id_line_division: .: (0.000218) test_id_line_entry_name: .: (0.001043) test_id_line_iterator: .: (0.000251) test_id_line_molecule_type: .: (0.000187) test_id_line_sequence_length: .: (0.000265) test_id_line_sequence_version: .: (0.000208) test_kw: .: (0.000690) test_molecule: .: (0.000245) test_oc: .: (0.000292) test_og: .: (0.000190) test_os: .: (0.000212) test_ref: .: (0.000237) test_references: .: (0.000457) test_seq: .: (0.000353) test_sequence_length: .: (0.000211) test_sq: .: (0.000189) test_sq_get: .: (0.000167) test_sv: .: (0.000296) test_version: .: (0.000195) Bio::TestEMBLAPI: test_ac: .: (0.000646) test_accessions: .: (0.000286) Bio::TestEMBLCommon: test_ac: .: (0.000387) test_accession: .: (0.000212) test_accessions: .: (0.000205) test_de: .: (0.000231) test_definition: .: (0.000214) test_description: .: (0.000222) test_dr: .: (0.000213) test_keywords: .: (0.000225) test_kw: .: (0.000214) test_oc: .: (0.000325) test_og: .: (0.000219) test_os: .: (0.000215) test_ref: .: (0.000239) test_references: .: (0.000206) Bio::TestEMBLDB: test_fetch: .: (0.000448) test_p_entry2hash: .: (0.000206) Bio::TestEMBLToBioSequence: test_classification: .: (0.002781) test_date_created: .: (0.000721) test_date_modified: .: (0.000575) test_definition: .: (0.000499) test_division: .: (0.000501) test_entry_id: .: (0.000480) test_entry_version: .: (0.000467) test_features: .: (0.000711) test_keywords: .: (0.000477) test_molecule_type: .: (0.000525) test_primary_accession: .: (0.000473) test_references: .: (0.000648) test_release_created: .: (0.000456) test_release_modified: .: (0.000568) test_secondary_accessions: .: (0.000513) test_sequence_version: .: (0.000502) test_species: .: (0.000525) test_topology: .: (0.000531) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.004325) test_date_created: .: (0.002594) test_date_modified: .: (0.002400) test_definition: .: (0.007836) test_division: .: (0.003180) test_entry_id: .: (0.002587) test_entry_version: .: (0.002464) test_features: .: (0.002715) test_keywords: .: (0.003056) test_molecule_type: .: (0.002187) test_primary_accession: .: (0.002357) test_references: .: (0.008417) test_release_created: .: (0.003439) test_release_modified: .: (0.002542) test_secondary_accessions: .: (0.002203) test_sequence_version: .: (0.002506) test_species: .: (0.002960) test_topology: .: (0.002294) Bio::TestFasta: test_db: .: (0.000405) test_format: .: (0.000205) test_format_arg_integer: .: (0.000227) test_format_arg_str: .: (0.000216) test_ktup: .: (0.000207) test_matrix: .: (0.000209) test_option: .: (0.000280) test_options: .: (0.000213) test_output: .: (0.000205) test_program: .: (0.000210) test_server: .: (0.000212) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000391) test_accession: .: (0.000251) test_accessions: .: (0.000247) test_description: .: (0.000228) test_descriptions: .: (0.000234) test_entry_id: .: (0.000283) test_get_all_by_type: .: (0.000243) test_gi: .: (0.000246) test_id_strings: .: (0.000311) test_list_ids: .: (0.000239) test_locus: .: (0.000249) test_words: .: (0.000287) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000445) test_accession: .: (0.000261) test_accessions: .: (0.000271) test_description: .: (0.000251) test_descriptions: .: (0.000262) test_emb: .: (0.000267) test_entry_id: .: (0.000248) test_get_all_by_type: .: (0.000241) test_get_emb: .: (0.000256) test_gi: .: (0.000244) test_id_strings: .: (0.000314) test_list_ids: .: (0.000247) test_locus: .: (0.000265) test_words: .: (0.000287) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000298) test_accession: .: (0.000274) test_accessions: .: (0.000193) test_description: .: (0.000207) test_descriptions: .: (0.000152) test_entry_id: .: (0.000144) test_get_all_by_type: .: (0.000160) test_gi: .: (0.000159) test_id_strings: .: (0.000270) test_list_ids: .: (0.000259) test_locus: .: (0.000274) test_sp: .: (0.000311) test_words: .: (0.000306) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000478) test_accession: .: (0.000341) test_accessions: .: (0.000333) test_description: .: (0.000300) test_descriptions: .: (0.000312) test_entry_id: .: (0.000268) test_get_all_by_type: .: (0.000275) test_gi: .: (0.000264) test_id_strings: .: (0.000433) test_list_ids: .: (0.000262) test_locus: .: (0.000324) test_words: .: (0.000486) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000500) test_accession: .: (0.000358) test_accessions: .: (0.000336) test_description: .: (0.000324) test_descriptions: .: (0.000302) test_entry_id: .: (0.000325) test_get_all_by_type: .: (0.000269) test_gi: .: (0.000311) test_id_strings: .: (0.000358) test_list_ids: .: (0.000274) test_locus: .: (0.000288) test_words: .: (0.000356) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000421) test_accession: .: (0.000275) test_accessions: .: (0.001033) test_description: .: (0.000249) test_descriptions: .: (0.000272) test_entry_id: .: (0.000262) test_get_all_by_type: .: (0.000251) test_gi: .: (0.000248) test_id_strings: .: (0.000278) test_list_ids: .: (0.000242) test_locus: .: (0.000256) test_words: .: (0.000320) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000448) test_accession: .: (0.000291) test_accessions: .: (0.000280) test_description: .: (0.000258) test_descriptions: .: (0.000243) test_entry_id: .: (0.000240) test_get: .: (0.000253) test_get_all_by_type: .: (0.000246) test_id_strings: .: (0.000510) test_list_ids: .: (0.000236) test_locus: .: (0.000266) test_sp: .: (0.000301) test_words: .: (0.000321) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000400) test_accession: .: (0.000278) test_accessions: .: (0.000306) test_description: .: (0.000241) test_descriptions: .: (0.000267) test_entry_id: .: (0.000278) test_get: .: (0.000256) test_get_all_by_type: .: (0.000249) test_id_strings: .: (0.000405) test_list_ids: .: (0.000271) test_locus: .: (0.000263) test_tr: .: (0.000285) test_words: .: (0.000408) Bio::TestFastaFirstName: test_first_name1: .: (0.000594) test_first_name_multi_identifier: .: (0.000277) test_first_name_single_worded_defintion: .: (0.000259) test_no_definition: .: (0.000223) test_space_before_first_name: .: (0.000237) test_tabbed_defintion: .: (0.000263) Bio::TestFastaFormat: test_aalen: .: (0.000474) test_aaseq: .: (0.000260) test_acc_version: .: (0.000364) test_accession: .: (0.000331) test_accessions: .: (0.000332) test_data: .: (0.000229) test_definition: .: (0.000230) test_entry: .: (0.000228) test_entry_id: .: (0.000284) test_entry_overrun: .: (0.000229) test_first_name: .: (0.000250) test_gi: .: (0.000328) test_identifiers: .: (0.000346) test_length: .: (0.000299) test_query: .: (0.000283) test_seq: .: (0.000254) Bio::TestFastaFormatConst: test_delimiter: .: (0.000340) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000472) test_data: .: (0.000277) test_definition: .: (0.000239) test_entry: .: (0.000254) test_entry_id: .: (0.000353) test_first_name: .: (0.000242) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000400) test_naseq: .: (0.000238) test_naseq_class: .: (0.000259) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000441) Bio::TestFastaInitialize: test_new_1: .: (0.000615) test_option: .: (0.000235) test_option_backward_compatibility: .: (0.000358) Bio::TestFastaNumericFormat: test_arg: .: (0.000444) test_data: .: (0.000288) test_definition: .: (0.000252) test_each: .: (0.000279) test_entry: .: (0.000234) test_entry_id: .: (0.000261) test_length: .: (0.000273) test_to_biosequence: .: (0.000998) Bio::TestFastaQuery: test_query: .: (0.002299) test_self_local: .: (0.000220) test_self_parser: .: (0.000174) test_self_remote: .: (0.000223) Bio::TestFastacmd: test_database: .: (0.000933) test_fastacmd: .: (0.001085) test_methods: .: (0.000278) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.003035) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.003892) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001541) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.002060) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.002762) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.003794) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.002837) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.001710) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.002357) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.002782) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.003742) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001850) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.002903) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.004552) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.005445) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.002342) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001761) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.001658) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.006552) test_error_probabilities_as_sanger: .: (0.002511) test_error_probabilities_as_solexa: .: (0.002277) test_quality_scores_as_illumina: .: (0.000568) test_quality_scores_as_sanger: .: (0.000556) test_quality_scores_as_solexa: .: (0.000488) test_validate_format: .: (0.000604) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.001280) test_entry_id: .: (0.000863) test_error_probabilities: .: (0.058631) test_nalen: .: (0.000933) test_naseq: .: (0.000850) test_quality_scores: .: (0.001278) test_quality_string: .: (0.002168) test_roundtrip: .: (0.081921) test_seq: .: (0.000636) test_sequence_string: .: (0.000437) test_to_biosequence: .: (0.048128) test_to_biosequence_and_output: .: (0.002934) test_to_s: .: (0.000548) test_validate_format: .: (0.000505) test_validate_format_with_array: .: (0.000516) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000737) test_mask_20_with_empty_string: .: (0.000275) test_mask_20_with_longer_string: .: (0.000255) test_mask_20_with_x: .: (0.000305) test_mask_60: .: (0.000250) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.002474) test_error_probabilities_as_sanger: .: (0.002722) test_error_probabilities_as_solexa: .: (0.002466) test_quality_scores_as_illumina: .: (0.003564) test_quality_scores_as_sanger: .: (0.000544) test_quality_scores_as_solexa: .: (0.000344) test_validate_format: .: (0.002172) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.002791) test_error_probabilities_as_sanger: .: (0.002283) test_error_probabilities_as_solexa: .: (0.001929) test_quality_scores_as_illumina: .: (0.000373) test_quality_scores_as_sanger: .: (0.000221) test_quality_scores_as_solexa: .: (0.000157) test_validate_format: .: (0.000337) Bio::TestFeature: test_append: .: (0.000189) test_append_nil: .: (0.000049) test_assoc: .: (0.000059) test_each: .: (0.000042) test_feature: .: (0.000036) test_locations: .: (0.000099) test_new: .: (0.000040) test_position: .: (0.000145) test_qualifiers: .: (0.000037) Bio::TestFeatures: test_append: .: (0.000188) test_arg: .: (0.000050) test_each: .: (0.000045) test_features: .: (0.000046) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000975) test_aaindex2: .: (0.000210) test_blast: .: (0.000142) test_blastxml: .: (0.000546) test_embl: .: (0.000195) test_embl_oldrelease: .: (0.000158) test_fastaformat: .: (0.000281) test_fastanumericformat: .: (0.000082) test_fastq: .: (0.000106) test_genbank: .: (0.000131) test_genpept: .: (0.000260) test_hmmer: .: (0.000149) test_maxml_cluster: .: (0.002567) test_maxml_sequence: .: (0.000233) test_medline: .: (0.000147) test_prosite: .: (0.003274) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002820) test_transfac: .: (0.001810) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000231) test_auto_1arg_filename: .: (0.000318) test_auto_1arg_io: .: (0.000209) test_auto_1arg_io_with_block: .: (0.000417) test_auto_1arg_with_block: .: (0.000376) test_auto_2arg_filename_mode: .: (0.000490) test_auto_2arg_filename_mode_with_block: .: (0.000430) test_auto_3arg: .: (0.000258) test_auto_3arg_with_block: .: (0.000377) test_foreach: .: (0.000321) test_new_2arg_class: .: (0.000111) test_new_2arg_nil: .: (0.000178) test_open_0arg: .: (0.000093) test_open_1arg_class: .: (0.000064) test_open_1arg_filename: .: (0.000198) test_open_1arg_io: .: (0.000186) test_open_1arg_io_with_block: .: (0.000377) test_open_1arg_nil: .: (0.000078) test_open_1arg_with_block: .: (0.000381) test_open_2arg_autodetect: .: (0.000208) test_open_2arg_autodetect_io: .: (0.000448) test_open_2arg_autodetect_io_with_block: .: (0.000420) test_open_2arg_autodetect_with_block: .: (0.000426) test_open_2arg_class: .: (0.000116) test_open_2arg_class_io: .: (0.000098) test_open_2arg_class_io_with_block: .: (0.000269) test_open_2arg_class_with_block: .: (0.000255) test_open_2arg_filename_mode: .: (0.000220) test_open_2arg_filename_mode_with_block: .: (0.000335) test_open_3arg: .: (0.000382) test_open_3arg_with_block: .: (0.000862) test_open_4arg: .: (0.001087) test_to_a: .: (0.000398) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000334) test_close: .: (0.000095) test_dbclass: .: (0.000071) test_dbclass_eq: .: (0.000091) test_dbclass_nil: .: (0.000138) test_each: .: (0.000178) test_each_entry: .: (0.000242) test_ended_pos: .: (0.000157) test_entry_pos_flag: .: (0.000095) test_entry_raw: .: (0.000200) test_eof?: .: (0.000171) test_next_entry: .: (0.000200) test_path: .: (0.000081) test_pos: .: (0.000383) test_raw: .: (0.000244) test_rewind: .: (0.000152) test_start_pos: .: (0.000142) test_start_pos_ended_pos_not_recorded: .: (0.000165) test_to_io: .: (0.000128) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000244) test_simpleformat2: .: (0.000117) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000148) test_eof_false_after_prefetch: .: (0.000110) test_eof_false_first: .: (0.000049) test_eof_true: .: (0.000080) test_getc: .: (0.000057) test_getc_after_prefetch: .: (0.000049) test_gets: .: (0.000047) test_gets_equal_prefetch_gets: .: (0.000055) test_gets_paragraph_mode: .: (0.003180) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000350) test_gets_paragraph_mode_within_buffer: .: (0.000224) test_gets_rs: .: (0.000080) test_gets_rs_equal_prefetch_gets: .: (0.000079) test_gets_rs_within_buffer: .: (0.000172) test_pos: .: (0.000071) test_pos=: .: (0.000071) test_prefetch_buffer: .: (0.000068) test_prefetch_gets: .: (0.000064) test_prefetch_gets_with_arg: .: (0.000078) test_rewind: .: (0.000059) test_skip_spaces: .: (0.000075) test_to_io: .: (0.000081) test_ungetc: .: (0.000065) test_ungetc_after_prefetch: .: (0.000062) test_ungets: .: (0.000074) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000947) test_self_open_file: .: (0.000142) test_self_open_file_with_block: .: (0.071468) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000245) test_parse_file_open_arg_int_perm: .: (0.000049) test_parse_file_open_arg_int_perm_opt: .: (0.000044) test_parse_file_open_arg_integer: .: (0.000063) test_parse_file_open_arg_nil: .: (0.000049) test_parse_file_open_arg_opt: .: (0.000073) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000053) test_parse_file_open_arg_str: .: (0.000047) test_parse_file_open_arg_str_opt: .: (0.000051) test_parse_file_open_arg_str_perm: .: (0.000045) test_parse_file_open_arg_str_perm_opt: .: (0.000048) test_parse_file_open_arg_str_with_enc: .: (0.000054) test_parse_file_open_arg_str_with_ext_enc: .: (0.000050) test_parse_file_open_mode_integer: .: (0.000044) test_parse_file_open_mode_nil: .: (0.000046) test_parse_file_open_mode_str: .: (0.000046) test_parse_file_open_mode_str_with_enc: .: (0.000046) test_parse_file_open_mode_str_with_ext_enc: .: (0.000042) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000449) test_entry: .: (0.000071) test_entry_ended_pos: .: (0.000050) test_entry_pos_flag: .: (0.000059) test_entry_start_pos: .: (0.000045) test_get_entry: .: (0.000096) test_rewind: .: (0.000065) test_skip_leader: .: (0.000055) test_stream: .: (0.000042) test_stream_pos: .: (0.000058) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000139) test_delimiter_overrun: .: (0.000045) test_entry: .: (0.000087) test_entry_ended_pos: .: (0.000060) test_entry_ended_pos_default_nil: .: (0.000053) test_entry_start_pos: .: (0.000055) test_entry_start_pos_default_nil: .: (0.000227) test_get_entry: .: (0.000165) test_get_parsed_entry: .: (0.000141) test_header: .: (0.000050) test_skip_leader: .: (0.000074) test_skip_leader_without_header: .: (0.000071) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000254) test_entry_ended_pos: .: (0.000129) test_entry_start_pos: .: (0.000097) test_flag_to_fetch_header: .: (0.000096) test_get_entry: .: (0.000131) test_get_parsed_entry: .: (0.000147) test_rewind: .: (0.000264) test_skip_leader: .: (0.000064) Bio::TestGCGMsf: test_alignment: .: (0.000716) test_checksum: .: (0.000128) test_compcheck: .: (0.000115) test_date: .: (0.000110) test_description: .: (0.000106) test_entry_id: .: (0.000302) test_gap_length_weight: .: (0.000113) test_gap_weight: .: (0.004407) test_heading: .: (0.000149) test_length: .: (0.000136) test_seq_type: .: (0.000112) test_symbol_comparison_table: .: (0.000115) test_validate_checksum: .: (0.000775) Bio::TestGFF: test_record_class: .: (0.000581) test_records: .: (0.000187) Bio::TestGFF2: test_const_version: .: (0.000376) test_gff_version: .: (0.000265) test_metadata: .: (0.000229) test_metadata_size: .: (0.000203) test_records_size: .: (0.004663) test_to_s: .: (0.000708) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000353) test_attributes_case2: .: (0.000238) test_attributes_incompatible_backslash_semicolon: .: (0.000279) Bio::TestGFF2MetaData: test_data: .: (0.000272) test_directive: .: (0.000171) test_parse: .: (0.000166) Bio::TestGFF2Record: test_attribute: .: (0.000571) test_attribute_nonexistent: .: (0.000286) test_attributes: .: (0.000309) test_attributes_to_hash: .: (0.005607) test_comment_only?: .: (0.000395) test_delete_attribute: .: (0.000351) test_delete_attribute_multiple: .: (0.000449) test_delete_attribute_multiple2: .: (0.000335) test_delete_attribute_multiple_nil: .: (0.000322) test_delete_attribute_nil: .: (0.000301) test_delete_attribute_nonexistent: .: (0.000307) test_delete_attributes: .: (0.000537) test_delete_attributes_multiple: .: (0.000308) test_delete_attributes_nonexistent: .: (0.000305) test_end: .: (0.000329) test_eqeq: .: (0.000600) test_eqeq_false: .: (0.000548) test_feature: .: (0.000281) test_frame: .: (0.000277) test_get_attribute: .: (0.000345) test_get_attribute_nonexistent: .: (0.000472) test_get_attributes: .: (0.000344) test_get_attributes_nonexistent: .: (0.000266) test_replace_attributes: .: (0.000304) test_replace_attributes_multiple_multiple_over: .: (0.000314) test_replace_attributes_multiple_multiple_same: .: (0.000306) test_replace_attributes_multiple_multiple_two: .: (0.000322) test_replace_attributes_multiple_single: .: (0.000292) test_replace_attributes_nonexistent: .: (0.000306) test_replace_attributes_nonexistent_multiple: .: (0.000294) test_replace_attributes_single_multiple: .: (0.000308) test_score: .: (0.000467) test_self_parse: .: (0.000629) test_seqname: .: (0.000307) test_set_attribute: .: (0.000296) test_set_attribute_multiple: .: (0.000447) test_set_attribute_nonexistent: .: (0.000312) test_sort_attributes_by_tag!: .: (0.000355) test_sort_attributes_by_tag_bang_test2: .: (0.000342) test_sort_attributes_by_tag_bang_with_block: .: (0.000341) test_source: .: (0.000273) test_start: .: (0.000272) test_strand: .: (0.000283) test_to_s: .: (0.000438) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000323) test_comment_eq: .: (0.000172) test_comment_only?: .: (0.000171) test_comment_only_false: .: (0.000160) test_to_s: .: (0.000184) test_to_s_not_empty: .: (0.000240) Bio::TestGFF3: test_const_version: .: (0.000720) test_gff_version: .: (0.000493) test_records: .: (0.000568) test_sequence_regions: .: (0.000458) test_sequences: .: (0.000511) test_to_s: .: (0.000786) Bio::TestGFF3MetaData: test_data: .: (0.000279) test_directive: .: (0.000148) test_parse: .: (0.000181) Bio::TestGFF3Record: test_attributes: .: (0.000434) test_end: .: (0.000265) test_feature: .: (0.000242) test_frame: .: (0.000241) test_id: .: (0.000243) test_score: .: (0.000247) test_seqname: .: (0.000244) test_source: .: (0.000267) test_start: .: (0.000240) test_strand: .: (0.000247) test_to_s: .: (0.000383) test_to_s_attr_order_changed: .: (0.000429) Bio::TestGFF3RecordEscape: test_escape: .: (0.000330) test_escape_attribute: .: (0.000206) test_escape_seqid: .: (0.000205) test_unescape: .: (0.000191) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000418) test_eqeq: .: (0.000253) test_new_from_sequences_na: .: (0.000266) test_new_from_sequences_na_aa: .: (0.000342) test_new_from_sequences_na_aa_boundary_gap: .: (0.000401) test_new_from_sequences_na_aa_example: .: (0.000356) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000305) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000303) test_process_sequences_na: .: (0.000267) test_process_sequences_na_aa: .: (0.000259) test_process_sequences_na_aa_reverse_frameshift: .: (0.000253) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000249) test_process_sequences_na_aa_tooshort: .: (0.000354) test_process_sequences_na_tooshort: .: (0.000326) test_to_s: .: (0.000267) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000366) test_attributes_one: .: (0.000202) test_attributes_with_escaping: .: (0.000222) test_id_multiple: .: (0.000327) test_id_multiple2: .: (0.000326) test_id_replace: .: (0.000230) test_id_set: .: (0.000345) test_initialize_9: .: (0.000167) test_phase: .: (0.000244) test_score: .: (0.000201) test_to_s_void: .: (0.000192) Bio::TestGFF3RecordTarget: test_end: .: (0.000287) test_parse: .: (0.000243) test_start: .: (0.000162) test_strand: .: (0.000157) test_target_id: .: (0.000157) test_to_s: .: (0.000329) Bio::TestGFF3SequenceRegion: test_end: .: (0.000317) test_parse: .: (0.000254) test_seqid: .: (0.000173) test_start: .: (0.000187) test_to_s: .: (0.000231) Bio::TestGFFRecord: test_attributes: .: (0.000350) test_comment: .: (0.000192) test_end: .: (0.000276) test_feature: .: (0.000196) test_frame: .: (0.000184) test_score: .: (0.000217) test_seqname: .: (0.000190) test_source: .: (0.000177) test_start: .: (0.000209) test_strand: .: (0.000180) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000287) Bio::TestGeneAssociation: test_aspect: .: (0.000407) test_assigned_by: .: (0.000168) test_date: .: (0.000169) test_db: .: (0.000169) test_db_object_id: .: (0.000174) test_db_object_name: .: (0.000170) test_db_object_symbol: .: (0.000178) test_db_object_synonym: .: (0.000181) test_db_object_type: .: (0.000164) test_db_reference: .: (0.000172) test_evidence: .: (0.000175) test_goid: .: (0.005862) test_parser: .: (0.000738) test_qualifier: .: (0.000202) test_taxon: .: (0.000184) test_to_str: .: (0.000200) test_with: .: (0.000194) Bio::TestGenscanReport: test_date_run: .: (0.000985) test_gccontent: .: (0.001637) test_genscan_version: .: (0.000724) test_isochore: .: (0.000649) test_length: .: (0.000671) test_matrix: .: (0.000954) test_predictions_size: .: (0.000636) test_query_name: .: (0.000647) test_time: .: (0.000633) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000957) test_donor_score: .: (0.000622) test_exon_type: .: (0.000657) test_exon_type_long: .: (0.000649) test_first: .: (0.000837) test_initiation_score: .: (0.000650) test_last: .: (0.000622) test_number: .: (0.002144) test_p_value: .: (0.000961) test_phase: .: (0.000653) test_range: .: (0.000632) test_score: .: (0.000624) test_strand: .: (0.000627) test_t_score: .: (0.000647) test_termination_score: .: (0.000619) Bio::TestGenscanReportGene: test_aaseq: .: (0.000815) test_naseq: .: (0.000702) test_number: .: (0.000686) test_polyA: .: (0.000664) test_promoter: .: (0.006991) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000967) test_reports_ary_contents: .: (0.000727) Bio::TestHMMERReportConstants: test_rs: .: (0.000316) Bio::TestHMMERReportHit: test_accession: .: (0.000863) test_append_hsp: .: (0.000698) test_bit_score: .: (0.001646) test_definition: .: (0.000694) test_description: .: (0.000659) test_each: .: (0.000690) test_each_hsp: .: (0.000679) test_entry_id: .: (0.001011) test_evalue: .: (0.000750) test_hit: .: (0.000670) test_hit_id: .: (0.000663) test_hsps: .: (0.000701) test_num: .: (0.000651) test_score: .: (0.000660) test_target_def: .: (0.000663) test_target_id: .: (0.000655) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000988) test_each: .: (0.000701) test_each_hit: .: (0.000652) test_histogram: .: (0.000638) test_hits: .: (0.000677) test_hsps: .: (0.000653) test_parameter: .: (0.000848) test_program: .: (0.000664) test_query_info: .: (0.000667) test_statistical_detail: .: (0.000651) test_total_seq_searched: .: (0.000691) test_whole_seq_top_hits: .: (0.000622) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000913) test_histogram: .: (0.000797) test_statistical_detail: .: (0.001290) test_total_seq_searched: .: (0.000733) test_whole_seq_top_hit: .: (0.000746) Bio::TestHMMERReportHsp: test_accession: .: (0.000816) test_bit_score: .: (0.000655) test_csline: .: (0.000621) test_domain: .: (0.000615) test_evalue: .: (0.000602) test_flatseq: .: (0.000633) test_hmm_f: .: (0.000641) test_hmm_t: .: (0.000610) test_hmmseq: .: (0.000631) test_hsp: .: (0.000641) test_midline: .: (0.000665) test_query_frame: .: (0.000648) test_query_from: .: (0.000612) test_query_seq: .: (0.000608) test_query_to: .: (0.000611) test_rfline: .: (0.000638) test_score: .: (0.000620) test_seq_f: .: (0.000617) test_seq_ft: .: (0.000614) test_seq_t: .: (0.007224) test_set_alignment: .: (0.000678) test_targat_to: .: (0.000685) test_target_frame: .: (0.000676) test_target_from: .: (0.000684) test_target_seq: .: (0.000660) Bio::TestHetatmFinder: test_each_hetatm: .: (0.001369) test_find_hetatm: .: (0.000284) test_hetatms: .: (0.000397) Bio::TestHeterogen: test_addAtom: .: (0.000404) test_each: .: (0.000263) test_each_hetatm: .: (0.000245) test_get_residue_id_from_atom: .: (0.000231) test_het_atom: .: (0.000508) test_iCode: .: (0.000212) test_inspect: .: (0.000284) test_resSeq: .: (0.000207) test_sort: .: (0.000255) test_square_bracket: .: (0.000240) test_to_s: .: (0.000303) test_update_resudue_id: .: (0.000207) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000349) test_find_heterogen: .: (0.000216) test_heterogens: .: (0.000220) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000362) test_match_description: .: (0.000212) test_match_evalue: .: (0.000202) test_match_ipr_description: .: (0.000203) test_match_ipr_id: .: (0.000206) test_match_match_end: .: (0.000200) test_match_match_start: .: (0.000201) test_match_method: .: (0.000203) test_matches_size: .: (0.000206) test_query_id: .: (0.000200) test_query_length: .: (0.000206) Bio::TestIprscanRawReport: test_entry_id: .: (0.001885) test_match_accession: .: (0.001408) test_match_crc64: .: (0.001379) test_match_date: .: (0.001867) test_match_description: .: (0.001303) test_match_evalue: .: (0.001305) test_match_go_terms: .: (0.007355) test_match_ipr_description: .: (0.002344) test_match_ipr_id: .: (0.001618) test_match_match_end: .: (0.001664) test_match_match_start: .: (0.001569) test_match_method: .: (0.001844) test_match_query_id: .: (0.001331) test_match_query_length: .: (0.005812) test_match_status: .: (0.002265) test_obj: .: (0.001614) test_query_id: .: (0.001672) test_query_length: .: (0.002014) test_self_reports_in_raw: .: (0.002640) Bio::TestIprscanReport: test_output_raw: .: (0.005047) test_to_raw: .: (0.000557) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000651) test_match_accession: .: (0.000516) test_match_date: .: (0.000489) test_match_description: .: (0.000463) test_match_evalue: .: (0.000491) test_match_go_terms: .: (0.000951) test_match_ipr_description: .: (0.000565) test_match_ipr_id: .: (0.000478) test_match_match_end: .: (0.000483) test_match_match_start: .: (0.000457) test_match_method: .: (0.000443) test_match_status: .: (0.000429) test_matches_size: .: (0.000434) test_query_id: .: (0.001500) test_query_length: .: (0.000488) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000648) test_to_hash_match?: .: (0.000544) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.001054) Bio::TestKeggCompound: test_comment: .: (0.000529) test_dblinks_as_hash: .: (0.000395) test_dblinks_as_strings: .: (0.000328) test_entry_id: .: (0.000340) test_enzymes: .: (0.000576) test_formula: .: (0.000340) test_kcf: .: (0.000309) test_mass: .: (0.000326) test_name: .: (0.000376) test_names: .: (0.000346) test_pathways_as_hash: .: (0.004874) test_pathways_as_strings: .: (0.000586) test_reactions: .: (0.000635) test_remark: .: (0.000361) test_rpairs: .: (0.000358) Bio::TestKeggEnzyme: test_all_reac: .: (0.000713) test_classes: .: (0.000511) test_cofactors: .: (0.001148) test_comment: .: (0.000574) test_dblinks_as_hash: .: (0.000561) test_dblinks_as_strings: .: (0.000510) test_diseases: .: (0.000506) test_entry: .: (0.000556) test_entry_id: .: (0.000569) test_genes: .: (0.052151) test_genes_as_hash: .: (0.011985) test_genes_as_strings: .: (0.005433) test_inhibitors: .: (0.000585) test_iubmb_reactions: .: (0.000580) test_kegg_reactions: .: (0.000558) test_motifs: .: (0.000466) test_name: .: (0.000545) test_names: .: (0.000543) test_obsolete?: .: (0.001515) test_orthologs_as_hash: .: (0.000548) test_orthologs_as_strings: .: (0.000459) test_pathways_as_hash: .: (0.000613) test_pathways_as_strings: .: (0.000581) test_products: .: (0.000615) test_reaction: .: (0.000596) test_structures: .: (0.000784) test_substrates: .: (0.000580) test_sysname: .: (0.000548) Bio::TestKeggGenesDblinks: test_data: .: (0.000388) test_dblinks_0: .: (0.000216) test_dblinks_1: .: (0.000204) test_dblinks_2: .: (0.000182) Bio::TestKeggGenesStructure: test_data: .: (0.000342) test_ids: .: (0.000241) test_ids_in_array: .: (0.000219) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004645) test_graphics__size: .: (0.004178) test_id: .: (0.004068) test_link: .: (0.004138) test_name: .: (0.004175) test_reaction: .: (0.004111) test_type: .: (0.004102) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.008183) test_graphics__size: .: (0.006483) test_id: .: (0.004489) test_link: .: (0.004380) test_name: .: (0.004519) test_reaction: .: (0.004381) test_type: .: (0.004407) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.004218) test_category: .: (0.004039) test_entry_id: .: (0.007422) test_fgcolor=: .: (0.005991) test_height=: .: (0.004516) test_label=: .: (0.004405) test_shape=: .: (0.004460) test_width=: .: (0.004567) test_x=: .: (0.004142) test_y=: .: (0.004112) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.004209) test_graphics__size: .: (0.007239) test_id: .: (0.005568) test_link: .: (0.004917) test_name: .: (0.004457) test_reaction: .: (0.004364) test_type: .: (0.004649) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000343) test_graphics=: .: (0.000178) test_id=: .: (0.000180) test_link=: .: (0.000177) test_name=: .: (0.000176) test_reaction=: .: (0.000166) test_type=: .: (0.000169) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000327) test_category=: .: (0.000204) test_entry_id=: .: (0.000187) test_fgcolor=: .: (0.000201) test_height=: .: (0.000201) test_label=: .: (0.000195) test_pathway=: .: (0.000170) test_shape=: .: (0.000216) test_width=: .: (0.000180) test_x=: .: (0.000175) test_y=: .: (0.000176) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.004230) test_coords: .: (0.004059) test_fgcolor: .: (0.006596) test_height: .: (0.005535) test_name: .: (0.004950) test_type: .: (0.004460) test_width: .: (0.004309) test_x: .: (0.004419) test_y: .: (0.004417) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.004195) test_coords: .: (0.004091) test_fgcolor: .: (0.006624) test_height: .: (0.005558) test_name: .: (0.004594) test_type: .: (0.004278) test_width: .: (0.004398) test_x: .: (0.004478) test_y: .: (0.004085) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000322) test_coords=: .: (0.000195) test_fgcolor=: .: (0.000174) test_height=: .: (0.000158) test_name=: .: (0.000175) test_type=: .: (0.000159) test_width=: .: (0.000150) test_x=: .: (0.000152) test_y=: .: (0.000158) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.004208) test_entries__size: .: (0.004082) test_image: .: (0.007268) test_link: .: (0.004904) test_name: .: (0.004310) test_number: .: (0.004460) test_org: .: (0.004211) test_reactions=: .: (0.004592) test_reactions__size: .: (0.004075) test_relations=: .: (0.003966) test_relations__size: .: (0.006266) test_title: .: (0.005526) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.008494) test_name: .: (0.008407) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000200) test_initialize_0: .: (0.000040) test_initialize_1: .: (0.000046) test_initialize_2: .: (0.000046) test_name=: .: (0.000301) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.004298) test_name: .: (0.004278) test_products: .: (0.004136) test_substrates: .: (0.007421) test_type: .: (0.004956) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000462) test_name=: .: (0.000186) test_products=: .: (0.000173) test_substraces=: .: (0.000173) test_type=: .: (0.000178) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000342) test_entry_id=: .: (0.000189) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.004602) test_entry2: .: (0.004367) test_name: .: (0.004937) test_type: .: (0.004129) test_value: .: (0.004206) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000330) test_node1=: .: (0.000186) test_node2=: .: (0.000177) test_rel=: .: (0.000183) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000294) test_entry2=: .: (0.000163) test_name=: .: (0.000161) test_type=: .: (0.000185) test_value=: .: (0.000166) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.011880) test_name: .: (0.008424) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000194) test_initialize_0: .: (0.000039) test_initialize_1: .: (0.000039) test_initialize_2: .: (0.000040) test_name=: .: (0.000056) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000229) test_initialize_0: .: (0.000038) test_initialize_1: .: (0.000039) test_initialize_2: .: (0.000042) test_name=: .: (0.000058) Bio::TestKeggModule: test_compounds: .: (0.000344) test_compounds_as_hash: .: (0.000158) test_compounds_as_strings: .: (0.000132) test_definition: .: (0.000135) test_entry_id: .: (0.000114) test_keggclass: .: (0.000106) test_name: .: (0.000107) test_new: .: (0.000110) test_orthologs: .: (0.000386) test_orthologs_as_array: .: (0.000257) test_orthologs_as_hash: .: (0.000176) test_orthologs_as_strings: .: (0.000134) test_pathways: .: (0.000272) test_pathways_as_hash: .: (0.000118) test_pathways_as_strings: .: (0.000093) test_reactions: .: (0.000160) test_reactions_as_hash: .: (0.000152) test_reactions_as_strings: .: (0.000123) Bio::TestKeggOrthology: test_dblinks: .: (0.000452) test_dblinks_as_hash: .: (0.000274) test_dblinks_as_strings: .: (0.000244) test_definition: .: (0.000265) test_entry_id: .: (0.000249) test_genes_as_hash: .: (0.038458) test_genes_as_strings: .: (0.020143) test_keggclass: .: (0.000633) test_keggclasses: .: (0.000584) test_modules: .: (0.000504) test_modules_as_hash: .: (0.000485) test_modules_as_strings: .: (0.000430) test_name: .: (0.000452) test_names: .: (0.000453) test_pathways_as_strings: .: (0.000445) test_pathways_in_keggclass: .: (0.000559) test_references: .: (0.001704) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000513) test_compounds_as_strings: .: (0.000300) test_dblinks_as_hash: .: (0.000312) test_dblinks_as_strings: .: (0.000281) test_description: .: (0.000337) test_diseases_as_hash: .: (0.000303) test_diseases_as_strings: .: (0.000292) test_entry_id: .: (0.000318) test_enzymes_as_strings: .: (0.000285) test_genes_as_hash: .: (0.000277) test_genes_as_strings: .: (0.000270) test_keggclass: .: (0.000330) test_ko_pathway: .: (0.000298) test_modules_as_hash: .: (0.000362) test_modules_as_strings: .: (0.000298) test_name: .: (0.000305) test_organism: .: (0.000310) test_orthologs_as_hash: .: (0.000288) test_orthologs_as_strings: .: (0.000273) test_pathways_as_hash: .: (0.000297) test_pathways_as_strings: .: (0.000290) test_reactions_as_hash: .: (0.000273) test_reactions_as_strings: .: (0.000309) test_references: .: (0.000277) test_rel_pathways_as_hash: .: (0.000319) test_rel_pathways_as_strings: .: (0.000289) Bio::TestKeggReaction: test_definition: .: (0.000489) test_entry_id: .: (0.000335) test_enzymes: .: (0.000334) test_equation: .: (0.000320) test_name: .: (0.000329) test_orthologs_as_hash: .: (0.000341) test_orthologs_as_strings: .: (0.000311) test_pathways_as_hash: .: (0.000333) test_pathways_as_strings: .: (0.000302) test_rpairs_as_hash: .: (0.000336) test_rpairs_as_strings: .: (0.000318) test_rpairs_as_tokens: .: (0.000332) Bio::TestLasergene: test_methods: .: (0.007159) Bio::TestLocations: test_complement: .: (0.000721) test_hat: .: (0.000251) test_normal: .: (0.000219) test_replace_single_base: .: (0.000208) test_should_not_modify_argument: .: (0.000191) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002394) test_locations_to_s: .: (0.001035) Bio::TestMEDLINE: test_authors: .: (0.000727) test_authors_with_last_name_all_caps: .: (0.000197) test_authors_with_suffix: .: (0.000188) Bio::TestMEDLINE_20146148: test_ab: .: (0.000545) test_ad: .: (0.000381) test_au: .: (0.000365) test_authors: .: (0.000413) test_doi: .: (0.001206) test_dp: .: (0.000452) test_ip: .: (0.000358) test_mh: .: (0.000386) test_pages: .: (0.000367) test_pg: .: (0.000361) test_pii: .: (0.000359) test_pmid: .: (0.000361) test_pt: .: (0.000371) test_reference: .: (0.000565) test_self_new: .: (0.000382) test_so: .: (0.000369) test_ta: .: (0.000409) test_ti: .: (0.000386) test_ui: .: (0.003781) test_vi: .: (0.000885) test_year: .: (0.000402) Bio::TestMapSimple: test_attributes: .: (0.000394) Bio::TestMapping: test_add_mapping_as_map: .: (0.000459) test_add_mapping_as_marker: .: (0.000269) test_contains_marker?: .: (0.000231) test_mapped_to?: .: (0.000214) test_mapping_location_comparison: .: (0.001145) test_mappings_as_map_each: .: (0.000218) test_mappings_as_marker_each: .: (0.000263) test_mappings_on: .: (0.000268) test_multiple_mappings_between_same_marker_and_map: .: (0.000405) test_positions_on: .: (0.000277) test_raise_error_kind_of: .: (0.000430) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000641) test_check_options_with_invalid_opts: .: (0.000312) test_check_options_with_valid_opts: .: (0.000245) test_command_to_be_run: .: (0.000255) test_config_defaults: .: (0.000249) test_minimal_config: .: (0.000239) test_more_config: .: (0.000224) test_run: .: (0.000189) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000565) test_report_has_motifs: .: (0.000338) Bio::TestModel: test_addChain: .: (0.000478) test_comp: .: (0.000238) test_each: .: (0.000206) test_each_chain: .: (0.000184) test_inspect: .: (0.000183) test_rehash: .: (0.000159) test_square_brace: .: (0.000180) test_to_s: .: (0.000183) Bio::TestModelFinder: test_find_model: .: (0.000331) Bio::TestMotif: test_creation_and_attributes: .: (0.000316) test_length: .: (0.000163) Bio::TestMyGraph: test_cliquishness: .: (0.000464) Bio::TestNA: test_accessor: .: (0.000276) test_na: .: (0.000166) test_name: .: (0.000165) test_names: .: (0.000156) test_to_re: .: (0.000297) test_weight: .: (0.000184) test_weight_rna: .: (0.000311) Bio::TestNAConstants: test_NAMES: .: (0.000276) test_NAMES_1_to_name: .: (0.000154) test_WEIGHT: .: (0.000165) Bio::TestNATranslate: test_translate: .: (0.000439) test_translate_1: .: (0.000269) test_translate_2: .: (0.000196) test_translate_3: .: (0.000179) test_translate_4: .: (0.000274) test_translate_5: .: (0.000186) test_translate_6: .: (0.000162) Bio::TestNCBIDB: test_fetch: .: (0.000348) test_p_entry2hash: .: (0.000173) test_p_subtag2array: .: (0.000142) test_p_toptag2array: .: (0.000135) Bio::TestNewick: test_reparse: .: (0.001196) test_reparse_before_lazy_parsing: .: (0.000451) test_string_tree: .: (0.000738) Bio::TestNewick2: test_string_tree: .: (0.000694) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000288) test_parse_newick_leaf: .: (0.000262) test_parse_newick_tokenize: .: (0.000363) Bio::TestNexus: test_nexus: .: (0.006399) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000391) test_uncapitalized_letter_Q32725_9POAL: .: (0.000225) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000326) test_load_parameters: .: (0.000200) test_parameters: .: (0.000167) test_set_default_parameters: .: (0.000188) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000650) test_expected_parameters_set_in_control_file: .: (0.000547) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000296) test_new_with_parameters: .: (0.000198) test_new_with_two_argument: .: (0.000182) test_new_without_argument: .: (0.000172) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001037) test_rates_hundred_and_fiftieth_position: .: (0.005864) test_rates_last_position: .: (0.001011) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.000771) test_tree: .: (0.000590) test_tree_length: .: (0.000599) test_tree_log_likelihood: .: (0.000562) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000718) test_parameters_should_be_loaded_from_control: .: (0.000353) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001218) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000415) test_dN_dS: .: (0.000293) test_kappa: .: (0.000250) test_lnL: .: (0.000239) test_m3_classes: .: (0.000332) test_m3_lnL: .: (0.000265) test_m3_to_s: .: (0.000247) test_m3_tree: .: (0.000296) test_omega: .: (0.000243) test_to_s: .: (0.000231) test_tree: .: (0.000289) test_tree_length: .: (0.000233) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000566) test_p: .: (0.000618) test_position: .: (0.000409) test_probability: .: (0.000420) test_w: .: (0.000414) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000563) test_graph_omega: .: (0.000624) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000389) test_footer: .: (0.000227) test_header: .: (0.000230) test_initialize: .: (0.000261) test_models: .: (0.000256) test_nb_sites: .: (0.000557) test_num_codons: .: (0.000257) test_num_sequences: .: (0.000244) test_significant: .: (0.000286) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000398) test_nb_sites: .: (0.000358) test_significant: .: (0.000281) test_sites: .: (0.001537) Bio::TestPDB: test_accession: .: (0.001060) test_addModel: .: (0.000707) test_authors: .: (0.000654) test_bracket: .: (0.000652) test_classification: .: (0.000711) test_dbref: .: (0.000766) test_definition: .: (0.000652) test_each: .: (0.000678) test_each_model: .: (0.000648) test_entry_id: .: (0.000642) test_helix: .: (0.000736) test_inspect: .: (0.000673) test_jrnl: .: (0.000652) test_keywords: .: (0.000648) test_record: .: (0.000627) test_remark: .: (0.000824) test_seqres: .: (0.000840) test_sheet: .: (0.000819) test_ssbond: .: (0.000653) test_to_s: .: (0.000825) test_turn: .: (0.000626) test_version: .: (0.000648) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000389) test_U12: .: (0.000203) test_U13: .: (0.000193) test_U22: .: (0.000210) test_U23: .: (0.000203) test_U33: .: (0.000197) test_altLoc: .: (0.000198) test_chainID: .: (0.000190) test_charge: .: (0.000188) test_element: .: (0.000185) test_iCode: .: (0.000191) test_name: .: (0.000188) test_resName: .: (0.000219) test_resSeq: .: (0.000212) test_segID: .: (0.000194) test_serial: .: (0.000207) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000310) test_anisou: .: (0.000177) test_chainID: .: (0.000168) test_charge: .: (0.000167) test_comparable: .: (0.000201) test_do_parse: .: (0.000167) test_element: .: (0.000169) test_iCode: .: (0.000178) test_name: .: (0.000171) test_occupancy: .: (0.000203) test_original_data: .: (0.000174) test_record_name: .: (0.000165) test_resName: .: (0.000167) test_resSeq: .: (0.000166) test_residue: .: (0.000166) test_segID: .: (0.000169) test_serial: .: (0.000156) test_sigatm: .: (0.000174) test_tempFactor: .: (0.000194) test_ter: .: (0.000200) test_to_a: .: (0.000178) test_to_s: .: (0.000213) test_x: .: (0.000197) test_xyz: .: (0.000221) test_y: .: (0.000189) test_z: .: (0.000179) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000615) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000344) test_idcode: .: (0.000196) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000381) test_chainID2: .: (0.000224) test_icode1: .: (0.000220) test_icode2: .: (0.000223) test_measure: .: (0.000212) test_modNum: .: (0.000206) test_pep1: .: (0.000202) test_pep2: .: (0.000210) test_seqNum1: .: (0.000201) test_seqNum2: .: (0.000202) test_serNum: .: (0.000206) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000343) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000843) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000332) test_alpha: .: (0.000197) test_b: .: (0.000186) test_beta: .: (0.000194) test_c: .: (0.000183) test_gamma: .: (0.000193) test_sGroup: .: (0.000194) test_z: .: (0.000188) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000401) test_database: .: (0.000228) test_dbAccession: .: (0.000248) test_dbIdCode: .: (0.000221) test_dbseqBegin: .: (0.000213) test_dbseqEnd: .: (0.000454) test_idCode: .: (0.000244) test_idbnsBeg: .: (0.000205) test_insertBegin: .: (0.000231) test_insertEnd: .: (0.000216) test_seqBegin: .: (0.000198) test_seqEnd: .: (0.000213) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000327) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000287) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000298) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000288) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000297) test_depDate: .: (0.000242) test_idCode: .: (0.000195) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000311) test_hetID: .: (0.000199) test_iCode: .: (0.000226) test_numHetAtoms: .: (0.000189) test_seqNum: .: (0.000194) test_text: .: (0.000201) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000307) test_anisou: .: (0.000180) test_chainID: .: (0.000173) test_charge: .: (0.000169) test_comparable: .: (0.000206) test_do_parse: .: (0.000181) test_element: .: (0.000168) test_iCode: .: (0.000168) test_name: .: (0.000154) test_occupancy: .: (0.000201) test_original_data: .: (0.000182) test_record_name: .: (0.000165) test_resName: .: (0.000377) test_resSeq: .: (0.000189) test_residue: .: (0.000169) test_segID: .: (0.000163) test_serial: .: (0.000169) test_sigatm: .: (0.000158) test_tempFactor: .: (0.000183) test_ter: .: (0.000171) test_to_a: .: (0.002101) test_to_s: .: (0.000770) test_x: .: (0.001305) test_xyz: .: (0.001318) test_y: .: (0.001335) test_z: .: (0.000205) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.002385) test_ChainH: .: (0.000258) test_ICode1: .: (0.000250) test_altLoc1: .: (0.001315) test_altLoc2: .: (0.000255) test_altLocH: .: (0.001271) test_chainID2: .: (0.002466) test_iCode2: .: (0.001545) test_iCodeH: .: (0.001434) test_name1: .: (0.002348) test_name2: .: (0.000288) test_nameH: .: (0.001210) test_resName1: .: (0.000318) test_resName2: .: (0.000239) test_resSeq1: .: (0.001301) test_resSeq2: .: (0.000230) test_resSeqH: .: (0.001387) test_sym1: .: (0.000250) test_sym2: .: (0.000215) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.001406) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000391) test_altLoc2: .: (0.001364) test_chainID1: .: (0.000252) test_chainID2: .: (0.002426) test_iCode1: .: (0.001346) test_iCode2: .: (0.000235) test_name1: .: (0.000221) test_name2: .: (0.001269) test_resName1: .: (0.001227) test_resName2: .: (0.000265) test_resSeq1: .: (0.001351) test_resSeq2: .: (0.000217) test_sym1: .: (0.001307) test_sym2: .: (0.000260) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.001430) test_numCoord: .: (0.000174) test_numHelix: .: (0.001714) test_numHet: .: (0.002113) test_numRemark: .: (0.000204) test_numSeq: .: (0.000169) test_numSheet: .: (0.000175) test_numSite: .: (0.000860) test_numTer: .: (0.000183) test_numTurn: .: (0.001045) test_numXform: .: (0.000178) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.003990) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.001356) test_comment: .: (0.001353) test_iCode: .: (0.002031) test_idCode: .: (0.000210) test_resName: .: (0.000199) test_seqNum: .: (0.000193) test_stdRes: .: (0.000191) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000353) test_Mn2: .: (0.000191) test_Mn3: .: (0.000183) test_Vn: .: (0.000200) test_iGiven: .: (0.000183) test_serial: .: (0.000176) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000332) test_Mn2: .: (0.000183) test_Mn3: .: (0.000187) test_Vn: .: (0.000175) test_iGiven: .: (0.000180) test_serial: .: (0.000201) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000501) test_Mn2: .: (0.000189) test_Mn3: .: (0.000179) test_Vn: .: (0.000174) test_iGiven: .: (0.000175) test_serial: .: (0.000174) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000363) test_rIdCode: .: (0.000200) test_repDate: .: (0.000203) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000318) test_On2: .: (0.000184) test_On3: .: (0.000177) test_Tn: .: (0.000179) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000329) test_modId: .: (0.000677) test_modNum: .: (0.000200) test_modType: .: (0.000206) test_record: .: (0.000193) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000324) test_text: .: (0.000169) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000309) test_Sn2: .: (0.000187) test_Sn3: .: (0.000176) test_Un: .: (0.000186) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000324) test_Sn2: .: (0.000188) test_Sn3: .: (0.000169) test_Un: .: (0.000166) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000310) test_Sn2: .: (0.000184) test_Sn3: .: (0.000179) test_Un: .: (0.000167) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000361) test_conflict: .: (0.000225) test_database: .: (0.000192) test_dbIdCode: .: (0.000194) test_dbRes: .: (0.000200) test_dbSeq: .: (0.000197) test_iCode: .: (0.000210) test_idCode: .: (0.000212) test_resName: .: (0.000208) test_seqNum: .: (0.000228) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000343) test_numRes: .: (0.000205) test_resName: .: (0.000206) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000360) test_curChainId: .: (0.000228) test_curICode: .: (0.000218) test_curResName: .: (0.000220) test_curResSeq: .: (0.000225) test_endChainID: .: (0.000448) test_endICode: .: (0.000220) test_endResName: .: (0.000233) test_endSeqNum: .: (0.000205) test_initChainID: .: (0.000223) test_initICode: .: (0.000229) test_initResName: .: (0.000229) test_initSeqNum: .: (0.000224) test_numStrands: .: (0.000219) test_prevAtom: .: (0.000229) test_prevChainId: .: (0.000237) test_prevICode: .: (0.000247) test_prevResName: .: (0.000244) test_prevResSeq: .: (0.000236) test_sense: .: (0.000354) test_sheetID: .: (0.000228) test_strand: .: (0.000212) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000384) test_chainID: .: (0.000249) test_charge: .: (0.000235) test_element: .: (0.000223) test_iCode: .: (0.000249) test_name: .: (0.000207) test_resName: .: (0.000216) test_resSeq: .: (0.000206) test_segID: .: (0.000202) test_serial: .: (0.000201) test_sigOcc: .: (0.000207) test_sigTemp: .: (0.000264) test_sigX: .: (0.000229) test_sigY: .: (0.000212) test_sigZ: .: (0.000214) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000354) test_SigmaU12: .: (0.000213) test_SigmaU13: .: (0.000200) test_SigmaU22: .: (0.000194) test_SigmaU23: .: (0.000208) test_SigmaU33: .: (0.000197) test_altLoc: .: (0.000210) test_chainID: .: (0.000238) test_charge: .: (0.000208) test_element: .: (0.000217) test_iCode: .: (0.000209) test_name: .: (0.000198) test_resName: .: (0.000190) test_resSeq: .: (0.000208) test_segID: .: (0.000266) test_serial: .: (0.000202) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000359) test_chainID2: .: (0.000216) test_chainID3: .: (0.000207) test_chainID4: .: (0.000201) test_iCode1: .: (0.000202) test_iCode2: .: (0.000213) test_iCode3: .: (0.000206) test_iCode4: .: (0.000198) test_numRes: .: (0.000201) test_resName1: .: (0.000207) test_resName2: .: (0.000200) test_resName3: .: (0.000206) test_resName4: .: (0.000235) test_seq1: .: (0.000260) test_seq2: .: (0.000215) test_seq3: .: (0.000200) test_seq4: .: (0.000200) test_seqNum: .: (0.000200) test_siteID: .: (0.000204) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000341) test_altLoc2: .: (0.000196) test_atom1: .: (0.000185) test_atom2: .: (0.000214) test_chainID1: .: (0.000202) test_chainID2: .: (0.000194) test_iCode1: .: (0.000205) test_iCode2: .: (0.000186) test_resName1: .: (0.000187) test_resName2: .: (0.000187) test_resSeq1: .: (0.000273) test_resSeq2: .: (0.000200) test_sym1: .: (0.000195) test_sym2: .: (0.000188) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000356) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000337) test_sIdCode: .: (0.000187) test_sprsdeDate: .: (0.000189) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000318) test_iCode: .: (0.000199) test_resName: .: (0.000181) test_resSeq: .: (0.000197) test_serial: .: (0.000253) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000284) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000246) test_t1: .: (0.000117) test_t2: .: (0.000115) test_t3: .: (0.000113) test_text: .: (0.000125) Bio::TestPROSITE: test_ac: .: (0.001060) test_cc: .: (0.008709) test_de: .: (0.000920) test_division: .: (0.000789) test_dr: .: (0.033195) test_dt: .: (0.012822) test_false_neg: .: (0.007782) test_false_pos: .: (0.001022) test_false_positive_sequences: .: (0.000869) test_list_falsenegative: .: (0.047957) test_list_falsepositive: .: (0.039046) test_list_potentialhit: .: (0.038586) test_list_truepositive: .: (0.035954) test_list_unknown: .: (0.033046) test_list_xref: .: (0.034566) test_ma: .: (0.007802) test_max_repeat: .: (0.000958) test_name: .: (0.000850) test_nr: .: (0.000811) test_pa: .: (0.000789) test_pa2re: .: (0.000863) test_partial: .: (0.000800) test_pdb_xref: .: (0.006256) test_pdoc_xref: .: (0.001110) test_positive: .: (0.006603) test_positive_hits: .: (0.003419) test_positive_sequences: .: (0.008321) test_release: .: (0.007736) test_ru: .: (0.001476) test_self_pa2re: .: (0.001188) test_site: .: (0.001066) test_skip_flag: .: (0.001492) test_swissprot_release_number: .: (0.000873) test_swissprot_release_sequences: .: (0.007813) test_taxon_range: .: (0.001003) test_total: .: (0.001027) test_total_hits: .: (0.003099) test_total_sequences: .: (0.006413) test_unknown: .: (0.001135) test_unknown_hits: .: (0.006565) test_unknown_sequences: .: (0.001190) Bio::TestPROSITEConst: test_delimiter: .: (0.000246) test_tagsize: .: (0.000092) Bio::TestPTS1: test_function_set: .: (0.000210) test_function_set_number_1: .: (0.000119) test_function_set_number_2: .: (0.000096) test_function_set_number_3: .: (0.000101) test_function_show: .: (0.000090) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000182) Bio::TestPTS1New: test_fungi: .: (0.000299) test_general: .: (0.000102) test_metazoa: .: (0.000119) Bio::TestQualifier: test_qualifier: .: (0.000184) test_value: .: (0.000087) Bio::TestREBASE: test_methods: .: (0.000671) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000841) test_bit_score: .: (0.004473) test_evalue: .: (0.000744) test_gaps: .: (0.000575) test_hit_from: .: (0.006320) test_hit_to: .: (0.000777) test_hseq: .: (0.000566) test_identity: .: (0.006290) test_midline: .: (0.000792) test_percent_identity: .: (0.000570) test_positive: .: (0.000517) test_qseq: .: (0.000534) test_query_from: .: (0.000515) test_query_to: .: (0.000530) test_score: .: (0.000526) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000643) test_hits_size: .: (0.002551) test_iterations_size: .: (0.011711) test_program: .: (0.000679) test_query_def: .: (0.000976) test_query_len: .: (0.000977) test_version: .: (0.000482) test_version_date: .: (0.000461) test_version_number: .: (0.000438) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000709) test_definition: .: (0.000746) test_evalue: .: (0.011143) test_hsps_size: .: (0.000902) test_identity: .: (0.000602) test_lap_at: .: (0.000606) test_len: .: (0.000555) test_midline: .: (0.004856) test_overlap: .: (0.007735) test_query_end: .: (0.001456) test_query_seq: .: (0.000818) test_query_start: .: (0.000564) test_target_def: .: (0.000521) test_target_end: .: (0.000575) test_target_len: .: (0.007485) test_target_seq: .: (0.000747) test_target_start: .: (0.000645) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000392) test_get_entry: .: (0.000289) test_rewind: .: (0.000073) test_skip_leader: .: (0.000108) Bio::TestReference: test_abstract: .: (0.000135) test_affiliations: .: (0.000047) test_authors: .: (0.000043) test_format_bibitem: .: (0.000087) test_format_bibtex: .: (0.000135) test_format_bibtex_with_arguments: .: (0.000102) test_format_cell: .: (0.000181) test_format_current: .: (0.000067) test_format_endnote: .: (0.000073) test_format_general: .: (0.000061) test_format_genome_biol: .: (0.000053) test_format_genome_res: .: (0.000055) test_format_nar: .: (0.004279) test_format_nature: .: (0.000143) test_format_rd: .: (0.000073) test_format_science: .: (0.000097) test_format_trends: .: (0.000051) test_issue: .: (0.000041) test_journal: .: (0.000043) test_mesh: .: (0.000046) test_pages: .: (0.000040) test_pubmed: .: (0.000059) test_pubmed_url: .: (0.000046) test_url: .: (0.000037) test_volume: .: (0.000034) test_year: .: (0.000037) Bio::TestReference_noURL: test_format_endnote: .: (0.000192) test_url: .: (0.000041) Bio::TestReferences: test_append: .: (0.000162) test_each: .: (0.000057) Bio::TestRelation: test_comparison_operator: .: (0.000142) test_uniq: .: (0.000072) Bio::TestResidue: test_addAtom: .: (0.000238) test_each: .: (0.000150) test_each_atom: .: (0.000100) test_get_residue_id_from_atom: .: (0.000086) test_het_atom: .: (0.000068) test_iCode: .: (0.000528) test_inspect: .: (0.000136) test_resSeq: .: (0.000077) test_sort: .: (0.000360) test_square_bracket: .: (0.000143) test_to_s: .: (0.000140) test_update_resudue_id: .: (0.000086) Bio::TestResidueFinder: test_each_residue: .: (0.000199) test_find_residue: .: (0.000106) test_residues: .: (0.000090) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.329611) test_cut_from_bio_sequence_na: .: (0.044995) test_cut_without_permutations: .: (0.026812) test_view_ranges: .: (0.036738) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001228) test_cuts_after_remove_incomplete_cuts: .: (0.005947) test_strands_for_display: .: (0.001775) test_strands_for_display_current: .: (0.000555) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000626) test_fragments_for_display_1: .: (0.000670) test_fragments_for_display_10: .: (0.000704) test_fragments_for_display_2: .: (0.000608) test_fragments_for_display_3: .: (0.000779) test_fragments_for_display_4: .: (0.004535) test_fragments_for_display_5: .: (0.000754) test_fragments_for_display_6: .: (0.000567) test_fragments_for_display_7: .: (0.000526) test_fragments_for_display_8: .: (0.000520) test_fragments_for_display_9: .: (0.000532) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000458) test_obj_3: .: (0.000296) test_obj_7: .: (0.000263) test_obj_z: .: (0.000264) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.005445) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000475) test_bracket_eq: .: (0.000257) test_concat: .: (0.000216) test_delete: .: (0.000226) test_dup: .: (0.003580) test_each: .: (0.000244) test_eqeq: .: (0.000197) test_eqeq_false: .: (0.000190) test_eqeq_other: .: (0.000165) test_eqeq_self: .: (0.000174) test_include?: .: (0.004106) test_internal_data: .: (0.000264) test_internal_data_eq: .: (0.000202) test_length: .: (0.000182) test_ltlt: .: (0.000199) test_ltlt_larger: .: (0.000185) test_ltlt_middle: .: (0.000184) test_plus: .: (0.000231) test_plus_error: .: (0.000243) test_push: .: (0.000472) test_reverse_each: .: (0.000260) test_self_bracket: .: (0.000186) test_self_new: .: (0.000207) test_size: .: (0.000174) test_sort!: .: (0.000160) test_to_a: .: (0.000180) test_uniq!: .: (0.000177) test_unshift: .: (0.000237) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.009086) test_complement: .: (0.003300) test_complement_with_cut_symbols: .: (0.008175) test_cut_locations: .: (0.006322) test_cut_locations_in_enzyme_notation: .: (0.003297) test_primary: .: (0.009547) test_primary_with_cut_symbols: .: (0.003004) test_to_re: .: (0.002802) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000948) test_align_with_cuts: .: (0.004105) test_argument_error: .: (0.007685) test_ds: .: (0.000979) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000537) test_complement: .: (0.000266) test_contents: .: (0.000574) test_primary: .: (0.000231) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000460) test_complement: .: (0.007004) test_contents: .: (0.000342) test_primary: .: (0.000293) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000407) test_contents: .: (0.000213) test_primary: .: (0.000540) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000389) test_complement_to_array_index: .: (0.000288) test_complement_to_array_index_class: .: (0.000266) test_contents: .: (0.000238) test_primary: .: (0.000226) test_primary_to_array_index: .: (0.000283) test_primary_to_array_index_class: .: (0.000285) test_to_array_index: .: (0.000454) test_to_array_index_class: .: (0.000619) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000475) test_rebase: .: (0.000224) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000849) test_creation_with_no_cuts: .: (0.000514) test_cut_locations: .: (0.000661) test_cut_locations_in_enzyme_notation: .: (0.003627) test_orientation: .: (0.000587) test_pattern: .: (0.000481) test_pattern_palindromic?: .: (0.000690) test_stripped: .: (0.000408) test_to_re: .: (0.000381) test_with_cut_symbols: .: (0.000562) test_with_spaces: .: (0.000785) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000957) test_creation_with_no_cuts: .: (0.000504) test_cut_locations: .: (0.000674) test_cut_locations_in_enzyme_notation: .: (0.000429) test_orientation: .: (0.000446) test_pattern: .: (0.000444) test_pattern_palindromic?: .: (0.000721) test_stripped: .: (0.000411) test_to_re: .: (0.000375) test_with_cut_symbols: .: (0.000424) test_with_spaces: .: (0.000520) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.007493) test_initialize_with_pattern: .: (0.003467) test_max: .: (0.000256) test_min: .: (0.000194) test_to_array_index: .: (0.007260) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.003004) test_bracket_eq: .: (0.000316) test_concat: .: (0.000185) test_delete: .: (0.001497) test_dup: .: (0.000243) test_each: .: (0.000435) test_eqeq: .: (0.001543) test_eqeq_false: .: (0.000172) test_eqeq_other: .: (0.000148) test_eqeq_self: .: (0.000799) test_include?: .: (0.000214) test_internal_data_hash: .: (0.000163) test_internal_data_hash_eq: .: (0.000178) test_length: .: (0.000225) test_ltlt: .: (0.000168) test_ltlt_noeffect: .: (0.000165) test_plus: .: (0.001451) test_plus_error: .: (0.001672) test_private_push_element: .: (0.000197) test_private_push_element_intermediate: .: (0.001770) test_private_push_element_last: .: (0.000260) test_private_push_element_noeffect: .: (0.000166) test_private_sorted_keys: .: (0.000168) test_private_unshift_element: .: (0.000208) test_private_unshift_element_first: .: (0.001765) test_private_unshift_element_intermediate: .: (0.000202) test_private_unshift_element_noeffect: .: (0.000162) test_push: .: (0.006364) test_reverse_each: .: (0.001581) test_self_bracket: .: (0.000191) test_self_new: .: (0.000192) test_size: .: (0.000225) test_sort!: .: (0.000216) test_to_a: .: (0.000187) test_uniq!: .: (0.000147) test_unshift: .: (0.003053) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000335) test_left_padding: .: (0.000284) test_right_padding: .: (0.001679) test_strip_padding: .: (0.000200) Bio::TestSOFT: test_dataset: .: (0.024750) test_series: .: (0.005390) Bio::TestSOSUIReport: test_entry_id: .: (0.000410) test_prediction: .: (0.000223) test_tmh: .: (0.000213) test_tmhs: .: (0.000246) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000276) test_rs: .: (0.000156) Bio::TestSOSUITMH: test_grade: .: (0.000654) test_range: .: (0.000214) test_sequence: .: (0.000208) Bio::TestSampleGraph: test_bellman_ford: .: (0.000471) test_bfs_shortest_path: .: (0.000251) test_breadth_first_search: .: (0.000242) test_depth_first_search: .: (0.000330) test_dijkstra: .: (0.000312) test_dump_list: .: (0.000275) test_dump_matrix: .: (0.000392) test_extract_subgraph_by_label: .: (0.000255) test_extract_subgraph_by_list: .: (0.000481) test_extract_subgraph_retains_disconnected_nodes: .: (0.000226) test_small_world_aka_node_degree_histogram: .: (0.000211) test_to_matrix: .: (0.000380) test_to_matrix_fixed_index: .: (0.000294) test_undirected_cliquishness: .: (0.000362) Bio::TestScf_version_2: test_complement: .: (0.005207) test_seq: .: (0.004542) test_to_biosequence: .: (0.004613) Bio::TestScf_version_3: test_complement: .: (0.012704) test_seq: .: (0.012889) test_to_biosequence: .: (0.012391) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000338) test_AA_new_sequence_all_legal_symbols: .: (0.000172) test_AA_new_sequence_removes_whitespace: .: (0.000162) test_AA_new_sequence_upcases_symbols: .: (0.000183) test_DNA_new_blank_sequence: .: (0.000158) test_DNA_new_sequence_downcases_symbols: .: (0.000166) test_DNA_new_sequence_removes_whitespace: .: (0.000168) test_NA_randomize_with_counts: .: (0.000625) test_NA_randomize_with_counts_and_block: .: (0.000642) test_RNA_new_sequence: .: (0.000166) test_ambiguous_dna_sequence_complement: .: (0.000179) test_ambiguous_rna_sequence_complement: .: (0.000174) test_amino_acid_codes: .: (0.000211) test_amino_acid_molecular_weight: .: (0.000266) test_amino_acid_names: .: (0.000199) test_amino_acid_randomize_can_be_chained: .: (0.000839) test_amino_acid_randomize_has_same_composition: .: (0.000527) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.005406) test_dna_composition: .: (0.000235) test_dna_gc_percent: .: (0.000202) test_dna_molecular_weight: .: (0.000241) test_dna_pikachu: .: (0.000188) test_dna_sequence_complement: .: (0.000168) test_dna_sequence_translate: .: (0.000477) test_dna_to_re: .: (0.000239) test_element_reference_operator_with_one_argument: .: (0.000205) test_element_reference_operator_with_two_arguments: .: (0.000173) test_invalid_nucleic_acid_illegal_bases: .: (0.000806) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000216) test_nucleic_acid_names: .: (0.000196) test_randomize_dna_can_be_chained: .: (0.000373) test_randomize_dna_retains_composition: .: (0.000292) test_randomize_dna_with_block: .: (0.000319) test_rna_composition: .: (0.000206) test_rna_gc_percent: .: (0.000189) test_rna_molecular_weight: .: (0.000221) test_rna_pikachu: .: (0.000184) test_rna_sequence_complement: .: (0.000168) test_rna_sequence_translate: .: (0.001166) test_rna_to_re: .: (0.000277) test_total: .: (0.000196) test_two_consecutive_dna_randomizations_not_equal: .: (0.000310) test_valid_dna_sequence_illegal_bases: .: (0.000179) Bio::TestSequenceAA: test_codes: .: (0.000325) test_molecular_weight: .: (0.000454) test_names: .: (0.000191) test_to_re: .: (0.000233) test_to_s: .: (0.000156) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000365) Bio::TestSequenceAANew: test_new: .: (0.000264) test_new_n: .: (0.000169) test_new_r: .: (0.000176) test_new_t: .: (0.000150) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000309) test_concat: .: (0.000174) test_push: .: (0.000151) test_seq: .: (0.000162) test_splicing: .: (0.001686) test_sum: .: (0.000220) test_to_s: .: (0.000152) test_to_str: .: (0.000154) test_total: .: (0.000165) test_window_search: .: (0.000281) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000276) test_normalize_A: .: (0.000186) test_normalize_a: .: (0.000163) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000917) test_randomize_with_block: .: (0.002684) test_randomize_with_hash: .: (0.001155) test_randomize_with_hash_block: .: (0.002833) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.001285) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.000971) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000348) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000193) test_subseq_returns_subsequence: .: (0.000164) test_to_s_returns_self_as_string: .: (0.000185) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000296) test_window_search_with_width_3_step_two_with_residual: .: (0.000186) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000303) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000264) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000329) test_na_self_randomize: .: (0.000257) Bio::TestSequenceDBLink: test_database: .: (0.000259) test_id: .: (0.000155) test_secondary_ids: .: (0.000150) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000293) test_parse_uniprot_DR_line: .: (0.000211) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000747) test_output_width_35: .: (0.000944) test_output_width_nil: .: (0.000367) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000480) test_output_after_adding_sequence: .: (0.000361) test_output_after_truncating_sequence: .: (0.000293) test_output_from_error_probabilities: .: (0.008228) test_output_width45: .: (0.000335) test_output_with_converting_score_phred2solexa: .: (0.000564) test_output_with_converting_score_solexa2phred: .: (0.000758) test_output_with_default_score: .: (0.000375) Bio::TestSequenceMasker: test_mask: .: (0.000404) test_mask_with_enumerator: .: (0.000241) test_mask_with_enumerator_empty_mask_char: .: (0.000237) test_mask_with_enumerator_excess: .: (0.000395) test_mask_with_enumerator_longer_mask_char: .: (0.000208) test_mask_with_enumerator_shorter: .: (0.000243) test_mask_with_error_probability: .: (0.000208) test_mask_with_quality_score: .: (0.000192) Bio::TestSequenceNA: test_at_content: .: (0.000789) test_at_skew: .: (0.000276) test_codon_usage: .: (0.000233) test_complement: .: (0.000181) test_dna: .: (0.000174) test_dna!: .: (0.000160) test_forward_complement: .: (0.000218) test_gc_content: .: (0.000298) test_gc_percent: .: (0.000236) test_gc_skew: .: (0.000326) test_iliegal_bases: .: (0.000214) test_molecular_weight: .: (0.000210) test_names: .: (0.000255) test_reverse_complement: .: (0.000213) test_rna: .: (0.000174) test_rna!: .: (0.000175) test_splicing: .: (0.000248) test_to_re: .: (0.000240) test_to_s: .: (0.000158) Bio::TestSequenceNACommon: test_composition: .: (0.000323) test_concat: .: (0.000486) test_push: .: (0.000160) test_seq: .: (0.000177) test_splicing: .: (0.000262) test_sum: .: (0.000156) test_to_s: .: (0.000146) test_to_str: .: (0.000154) test_total: .: (0.000161) test_window_search: .: (0.000276) Bio::TestSequenceNANew: test_new: .: (0.000286) test_new_n: .: (0.000170) test_new_r: .: (0.000153) test_new_t: .: (0.000161) Bio::TestSequenceNATranslation: test_translate: .: (0.000504) test_translate_0: .: (0.000850) test_translate_1: .: (0.000311) test_translate_2: .: (0.000283) test_translate_3: .: (0.000319) test_translate_4: .: (0.000307) test_translate_5: .: (0.000296) test_translate_6: .: (0.000289) test_translate_7: .: (0.000456) test_translate_given_codon_table: .: (0.031519) test_translate_n1: .: (0.000559) test_translate_n2: .: (0.000568) test_translate_n3: .: (0.000444) test_translate_unknown_o: .: (0.000336) test_translate_unknown_x: .: (0.000302) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000284) test_convert_scores_from_phred_to_solexa: .: (0.000452) test_convert_scores_from_solexa_to_phred: .: (0.000209) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000267) test_convert_scores_from_phred: .: (0.000158) test_convert_scores_from_phred_to_solexa: .: (0.004462) test_convert_scores_from_solexa: .: (0.000291) test_convert_scores_from_solexa_to_phred: .: (0.000217) test_convert_scores_to_phred: .: (0.000158) test_convert_scores_to_solexa: .: (0.000436) test_p2q: .: (0.000201) test_phred_p2q: .: (0.000177) test_phred_q2p: .: (0.001439) test_q2p: .: (0.001448) test_quality_score_type: .: (0.000159) test_self_convert_scores_to_solexa: .: (0.000350) test_self_p2q: .: (0.005313) test_self_q2p: .: (0.001544) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000299) test_convert_scores_from_phred: .: (0.000435) test_convert_scores_from_phred_to_solexa: .: (0.000329) test_convert_scores_from_solexa: .: (0.000163) test_convert_scores_from_solexa_to_phred: .: (0.000189) test_convert_scores_to_phred: .: (0.000193) test_convert_scores_to_solexa: .: (0.000152) test_p2q: .: (0.000239) test_q2p: .: (0.001593) test_quality_score_type: .: (0.000169) test_self_convert_scores_to_phred: .: (0.000219) test_self_p2q: .: (0.000245) test_self_q2p: .: (0.009352) test_solexa_p2q: .: (0.000274) test_solexa_q2p: .: (0.002559) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000347) test_center: .: (0.000185) test_chomp: .: (0.000192) test_chop: .: (0.000192) test_delete: .: (0.000178) test_delete_prefix: .: (0.000185) test_delete_suffix: .: (0.000519) test_downcase: .: (0.000205) test_each_char: .: (0.000218) test_each_char_enum: .: (0.000213) test_each_grapheme_cluster: .: (0.000571) test_each_grapheme_cluster_enum: .: (0.000225) test_each_line: .: (0.000210) test_each_line_enum: .: (0.000205) test_gsub: .: (0.000204) test_gsub_with_block: .: (0.000464) test_ljust: .: (0.000180) test_lstrip: .: (0.000173) test_multiply: .: (0.002932) test_next: .: (0.000265) test_reverse: .: (0.000276) test_rjust: .: (0.000176) test_rstrip: .: (0.000163) test_slice: .: (0.000170) test_slice2: .: (0.000164) test_split: .: (0.000214) test_squeeze: .: (0.000176) test_strip: .: (0.000166) test_sub: .: (0.000197) test_sub_with_block: .: (0.000344) test_succ: .: (0.000186) test_swapcase: .: (0.000204) test_tr: .: (0.000177) test_tr_s: .: (0.000172) test_upcase: .: (0.000173) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000649) test_partition_nomatch: .: (0.000202) test_partition_sep_TSeq: .: (0.000192) test_partition_sep_regexp: .: (0.000343) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000283) test_rpartition_nomatch: .: (0.000134) test_rpartition_sep_TSeq: .: (0.000127) test_rpartition_sep_regexp: .: (0.000133) Bio::TestShRNA: test_blocK_it: .: (0.046255) test_blocK_it_: .: (0.039793) test_blocK_it_BLOCK_IT: .: (0.031289) test_blocK_it_BLOCK_iT: .: (0.036334) test_blocK_it_piGene: .: (0.039975) test_bottom_strand: .: (0.039715) test_bottom_strand_class: .: (0.035672) test_bottom_strand_nil: .: (0.036741) test_design: .: (0.038784) test_design_BLOCK_IT: .: (0.034861) test_report: .: (0.035311) test_report_before_design: .: (0.036997) test_top_strand: .: (0.036675) test_top_strand_class: .: (0.036131) test_top_strand_nil: .: (0.038540) Bio::TestShRNANew: test_new: .: (0.000549) Bio::TestSiRNA: test_antisense_size: .: (0.000323) test_design: .: (0.036686) test_design_reynolds: .: (0.045675) test_design_uitei: .: (0.037227) test_max_gc_percent: .: (0.000187) test_min_gc_percent: .: (0.000160) test_reynolds: .: (0.045837) test_reynolds?: .: (0.006826) test_uitei: .: (0.032887) test_uitei?: .: (0.000206) Bio::TestSiRNANew: test_new: .: (0.000551) Bio::TestSiRNAPair: test_antisense: .: (0.042139) test_gc_percent: .: (0.024726) test_report: .: (0.020778) test_rule: .: (0.019882) test_sense: .: (0.019794) test_start: .: (0.021261) test_stop: .: (0.019381) test_target: .: (0.021951) Bio::TestSiRNAPairNew: test_new: .: (0.000491) Bio::TestSim4Report: test_all_hits: .: (0.000542) test_each: .: (0.000334) test_each_hit: .: (0.000284) test_hits: .: (0.000297) test_num_hits: .: (0.000252) test_query_def: .: (0.000253) test_query_id: .: (0.000240) test_query_len: .: (0.000251) test_seq1: .: (0.000441) Bio::TestSim4Report2: test_all_hits: .: (0.000440) test_each: .: (0.000266) test_each_hit: .: (0.000256) test_hits: .: (0.000269) test_num_hits: .: (0.000250) test_query_def: .: (0.000252) test_query_id: .: (0.000244) test_query_len: .: (0.000261) test_seq1: .: (0.000335) Bio::TestSim4Report4: test_all_hits: .: (0.000446) test_each: .: (0.000434) test_each_hit: .: (0.000283) test_hits: .: (0.000272) test_num_hits: .: (0.000247) test_query_def: .: (0.000245) test_query_id: .: (0.000274) test_query_len: .: (0.000716) test_seq1: .: (0.000335) Bio::TestSim4ReportHit: test_align: .: (0.000497) test_complement?: .: (0.000249) test_definition: .: (0.000245) test_each: .: (0.000421) test_exons: .: (0.000399) test_hit_id: .: (0.000244) test_hsps: .: (0.000394) test_introns: .: (0.000376) test_len: .: (0.000235) test_query_def: .: (0.000242) test_query_id: .: (0.000239) test_query_len: .: (0.000239) test_segmentpairs: .: (0.000377) test_seq1: .: (0.000311) test_seq2: .: (0.000270) test_target_def: .: (0.000245) test_target_id: .: (0.000237) test_target_len: .: (0.000240) Bio::TestSim4ReportHit2: test_align: .: (0.000433) test_complement?: .: (0.000234) test_definition: .: (0.000235) test_each: .: (0.000375) test_exons: .: (0.000359) test_hit_id: .: (0.000237) test_hsps: .: (0.000356) test_introns: .: (0.000334) test_len: .: (0.000254) test_query_def: .: (0.000234) test_query_id: .: (0.000235) test_query_len: .: (0.000310) test_segmentpairs: .: (0.000483) test_seq1: .: (0.000387) test_seq2: .: (0.000348) test_target_def: .: (0.000336) test_target_id: .: (0.000339) test_target_len: .: (0.000336) Bio::TestSim4ReportHit4: test_align: .: (0.000568) test_complement?: .: (0.000355) test_definition: .: (0.000349) test_each: .: (0.000601) test_exons: .: (0.000563) test_hit_id: .: (0.000299) test_hsps: .: (0.000518) test_introns: .: (0.000516) test_len: .: (0.000307) test_query_def: .: (0.000329) test_query_id: .: (0.000356) test_query_len: .: (0.000318) test_segmentpairs: .: (0.000527) test_seq1: .: (0.000393) test_seq2: .: (0.000389) test_target_def: .: (0.000362) test_target_id: .: (0.000307) test_target_len: .: (0.000321) Bio::TestSim4ReportSegment: test_from: .: (0.000383) test_self_new: .: (0.000271) test_seq: .: (0.000330) test_to: .: (0.000245) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000695) test_direction: .: (0.000496) test_hit_from: .: (0.000469) test_hit_to: .: (0.000498) test_hseq: .: (0.000411) test_midline: .: (0.000434) test_percent_identity: .: (0.000456) test_qseq: .: (0.001252) test_query_from: .: (0.000791) test_query_to: .: (0.000456) test_seq1: .: (0.000473) test_seq2: .: (0.000448) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000694) test_direction: .: (0.000484) test_hit_from: .: (0.000485) test_hit_to: .: (0.000778) test_hseq: .: (0.000519) test_midline: .: (0.000452) test_percent_identity: .: (0.000429) test_qseq: .: (0.000461) test_query_from: .: (0.000420) test_query_to: .: (0.000408) test_seq1: .: (0.000442) test_seq2: .: (0.000461) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000579) test_direction: .: (0.000719) test_hit_from: .: (0.000463) test_hit_to: .: (0.000487) test_hseq: .: (0.000535) test_midline: .: (0.000444) test_percent_identity: .: (0.000462) test_qseq: .: (0.000448) test_query_from: .: (0.000471) test_query_to: .: (0.000739) test_seq1: .: (0.000588) test_seq2: .: (0.000547) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000555) test_direction: .: (0.000427) test_hit_from: .: (0.000494) test_hit_to: .: (0.000480) test_hseq: .: (0.000533) test_midline: .: (0.000476) test_percent_identity: .: (0.000480) test_qseq: .: (0.000477) test_query_from: .: (0.000457) test_query_to: .: (0.000434) test_seq1: .: (0.000450) test_seq2: .: (0.000495) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000523) test_direction: .: (0.000587) test_hit_from: .: (0.000479) test_hit_to: .: (0.000453) test_hseq: .: (0.000416) test_midline: .: (0.000413) test_percent_identity: .: (0.001291) test_qseq: .: (0.000570) test_query_from: .: (0.000462) test_query_to: .: (0.000485) test_seq1: .: (0.000526) test_seq2: .: (0.000510) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000515) test_direction: .: (0.000384) test_hit_from: .: (0.000375) test_hit_to: .: (0.000372) test_hseq: .: (0.000428) test_midline: .: (0.000365) test_percent_identity: .: (0.000365) test_qseq: .: (0.000403) test_query_from: .: (0.000390) test_query_to: .: (0.000392) test_seq1: .: (0.000423) test_seq2: .: (0.000415) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000554) test_direction: .: (0.000424) test_hit_from: .: (0.000402) test_hit_to: .: (0.000364) test_hseq: .: (0.000461) test_midline: .: (0.000408) test_percent_identity: .: (0.000360) test_qseq: .: (0.000383) test_query_from: .: (0.000354) test_query_to: .: (0.000421) test_seq1: .: (0.000451) test_seq2: .: (0.000444) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000394) test_entry_id: .: (0.000232) test_filename: .: (0.000204) test_len: .: (0.000201) test_self_new: .: (0.000243) test_self_parse: .: (0.003519) Bio::TestTMHMMReport: test_entry_id: .: (0.000691) test_exp_aas_in_tmhs: .: (0.000478) test_exp_first_60aa: .: (0.000598) test_helix: .: (0.000505) test_predicted_tmhs: .: (0.000425) test_query_len: .: (0.000420) test_tmhs: .: (0.000451) test_to_s: .: (0.001421) test_total_prob_of_N_in: .: (0.000375) Bio::TestTMHMMReport_reports: test_reports: .: (0.000440) Bio::TestTMHMMTMH: test_entry_id: .: (0.000577) test_pos: .: (0.000478) test_range: .: (0.000467) test_status: .: (0.000435) test_version: .: (0.000469) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000562) test_cutoff: .: (0.000741) test_entry_id: .: (0.000392) test_length: .: (0.000356) test_loc: .: (0.000358) test_name: .: (0.000352) test_networks: .: (0.000336) test_prediction: .: (0.000513) test_query_len: .: (0.000326) test_query_sequences: .: (0.000290) test_rc: .: (0.000299) test_version: .: (0.000325) Bio::TestTargetPReportConst: test_delimiter: .: (0.000361) test_rs: .: (0.000223) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000339) test_togows_access_wait: .: (2.002915) Bio::TestTogoWSREST: test_debug: .: (0.000691) test_debug_default: .: (0.000346) test_internal_http: .: (0.000256) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000257) test_entry: .: (0.000129) test_entry_database_list: .: (0.000114) test_new: .: (0.000263) test_new_with_uri_object: .: (0.000252) test_new_with_uri_string: .: (0.000246) test_retrieve: .: (0.000127) test_search: .: (0.000111) test_search_database_list: .: (0.000120) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000398) test_prepare_return_value: .: (0.005486) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000481) Bio::TestTree: test_get_edge_distance: .: (0.000312) test_get_edge_distance_string: .: (0.000180) test_get_node_name: .: (0.000141) test_initialize: .: (0.000151) test_options: .: (0.000131) test_root: .: (0.000126) test_root=: .: (0.000138) Bio::TestTree2: test_add_edge: .: (0.000499) test_add_node: .: (0.000292) test_adjacency_matrix: .: (0.000251) test_adjacency_matrix_with_block: .: (0.000249) test_adjacent_nodes: .: (0.000215) test_adjacent_nodes_nonexistent: .: (0.000163) test_ancestors: .: (0.000201) test_children: .: (0.000182) test_clear: .: (0.000189) test_clear_node: .: (0.000219) test_clear_node_nonexistent: .: (0.000236) test_collect_edge!: .: (0.000268) test_collect_node!: .: (0.000310) test_concat: .: (0.000259) test_descendents: .: (0.000201) test_distance_matrix: .: (0.007104) test_each_edge: .: (0.000396) test_each_node: .: (0.000322) test_each_out_edge: .: (0.000315) test_each_out_edge_chimpanzee: .: (0.000277) test_each_out_edge_human: .: (0.000269) test_each_out_edge_mammals: .: (0.000223) test_each_out_edge_nonexistent: .: (0.000183) test_each_out_edge_primates: .: (0.000217) test_each_out_edge_rat: .: (0.000189) test_each_out_edge_rodents: .: (0.000216) test_edges: .: (0.000184) test_get_edge: .: (0.000321) test_get_edge_indirect: .: (0.000169) test_get_edge_merged: .: (0.000192) test_get_edge_nonexistent: .: (0.000170) test_get_node_bootstrap: .: (0.000187) test_get_node_bootstrap_string=: .: (0.000177) test_get_node_by_name: .: (0.000221) test_get_node_by_name_noexistent: .: (0.000158) test_include?: .: (0.000189) test_include_nonexistent: .: (0.000168) test_insert_node: .: (0.000276) test_leaves: .: (0.000213) test_leaves_noargs: .: (0.011341) test_lowest_common_ancestor: .: (0.000386) test_nodes: .: (0.000295) test_number_of_edges: .: (0.000206) test_number_of_nodes: .: (0.000185) test_out_degree: .: (0.000217) test_out_degree_nonexistent: .: (0.000466) test_out_edges: .: (0.000216) test_out_edges_mammals: .: (0.000370) test_out_edges_nonexistent: .: (0.000306) test_out_edges_primates: .: (0.000374) test_out_edges_rodents: .: (0.000353) test_parent: .: (0.001080) test_path: .: (0.000300) test_remove_edge: .: (0.000310) test_remove_edge_if: .: (0.000309) test_remove_edge_if_nothing_removed: .: (0.000315) test_remove_edge_nonexistent: .: (0.000570) test_remove_node: .: (0.000248) test_remove_node_if: .: (0.000195) test_remove_node_if_false: .: (0.005457) test_remove_node_nonexistent: .: (0.000371) test_remove_nonsense_nodes: .: (0.000278) test_subtree: .: (0.000275) test_subtree_with_all_paths: .: (0.000577) test_total_distance: .: (0.000193) Bio::TestTreeEdge: test_distance: .: (0.000270) test_distance=: .: (0.000154) test_distance_string: .: (0.000119) test_distance_string=: .: (0.000150) test_initialize: .: (0.000181) test_inspect: .: (0.000138) test_to_s: .: (0.000123) Bio::TestTreeNode: test_bootstrap: .: (0.000246) test_bootstrap=: .: (0.000153) test_bootstrap_string: .: (0.000111) test_bootstrap_string=: .: (0.000165) test_initialize: .: (0.000155) test_inspect: .: (0.000309) test_name: .: (0.000351) test_to_s: .: (0.000236) Bio::TestUniProt: test_gene_name: .: (0.007685) Bio::TestUniProtKB: test_ac: .: (0.003036) test_accession: .: (0.007857) test_cc: .: (0.015581) test_cc_alternative_products: .: (0.004249) test_cc_database: .: (0.019060) test_cc_mass_spectrometry: .: (0.004032) test_de: .: (0.014735) test_dr: .: (0.004174) test_dr_with_key: .: (0.006996) test_dr_with_key_empty: .: (0.004786) test_dt: .: (0.003565) test_dt_annotation: .: (0.001991) test_dt_created: .: (0.004565) test_dt_sequence: .: (0.002596) test_entry: .: (0.002548) test_ft: .: (0.022538) test_gene_name: .: (0.037396) test_gene_names: .: (0.004076) test_gn: .: (0.002595) test_gn_old_parser: .: (0.002326) test_gn_uniprot_parser: .: (0.002742) test_id_line: .: (0.002086) test_id_line_data_class: .: (0.001988) test_id_line_entry_name: .: (0.004924) test_id_line_molecule_type: .: (0.003004) test_id_line_sequence_length: .: (0.002222) test_kw: .: (0.002226) test_molecule: .: (0.002367) test_oc: .: (0.002022) test_og_1: .: (0.002025) test_og_2: .: (0.005480) test_og_3: .: (0.002508) test_og_4: .: (0.002318) test_og_5: .: (0.002663) test_og_6: .: (0.001982) test_os: .: (0.001979) test_os_access: .: (0.003929) test_os_access2: .: (0.003643) test_ox: .: (0.002391) test_protein_name: .: (0.002273) test_ref: .: (0.005422) test_seq: .: (0.004852) test_sequence_length: .: (0.002909) test_sq: .: (0.002215) test_sq_crc64: .: (0.002276) test_sq_len: .: (0.002440) test_sq_mw: .: (0.002057) test_synonyms: .: (0.003764) Bio::TestUniProtKB_CC: test_allergen: .: (0.000363) test_alternative_products_access_as_hash: .: (0.000245) test_alternative_products_ai: .: (0.000282) test_alternative_products_apu: .: (0.000407) test_alternative_products_as: .: (0.000976) test_alternative_products_rf: .: (0.000121) test_biophysicochemical_properties: .: (0.000665) test_biotechnology: .: (0.000286) test_catalytic_activity: .: (0.000194) test_caution: .: (0.000205) test_cofactor: .: (0.000225) test_developmental_stage: .: (0.000222) test_disease: .: (0.000285) test_domain: .: (0.000300) test_enzyme_regulation: .: (0.000197) test_function: .: (0.000210) test_induction: .: (0.000175) test_interaction: .: (0.000272) test_mass_spectrometry: .: (0.000282) test_miscellaneous: .: (0.000175) test_pathway: .: (0.000219) test_pharmaceutical: .: (0.000400) test_polymorphism: .: (0.000301) test_ptm: .: (0.000187) test_rna_editing: .: (0.000269) test_similarity: .: (0.000185) test_subcellular_location: .: (0.000220) test_subunit: .: (0.000159) test_tissue_specificity: .: (0.000208) test_toxic_dose: .: (0.000414) test_web_resource: .: (0.000280) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000391) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000436) test_protein_name: .: (0.000261) test_synonyms: .: (0.000293) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000390) test_entry: .: (0.000118) test_entry_id: .: (0.000103) test_entry_name: .: (0.000111) test_id_line: .: (0.000117) test_molecule: .: (0.000117) test_sequence_length: .: (0.000109) Bio::TestUniProtKB_P03589: test_ac: .: (0.000576) test_accession: .: (0.000345) test_cc: .: (0.000637) test_cc_alternative_products: .: (0.000508) test_cc_database: .: (0.000480) test_cc_mass_spectrometry: .: (0.000468) test_de: .: (0.000452) test_dr: .: (0.000540) test_dr_with_key: .: (0.000528) test_dr_with_key_empty: .: (0.000515) test_dt: .: (0.000434) test_dt_annotation: .: (0.000318) test_dt_created: .: (0.000884) test_dt_sequence: .: (0.000313) test_entry: .: (0.000338) test_ft: .: (0.000488) test_gene_name: .: (0.000397) test_gene_names: .: (0.000351) test_gn: .: (0.000343) test_gn_old_parser: .: (0.000374) test_gn_uniprot_parser: .: (0.000378) test_id_line: .: (0.000321) test_id_line_data_class: .: (0.000308) test_id_line_entry_name: .: (0.000290) test_id_line_sequence_length: .: (0.000320) test_kw: .: (0.000368) test_oc: .: (0.000368) test_oh: .: (0.000535) test_os: .: (0.000342) test_os_access: .: (0.000317) test_os_access2: .: (0.000364) test_ox: .: (0.000324) test_protein_name: .: (0.000344) test_protein_name_after_calling_de: .: (0.000384) test_ref: .: (0.000371) test_seq: .: (0.000550) test_sequence_length: .: (0.000314) test_sq: .: (0.000320) test_sq_crc64: .: (0.000322) test_sq_len: .: (0.000337) test_sq_mw: .: (0.000318) test_synonyms: .: (0.000375) Bio::TestUniProtKB_P28907: test_ac: .: (0.001009) test_accession: .: (0.003579) test_cc: .: (0.002380) test_cc_alternative_products: .: (0.002254) test_cc_database: .: (0.001708) test_cc_mass_spectrometry: .: (0.001596) test_de: .: (0.001071) test_dr: .: (0.003227) test_dr_with_key: .: (0.005004) test_dr_with_key_empty: .: (0.003858) test_dt: .: (0.001214) test_dt_annotation: .: (0.001551) test_dt_created: .: (0.000818) test_dt_sequence: .: (0.000795) test_entry: .: (0.000837) test_ft: .: (0.001674) test_gene_name: .: (0.000913) test_gene_names: .: (0.000931) test_gn: .: (0.003938) test_gn_old_parser: .: (0.001971) test_gn_uniprot_parser: .: (0.001538) test_id_line: .: (0.001111) test_id_line_data_class: .: (0.001010) test_id_line_entry_name: .: (0.000957) test_id_line_sequence_length: .: (0.000948) test_kw: .: (0.001084) test_oc: .: (0.000982) test_os: .: (0.000959) test_os_access: .: (0.001396) test_os_access2: .: (0.000855) test_ox: .: (0.000865) test_protein_name: .: (0.000902) test_protein_name_after_calling_de: .: (0.000952) test_ref: .: (0.001466) test_seq: .: (0.003909) test_sequence_length: .: (0.001849) test_sq: .: (0.001517) test_sq_crc64: .: (0.001022) test_sq_len: .: (0.001129) test_sq_mw: .: (0.001197) test_synonyms: .: (0.001104) test_synonyms_after_calling_de: .: (0.001098) Bio::TestUniProtKB_P49144: test_ac: .: (0.000646) test_accession: .: (0.000585) test_cc: .: (0.000842) test_cc_alternative_products: .: (0.000824) test_cc_database: .: (0.001310) test_cc_mass_spectrometry: .: (0.000757) test_de: .: (0.000486) test_dr: .: (0.000786) test_dr_with_key: .: (0.000801) test_dr_with_key_empty: .: (0.000823) test_dt: .: (0.000517) test_dt_annotation: .: (0.002872) test_dt_created: .: (0.000574) test_dt_sequence: .: (0.001323) test_entry: .: (0.000556) test_ft: .: (0.001689) test_gene_name: .: (0.000729) test_gene_names: .: (0.000797) test_gn: .: (0.000513) test_gn_old_parser: .: (0.000568) test_gn_uniprot_parser: .: (0.000692) test_id_line: .: (0.000513) test_id_line_data_class: .: (0.000491) test_id_line_entry_name: .: (0.000475) test_id_line_sequence_length: .: (0.000574) test_kw: .: (0.000684) test_oc: .: (0.000549) test_os: .: (0.000527) test_os_access: .: (0.000625) test_os_access2: .: (0.000509) test_ox: .: (0.000489) test_protein_name: .: (0.000584) test_protein_name_after_calling_de: .: (0.000549) test_ref: .: (0.000945) test_seq: .: (0.000564) test_sequence_length: .: (0.000488) test_sq: .: (0.000505) test_sq_crc64: .: (0.000466) test_sq_len: .: (0.000493) test_sq_mw: .: (0.000492) test_synonyms: .: (0.000527) test_synonyms_after_calling_de: .: (0.000541) Bio::TestUniProtKB_Ref: test_RA: .: (0.000427) test_RC: .: (0.000226) test_RG: .: (0.000205) test_RL: .: (0.000222) test_RN: .: (0.000208) test_RP: .: (0.000208) test_RT: .: (0.000217) test_RX: .: (0.000226) test_ref: .: (0.000231) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000281) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000437) test_alternative_products_with_ft: .: (0.000611) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000314) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000297) test_RL_lines: .: (0.000140) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.003271) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000298) test_RG_line: .: (0.000161) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000469) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000330) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000231) test_RL_line: .: (0.000170) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000754) test_RP_line: .: (0.000276) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000164) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000293) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000212) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000190) test_CC_interaction_isoform: .: (0.000239) test_CC_interaction_no_gene_name: .: (0.000190) test_CC_interaction_self_association: .: (0.000228) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000344) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000280) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000347) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000282) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000267) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000261) test_DT_line: .: (0.000163) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.002783) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000665) test_CC_web_resource: .: (0.000100) test_FT_VER_SEQ: .: (0.000200) test_OH_line_exception: .: (0.000239) test_OH_lines: .: (0.000296) Bio::TestUtils: test_centreOfGravity: .: (0.000640) test_dihedral_angle: .: (0.000314) test_distance: .: (0.000391) test_geometricCentre: .: (0.000228) test_rad2deg: .: (0.000147) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000297) test_dijkstra_on_weighted_graph: .: (0.000156) Finished in 13.80696456 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 285.44 tests/s, 1564.50 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.5-1_arm64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1784902 and its subdirectories I: Current time: Mon Mar 2 13:36:36 -12 2026 I: pbuilder-time-stamp: 1772501796 Tue Jan 28 19:13:38 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Jan 28 19:13:38 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Jan 28 19:14:55 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Jan 28 19:14:56 UTC 2025 I: ruby-bio_2.0.5-1_arm64.changes: Format: 1.8 Date: Sun, 03 Mar 2024 14:21:49 +0100 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.5-1 Distribution: unstable Urgency: medium Maintainer: Debian Ruby Team Changed-By: Lucas Nussbaum Description: ruby-bio - Ruby tools for computational molecular biology Changes: ruby-bio (2.0.5-1) unstable; urgency=medium . [ Debian Janitor ] * Update standards version to 4.6.2, no changes needed. . [ Lucas Nussbaum ] * New upstream version 2.0.5 Checksums-Sha1: 1f09a2591e5cf4b31591e407f53b2f6c5881d609 656832 ruby-bio_2.0.5-1_all.deb 852ce2de21193d54c5386aa349433929f3ff9ded 8343 ruby-bio_2.0.5-1_arm64.buildinfo Checksums-Sha256: 9f50f668237d86011e1cb40b1f1bb964dfb322d827a0a1a7423df712652ac5f3 656832 ruby-bio_2.0.5-1_all.deb 17bac7a6900bd03ca4591d645dd1b4008b49fe462720420648ee63cbef8f7dc1 8343 ruby-bio_2.0.5-1_arm64.buildinfo Files: 6b30eeea4b84581b7c9732444564d65b 656832 ruby optional ruby-bio_2.0.5-1_all.deb 8a1916c293bd990bd54b78d3afa3690f 8343 ruby optional ruby-bio_2.0.5-1_arm64.buildinfo Tue Jan 28 19:14:57 UTC 2025 I: diffoscope 286 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_6-77287.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/ruby-bio_2.0.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/ruby-bio_2.0.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/ruby-bio_2.0.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/b1/ruby-bio_2.0.5-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.UBezSGM3/b2/ruby-bio_2.0.5-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 234ms CPU time consumed: 233ms Tue Jan 28 19:14:58 UTC 2025 I: diffoscope 286 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 28 19:14:58 UTC 2025 I: ruby-bio from trixie built successfully and reproducibly on arm64. Tue Jan 28 19:14:59 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Jan 28 19:14:59 UTC 2025 I: Submitting 12K b1/ruby-bio_2.0.5-1_arm64.buildinfo.asc Tue Jan 28 19:14:59 UTC 2025 I: Submitting 12K b2/ruby-bio_2.0.5-1_arm64.buildinfo.asc Tue Jan 28 19:15:00 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 28 19:15:00 UTC 2025 I: Done submitting .buildinfo files. Tue Jan 28 19:15:00 UTC 2025 I: Removing signed ruby-bio_2.0.5-1_arm64.buildinfo.asc files: removed './b1/ruby-bio_2.0.5-1_arm64.buildinfo.asc' removed './b2/ruby-bio_2.0.5-1_arm64.buildinfo.asc'