Mon Sep 29 12:42:57 UTC 2025 I: starting to build ruby-bio/forky/arm64 on jenkins on '2025-09-29 12:42' Mon Sep 29 12:42:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_11/126025/console.log Mon Sep 29 12:42:57 UTC 2025 I: Downloading source for forky/ruby-bio=2.0.6-1 --2025-09-29 12:42:58-- http://deb.debian.org/debian/pool/main/r/ruby-bio/ruby-bio_2.0.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1494 (1.5K) [text/prs.lines.tag] Saving to: ‘ruby-bio_2.0.6-1.dsc’ 0K . 100% 174M=0s 2025-09-29 12:42:58 (174 MB/s) - ‘ruby-bio_2.0.6-1.dsc’ saved [1494/1494] Mon Sep 29 12:42:58 UTC 2025 I: ruby-bio_2.0.6-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Homepage: https://bioruby.org/ Standards-Version: 4.7.2 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: a0cd4e46dd790e55ce38de08e2991a0a9b2fc4d1 1452516 ruby-bio_2.0.6.orig.tar.gz 6c20e105f27e196f76781c9d9342544db3970492 14552 ruby-bio_2.0.6-1.debian.tar.xz Checksums-Sha256: c96e0c54dcd9b9d413afad6b8702e4b1be290631b459402024c446ef922605b3 1452516 ruby-bio_2.0.6.orig.tar.gz d712ccb6ae91730a86227eb075ac8fc21db0250cdfc554e902697b23f656234f 14552 ruby-bio_2.0.6-1.debian.tar.xz Files: 9c4372512937a004ed39a200510677fd 1452516 ruby-bio_2.0.6.orig.tar.gz 6ac08c031b6ab46f3064d31334fd4e5e 14552 ruby-bio_2.0.6-1.debian.tar.xz Ruby-Versions: all -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaNZ5ixIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtpiGwD/Yv1EvwHHbzBVJFBwa56R8+C8lUrse+jE bNhr8Y9mgEQBANh5HuGu+dWyvwlxgf0tnSTtdOSIdt/MNxVmxrBpQ3oH =AK7i -----END PGP SIGNATURE----- Mon Sep 29 12:42:58 UTC 2025 I: Checking whether the package is not for us Mon Sep 29 12:42:58 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon Sep 29 12:42:58 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon Sep 29 12:43:57 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 29 00:42:59 -12 2025 I: pbuilder-time-stamp: 1759149779 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_2.0.6-1.dsc] I: copying [./ruby-bio_2.0.6.orig.tar.gz] I: copying [./ruby-bio_2.0.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.6-1.dsc: no acceptable signature found dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.6 dpkg-source: info: unpacking ruby-bio_2.0.6.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.6-1.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/515837/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='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0a9a5394c8d64090938d536e1b5faa11' 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='515837' 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.P5Ot3IT8/pbuilderrc_LSNI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/b1 --logfile b1/build.log ruby-bio_2.0.6-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' 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 codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/515837/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 ... 20022 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} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{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} 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} 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} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libksba8{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{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} libruby3.3{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2-16{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} rsopv{a} ruby{a} ruby-all-dev{a} ruby-csv{a} ruby-did-you-mean{a} ruby-libxml{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rd{a} ruby-ruby2-keywords{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} ruby3.3-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{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 debian-tag2upload-keyring dput dput-ng dupload equivs fonts-lato git-debpush gnupg libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgitlab-api-v4-perl libgpg-error-l10n libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmetacpan-client-perl libnamespace-clean-perl libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx lzip pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby-sdbm ruby3.3-doc strace unzip wget zip 0 packages upgraded, 129 newly installed, 0 to remove and 0 not upgraded. Need to get 37.0 MB of archives. After unpacking 148 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.7-1 [857 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.7-1 [2001 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.7-1 [1895 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 openssl arm64 3.5.3-1 [1457 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 ca-certificates all 20250419 [162 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.27 [92.2 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 debhelper all 13.27 [940 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libgpg-error0 arm64 1.55-2 [83.9 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libgcrypt20 arm64 1.11.2-2 [772 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 gpgconf arm64 2.4.8-3 [122 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 gpg arm64 2.4.8-3 [579 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 pinentry-curses arm64 1.3.2-3 [85.0 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 gpg-agent arm64 2.4.8-3 [248 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 56 http://deb.debian.org/debian forky/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 59 http://deb.debian.org/debian forky/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 86 http://deb.debian.org/debian forky/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libio-socket-ssl-perl all 2.095-1 [226 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 rsopv arm64 0.6.4-1 [1180 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 wdiff arm64 1.2.2-9 [122 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 devscripts all 2.25.19 [1047 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 docbook all 4.5-11 [126 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libosp5 arm64 1.5.2-15.2 [922 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 opensp arm64 1.5.2-15.2 [442 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 docbook-to-man arm64 1:2.0.0-49 [71.2 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 rubygems-integration all 1.19 [5488 B] Get: 105 http://deb.debian.org/debian forky/main arm64 ruby-csv all 3.3.4-1 [42.2 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get: 109 http://deb.debian.org/debian forky/main arm64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libruby3.3 arm64 3.3.8-2 [6142 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 ruby3.3 arm64 3.3.8-2 [834 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libruby arm64 1:3.3+b1 [5436 B] Get: 115 http://deb.debian.org/debian forky/main arm64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 ruby arm64 1:3.3+b1 [6560 B] Get: 117 http://deb.debian.org/debian forky/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 ruby-minitest all 5.25.4-3 [66.3 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 gem2deb-test-runner arm64 2.2.5 [17.9 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 ruby3.3-dev arm64 3.3.8-2 [1045 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 ruby-all-dev arm64 1:3.3+b1 [6496 B] Get: 126 http://deb.debian.org/debian forky/main arm64 gem2deb arm64 2.2.5 [48.0 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 ruby-rd all 0.6.38-5 [62.0 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 rdtool all 0.6.38-5 [42.5 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 ruby-libxml arm64 5.0.5-1 [75.8 kB] Fetched 37.0 MB in 0s (119 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 20022 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.7-1) ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_arm64.deb ... Unpacking python3.13 (3.13.7-1) ... 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Preparing to unpack .../071-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../072-libnet-ssleay-perl_1.94-3_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-3) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../073-libio-socket-ssl-perl_2.095-1_all.deb ... Unpacking libio-socket-ssl-perl (2.095-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../074-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 .../075-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 .../076-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 .../077-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../078-libwww-perl_6.78-1_all.deb ... Unpacking libwww-perl (6.78-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../079-patchutils_0.4.2-1+b1_arm64.deb ... Unpacking patchutils (0.4.2-1+b1) ... Selecting previously unselected package rsopv. Preparing to unpack .../080-rsopv_0.6.4-1_arm64.deb ... Unpacking rsopv (0.6.4-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../081-wdiff_1.2.2-9_arm64.deb ... Unpacking wdiff (1.2.2-9) ... Selecting previously unselected package devscripts. Preparing to unpack .../082-devscripts_2.25.19_all.deb ... Unpacking devscripts (2.25.19) ... Selecting previously unselected package sgml-base. Preparing to unpack .../083-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../084-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../085-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../086-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../087-libosp5_1.5.2-15.2_arm64.deb ... Unpacking libosp5 (1.5.2-15.2) ... Selecting previously unselected package opensp. Preparing to unpack .../088-opensp_1.5.2-15.2_arm64.deb ... Unpacking opensp (1.5.2-15.2) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../089-docbook-to-man_1%3a2.0.0-49_arm64.deb ... Unpacking docbook-to-man (1:2.0.0-49) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../090-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package ruby-csv. Preparing to unpack .../091-ruby-csv_3.3.4-1_all.deb ... Unpacking ruby-csv (3.3.4-1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../092-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../093-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-ruby2-keywords. Preparing to unpack .../094-ruby-ruby2-keywords_0.0.5-1_all.deb ... Unpacking ruby-ruby2-keywords (0.0.5-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../095-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../096-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../097-libyaml-0-2_0.2.5-2_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-2) ... Selecting previously unselected package libruby3.3:arm64. Preparing to unpack .../098-libruby3.3_3.3.8-2_arm64.deb ... Unpacking libruby3.3:arm64 (3.3.8-2) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../099-ruby3.3_3.3.8-2_arm64.deb ... Unpacking ruby3.3 (3.3.8-2) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../100-libruby_1%3a3.3+b1_arm64.deb ... Unpacking libruby:arm64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../101-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../102-ruby_1%3a3.3+b1_arm64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package rake. Preparing to unpack .../103-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../104-ruby-minitest_5.25.4-3_all.deb ... Unpacking ruby-minitest (5.25.4-3) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../105-ruby-power-assert_2.0.3-1_all.deb ... Unpacking ruby-power-assert (2.0.3-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../106-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../107-gem2deb-test-runner_2.2.5_arm64.deb ... Unpacking gem2deb-test-runner (2.2.5) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../108-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../109-libgmp-dev_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package ruby3.3-dev:arm64. Preparing to unpack .../110-ruby3.3-dev_3.3.8-2_arm64.deb ... Unpacking ruby3.3-dev:arm64 (3.3.8-2) ... Selecting previously unselected package ruby-all-dev:arm64. Preparing to unpack .../111-ruby-all-dev_1%3a3.3+b1_arm64.deb ... Unpacking ruby-all-dev:arm64 (1:3.3+b1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../112-gem2deb_2.2.5_arm64.deb ... Unpacking gem2deb (2.2.5) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../113-ruby-rd_0.6.38-5_all.deb ... Unpacking ruby-rd (0.6.38-5) ... Selecting previously unselected package rdtool. Preparing to unpack .../114-rdtool_0.6.38-5_all.deb ... Unpacking rdtool (0.6.38-5) ... Selecting previously unselected package ruby-libxml:arm64. Preparing to unpack .../115-ruby-libxml_5.0.5-1_arm64.deb ... Unpacking ruby-libxml:arm64 (5.0.5-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up wdiff (1.2.2-9) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up bsdextrautils (2.41.2-1) ... Setting up libgpg-error0:arm64 (1.55-2) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.46-5) ... 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 libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.27) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:arm64 (1.11.2-2) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up libosp5 (1.5.2-15.2) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Sep 29 12:43:23 UTC 2025. Universal Time is now: Mon Sep 29 12:43:23 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ruby-minitest (5.25.4-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20240727.1) ... Setting up rsopv (0.6.4-1) ... update-alternatives: using /usr/bin/rsopv to provide /usr/bin/sopv (sopv) in auto mode Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.4-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-2) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up autoconf (2.72-3.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.5.3-1) ... Setting up readline-common (8.3-3) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up liburi-perl (5.30-1) ... Setting up ruby-rd (0.6.38-5) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.2-3) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.5.4-5) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15.2) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up patchutils (0.4.2-1+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.4.8-3) ... Setting up libpython3.13-stdlib:arm64 (3.13.7-1) ... Setting up libio-socket-ssl-perl (2.095-1) ... Setting up gpg (2.4.8-3) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.4.8-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.7-1) ... 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 python3 (3.13.7-1) ... Setting up rubygems-integration (1.19) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmodule-runtime-perl (0.018-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.27) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.78-1) ... Setting up libruby3.3:arm64 (3.3.8-2) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up devscripts (2.25.19) ... Setting up ruby3.3-dev:arm64 (3.3.8-2) ... Setting up ruby3.3 (3.3.8-2) ... Setting up libruby:arm64 (1:3.3+b1) ... Setting up ruby-all-dev:arm64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up rdtool (0.6.38-5) ... Setting up ruby-libxml:arm64 (5.0.5-1) ... Setting up gem2deb-test-runner (2.2.5) ... Setting up gem2deb (2.2.5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-to-man (1:2.0.0-49) ... Processing triggers for ca-certificates (20250419) ... 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-2.0.6/ && 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_2.0.6-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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-2.0.6' 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-2.0.6' 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-2.0.6' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/pts1.rb 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/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/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-2.0.6/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.6.gemspec /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-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.6/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: .: (0.000414) test_dbs: .: (0.000130) test_go_ids: .: (0.000113) test_go_terms: .: (0.000108) test_parser: .: (0.000259) test_set_date: .: (0.000120) test_set_desc: .: (0.000108) test_to_str: .: (0.000117) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000494) test_mktmpdir_without_block: .: (0.000325) test_remove_entry_secure: .: (0.000259) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.003102) test_call_command_fork: .: (0.000110) test_call_command_open3: .: (0.002681) test_call_command_popen: .: (0.002177) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.002414) test_call_command_fork: .: (0.000091) test_call_command_open3: .: (0.002204) test_call_command_popen: .: (0.001653) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.001577) test_call_command_fork: .: (0.000090) test_call_command_open3: .: (0.002219) test_call_command_popen: .: (0.002214) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.002508) test_call_command_fork_chdir: .: (0.000218) test_call_command_popen_chdir: .: (0.001370) test_query_command_chdir: .: (0.002306) test_query_command_fork_chdir: .: (0.000217) test_query_command_popen_chdir: .: (0.002362) Bio::FuncTestCommandQuery: test_query_command: .: (0.004473) test_query_command_fork: .: (0.001772) test_query_command_open3: .: (0.003512) test_query_command_popen: .: (0.004932) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000584) test_initialize: .: (0.000208) test_path: .: (0.000131) test_path_after_close: .: (0.000243) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.014581) test_output_fasta: .: (0.004422) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000452) test_accession: .: (0.000143) test_accessions: .: (0.000093) test_comment: .: (0.000072) test_common_name: .: (0.000107) test_definition: .: (0.000094) test_features: .: (0.000213) test_gi: .: (0.000083) test_keywords: .: (0.000074) test_locus: .: (0.000050) test_nid: .: (0.000074) test_organism: .: (0.000092) test_origin: .: (0.000096) test_references: .: (0.000376) test_segment: .: (0.000096) test_source: .: (0.000171) test_taxonomy: .: (0.000100) test_version: .: (0.000088) test_versions: .: (0.000072) Bio::TestAA: test_13: .: (0.000148) test_1n: .: (0.000050) test_name2one: .: (0.000085) test_name2three: .: (0.000051) test_one2name: .: (0.000042) test_one2three: .: (0.000038) test_three2name: .: (0.000036) test_three2one: .: (0.000048) test_to_1_1: .: (0.000039) test_to_1_3: .: (0.000049) test_to_1_name: .: (0.000047) test_to_3_1: .: (0.000038) test_to_3_3: .: (0.000036) test_to_3_name: .: (0.000047) test_to_re: .: (0.000071) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000117) Bio::TestAAindex: test_api: .: (0.000078) test_auto_aax1: .: (0.000180) test_auto_aax2: .: (0.000119) Bio::TestAAindex1: test_author: .: (0.000193) test_comment: .: (0.000120) test_correlation_coefficient: .: (0.000235) test_dblinks: .: (0.000113) test_definition: .: (0.000107) test_entry_id: .: (0.000121) test_index: .: (0.000172) test_journal: .: (0.000129) test_title: .: (0.000114) Bio::TestAAindex2: test_access_A_R: .: (0.000531) test_access_R_A: .: (0.000401) test_author: .: (0.000133) test_cols: .: (0.000114) test_comment: .: (0.000113) test_dblinks: .: (0.000112) test_definition: .: (0.000115) test_entry_id: .: (0.000106) test_journal: .: (0.000123) test_matrix: .: (0.000407) test_matrix_1_2: .: (0.000404) test_matrix_2_2: .: (0.008501) test_matrix_A_R: .: (0.000502) test_matrix_R_A: .: (0.000424) test_matrix_determinant: .: (0.001701) test_matrix_rank: .: (0.001333) test_matrix_transpose: .: (0.000495) test_rows: .: (0.000151) test_title: .: (0.000150) Bio::TestAAindexConstant: test_delimiter: .: (0.000154) test_tagsize: .: (0.000043) Bio::TestAbif: test_complement: .: (0.005621) test_seq: .: (0.005566) test_to_biosequence: .: (0.005955) Bio::TestActsLikeMap: test_mixin: .: (0.000236) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000191) Bio::TestActsLikeMarker: test_mixin: .: (0.000116) Bio::TestAlignment: test_add_seq_no_key: .: (0.000203) test_add_seq_using_seq_with_aaseq_method: .: (0.000082) test_add_seq_using_seq_with_definition_method: .: (0.000054) test_add_seq_using_seq_with_entry_id_method: .: (0.000057) test_add_seq_using_seq_with_naseq_method: .: (0.000065) test_add_seq_using_seq_with_seq_method: .: (0.000064) test_consensus_iupac_gap_modes: .: (0.000274) test_consensus_iupac_missing_char: .: (0.000097) test_consensus_iupac_missing_char_option: .: (0.000106) test_consensus_iupac_no_gaps: .: (0.000150) test_consensus_iupac_of_ambiguous_bases: .: (0.000201) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002585) test_consensus_opt_gap_mode: .: (0.000323) test_consensus_opt_missing_char: .: (0.000195) test_consensus_string_no_gaps: .: (0.000128) test_consensus_threshold_four_sequences: .: (0.000165) test_consensus_threshold_two_sequences: .: (0.000191) test_convert_match: .: (0.000186) test_convert_unmatch: .: (0.000086) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000076) test_convert_unmatch_different_match_char: .: (0.000067) test_convert_unmatch_multiple_sequences: .: (0.000102) test_default_gap_char: .: (0.000041) test_default_gap_regexp_matches_default_gap_char: .: (0.000050) test_default_missing_char: .: (0.000051) test_each_site_equal_length: .: (0.000093) test_each_site_unequal_length: .: (0.000081) test_equals: .: (0.000115) test_match_line_protein: .: (0.000277) test_normalizebang_extends_sequences_with_gaps: .: (0.000083) test_seq_length_is_max_seq_length: .: (0.000053) test_seq_length_when_one_sequence: .: (0.000102) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000059) test_seqclass_when_seqclass_set: .: (0.000063) test_seqclass_when_sequence_used: .: (0.000047) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000046) test_set_and_get_gap_char: .: (0.000042) test_store_cannot_override_key: .: (0.000048) test_store_with_default_keys_and_user_defined_keys: .: (0.000052) test_store_with_nil_key_uses_next_number_for_key: .: (0.000045) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000168) test_alignment_concat: .: (0.000086) test_alignment_length: .: (0.000041) test_alignment_lstrip!: .: (0.000097) test_alignment_lstrip_nil: .: (0.000131) test_alignment_normalize!: .: (0.000053) test_alignment_rstrip!: .: (0.000126) test_alignment_rstrip_nil: .: (0.000054) test_alignment_site: .: (0.000054) test_alignment_slice: .: (0.007794) test_alignment_strip!: .: (0.000162) test_alignment_strip_nil: .: (0.000074) test_alignment_subseq: .: (0.000191) test_alignment_window: .: (0.000058) test_collect_each_site: .: (0.000097) test_consensus_each_site_default: .: (0.000098) test_consensus_each_site_gap_mode_1: .: (0.000091) test_consensus_each_site_gap_mode_minus1: .: (0.000091) test_consensus_iupac: .: (0.000238) test_consensus_string_default: .: (0.000097) test_consensus_string_half: .: (0.000075) test_convert_match: .: (0.000084) test_convert_unmatch: .: (0.000091) test_each_seq: .: (0.000060) test_each_site: .: (0.000103) test_each_site_step: .: (0.000066) test_each_window: .: (0.000099) test_match_line: .: (0.000596) test_match_line_amino: .: (0.000981) test_match_line_nuc: .: (0.000107) test_private_alignment_site: .: (0.000066) test_remove_all_gaps!: .: (0.000077) test_seqclass: .: (0.000057) test_seqclass=: .: (0.000073) test_seqclass_default: .: (0.000185) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002267) test_determine_seq_method: .: (0.012404) test_entries: .: (0.002963) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.001581) test_avoid_same_name_numbering: .: (0.000176) test_clustal_have_same_name_true: .: (0.002910) test_have_same_name_false: .: (0.000113) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000947) test_gap_char_default: .: (0.000074) test_gap_char_never_nil: .: (0.000043) test_gap_regexp: .: (0.000045) test_gap_regexp=: .: (0.001352) test_gap_regexp_never_nil: .: (0.001169) test_get_all_property_default: .: (0.001607) test_get_all_property_nodefault: .: (0.001200) test_is_gap_default_false: .: (0.001257) test_is_gap_default_true: .: (0.001093) test_is_gap_nodefault_false: .: (0.001427) test_is_gap_nodefault_true: .: (0.001999) test_missing_char=: .: (0.000685) test_missing_char_default: .: (0.001429) test_missing_char_never_nil: .: (0.000052) test_seqclass=: .: (0.000061) test_seqclass_default: .: (0.000045) test_seqclass_never_nil: .: (0.000041) test_set_all_property: .: (0.000062) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000524) test_consensus_string_50percent: .: (0.000075) test_consensus_string_50percent_nil: .: (0.000057) test_consensus_string_default: .: (0.000045) test_consensus_string_default_nil: .: (0.000046) test_has_gap_false: .: (0.000062) test_has_gap_true: .: (0.000044) test_match_line_amino_100percent: .: (0.000072) test_match_line_amino_missing: .: (0.000100) test_match_line_amino_strong: .: (0.000066) test_match_line_amino_weak: .: (0.000502) test_match_line_nuc_100percent: .: (0.000092) test_match_line_nuc_missing: .: (0.000075) test_remove_gaps!: .: (0.000057) test_remove_gaps_bang_not_removed: .: (0.000045) Bio::TestAtomFinder: test_atoms: .: (0.012661) test_each_atom: .: (0.000139) test_find_atom: .: (0.000221) Bio::TestBioFastaDefline: test_acc_version: .: (0.000352) test_accession: .: (0.000276) test_accessions: .: (0.000206) test_description: .: (0.000165) test_descriptions: .: (0.000160) test_entry_id: .: (0.000152) test_get: .: (0.000184) test_get_all_by_type: .: (0.000163) test_get_by_type: .: (0.000155) test_gi: .: (0.000133) test_id_strings: .: (0.000377) test_locus: .: (0.000136) test_method_missing: .: (0.000191) test_to_s: .: (0.000189) test_words: .: (0.000408) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000651) test_goid2term: .: (0.000227) test_parse_goids: .: (0.000210) Bio::TestBioGenBank: test_basecount: .: (0.000289) test_circular: .: (0.000164) test_classification: .: (0.000199) test_date: .: (0.000168) test_date_modified: .: (0.000484) test_division: .: (0.000174) test_each_cds_feature: .: (0.000477) test_each_cds_qualifiers: .: (0.005326) test_each_gene: .: (0.000586) test_entry_id: .: (0.000179) test_length: .: (0.000153) test_locus_circular: .: (0.000199) test_locus_class: .: (0.000233) test_locus_date: .: (0.000179) test_locus_division: .: (0.000166) test_locus_entry_id: .: (0.000171) test_locus_length: .: (0.000257) test_locus_natype: .: (0.000161) test_locus_strand: .: (0.000158) test_natype: .: (0.000136) test_seq: .: (0.000188) test_seq_len: .: (0.000168) test_strand: .: (0.000139) test_strandedness: .: (0.000147) test_to_biosequence: .: (0.001656) Bio::TestBioGenPept: test_circular: .: (0.000297) test_date: .: (0.000142) test_dbsource: .: (0.000112) test_division: .: (0.000109) test_entry_id: .: (0.000104) test_length: .: (0.000102) test_locus: .: (0.000107) test_seq: .: (0.000131) test_seq_len: .: (0.000116) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000874) test_aaseq: .: (0.000210) test_chromosome: .: (0.000143) test_codon_usage: .: (0.000219) test_cu_list: .: (0.000117) test_dblinks_as_hash: .: (0.000156) test_dblinks_as_strings: .: (0.000124) test_definition: .: (0.000138) test_division: .: (0.000161) test_eclinks: .: (0.000163) test_entry: .: (0.000126) test_entry_id: .: (0.000115) test_gbposition: .: (0.000149) test_gene: .: (0.000146) test_genes: .: (0.000125) test_keggclass: .: (0.000143) test_keggclasses: .: (0.000153) test_locations: .: (0.000262) test_motifs_as_hash: .: (0.000189) test_motifs_as_strings: .: (0.000122) test_name: .: (0.000128) test_names_as_array: .: (0.000374) test_new: .: (0.000136) test_ntlen: .: (0.000183) test_ntseq: .: (0.000215) test_organism: .: (0.000122) test_orthologs_as_hash: .: (0.000150) test_orthologs_as_strings: .: (0.000112) test_pathway: .: (0.000138) test_pathway_after_pathways_as_strings: .: (0.000186) test_pathway_before_pathways_as_strings: .: (0.000174) test_pathways_as_hash: .: (0.000142) test_pathways_as_strings: .: (0.000115) test_position: .: (0.000139) test_structure: .: (0.000155) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000841) test_comment: .: (0.000248) test_data_source: .: (0.000226) test_definition: .: (0.000212) test_disease: .: (0.000206) test_entry_id: .: (0.000199) test_lineage: .: (0.000222) test_nalen: .: (0.000211) test_name: .: (0.000200) test_new: .: (0.000226) test_num_gene: .: (0.000207) test_num_rna: .: (0.000201) test_original_databases: .: (0.000247) test_original_db: .: (0.000212) test_plasmids: .: (0.000197) test_references: .: (0.001736) test_statistics: .: (0.000250) test_taxid: .: (0.000228) test_taxonomy: .: (0.000232) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000355) test_comment: .: (0.000275) test_data_source: .: (0.000147) test_definition: .: (0.000135) test_disease: .: (0.000119) test_entry_id: .: (0.005620) test_lineage: .: (0.000436) test_nalen: .: (0.000155) test_name: .: (0.000144) test_new: .: (0.000140) test_num_gene: .: (0.000132) test_num_rna: .: (0.000129) test_original_databases: .: (0.000157) test_original_db: .: (0.000151) test_plasmids: .: (0.000227) test_references: .: (0.000292) test_statistics: .: (0.000159) test_taxid: .: (0.000646) test_taxonomy: .: (0.000312) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000314) test_compounds_as_strings: .: (0.000133) test_dblinks_as_hash: .: (0.000108) test_dblinks_as_strings: .: (0.000096) test_description: .: (0.000128) test_diseases_as_hash: .: (0.000107) test_diseases_as_strings: .: (0.000095) test_entry_id: .: (0.000117) test_enzymes_as_strings: .: (0.000115) test_genes_as_hash: .: (0.000102) test_genes_as_strings: .: (0.000331) test_keggclass: .: (0.000163) test_ko_pathway: .: (0.000112) test_modules_as_hash: .: (0.000118) test_modules_as_strings: .: (0.000100) test_name: .: (0.000129) test_new: .: (0.000129) test_organism: .: (0.000115) test_orthologs_as_hash: .: (0.000100) test_orthologs_as_strings: .: (0.000090) test_pathways_as_hash: .: (0.000105) test_pathways_as_strings: .: (0.000095) test_reactions_as_hash: .: (0.000093) test_reactions_as_strings: .: (0.000090) test_references: .: (0.000094) test_rel_pathways_as_hash: .: (0.000122) test_rel_pathways_as_strings: .: (0.000329) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000385) test_compounds_as_strings: .: (0.000181) test_dblinks_as_hash: .: (0.000129) test_dblinks_as_strings: .: (0.000114) test_description: .: (0.000129) test_diseases_as_hash: .: (0.000127) test_diseases_as_strings: .: (0.000115) test_entry_id: .: (0.000128) test_enzymes_as_strings: .: (0.000137) test_genes_as_hash: .: (0.000178) test_genes_as_strings: .: (0.000144) test_keggclass: .: (0.000133) test_ko_pathway: .: (0.000353) test_modules_as_hash: .: (0.000132) test_modules_as_strings: .: (0.000113) test_name: .: (0.000125) test_new: .: (0.000129) test_organism: .: (0.000125) test_orthologs_as_hash: .: (0.000416) test_orthologs_as_strings: .: (0.000116) test_pathways_as_hash: .: (0.000118) test_pathways_as_strings: .: (0.000108) test_reactions_as_hash: .: (0.000105) test_reactions_as_strings: .: (0.000099) test_references: .: (0.000105) test_rel_pathways_as_hash: .: (0.000134) test_rel_pathways_as_strings: .: (0.000118) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000246) test_compounds_as_strings: .: (0.000110) test_dblinks_as_hash: .: (0.000096) test_dblinks_as_strings: .: (0.000087) test_description: .: (0.000136) test_diseases_as_hash: .: (0.000102) test_diseases_as_strings: .: (0.000211) test_entry_id: .: (0.000128) test_enzymes_as_strings: .: (0.000111) test_genes_as_hash: .: (0.000101) test_genes_as_strings: .: (0.000091) test_keggclass: .: (0.000111) test_ko_pathway: .: (0.000100) test_modules_as_hash: .: (0.000091) test_modules_as_strings: .: (0.000085) test_name: .: (0.000101) test_new: .: (0.000105) test_organism: .: (0.000099) test_orthologs_as_hash: .: (0.000136) test_orthologs_as_strings: .: (0.000110) test_pathways_as_hash: .: (0.000099) test_pathways_as_strings: .: (0.000091) test_reactions_as_hash: .: (0.000091) test_reactions_as_strings: .: (0.000088) test_references: .: (0.000087) test_rel_pathways_as_hash: .: (0.000101) test_rel_pathways_as_strings: .: (0.000097) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000251) test_compounds_as_strings: .: (0.000116) test_dblinks_as_hash: .: (0.000124) test_dblinks_as_strings: .: (0.000110) test_description: .: (0.000203) test_diseases_as_hash: .: (0.000143) test_diseases_as_strings: .: (0.000121) test_entry_id: .: (0.000129) test_enzymes_as_strings: .: (0.000107) test_genes_as_hash: .: (0.000107) test_genes_as_strings: .: (0.000103) test_keggclass: .: (0.000129) test_ko_pathway: .: (0.000121) test_modules_as_hash: .: (0.000168) test_modules_as_strings: .: (0.000125) test_name: .: (0.000121) test_new: .: (0.000127) test_organism: .: (0.000127) test_orthologs_as_hash: .: (0.000109) test_orthologs_as_strings: .: (0.000105) test_pathways_as_hash: .: (0.000122) test_pathways_as_strings: .: (0.000109) test_reactions_as_hash: .: (0.000108) test_reactions_as_strings: .: (0.000103) test_references: .: (0.000482) test_rel_pathways_as_hash: .: (0.000175) test_rel_pathways_as_strings: .: (0.000125) Bio::TestBioKeggDRUG: test_activity: .: (0.000294) test_comment: .: (0.000144) test_dblinks_as_hash: .: (0.005874) test_dblinks_as_strings: .: (0.000452) test_entry_id: .: (0.000179) test_formula: .: (0.000143) test_kcf: .: (0.000124) test_mass: .: (0.000140) test_name: .: (0.000158) test_names: .: (0.000160) test_pathways_as_hash: .: (0.000165) test_pathways_as_strings: .: (0.000138) test_products: .: (0.000151) test_remark: .: (0.000169) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000702) test_composition: .: (0.000296) test_compounds: .: (0.000155) test_dblinks_as_hash: .: (0.000625) test_dblinks_as_strings: .: (0.000205) test_entry_id: .: (0.000150) test_enzymes: .: (0.000152) test_kcf: .: (0.000117) test_keggclass: .: (0.000464) test_mass: .: (0.000160) test_name: .: (0.000125) test_orthologs_as_hash: .: (0.000187) test_orthologs_as_strings: .: (0.000174) test_pathways_as_hash: .: (0.000151) test_pathways_as_strings: .: (0.000121) test_reactions: .: (0.000137) test_references: .: (0.000192) test_remark: .: (0.000143) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000243) test_composition: .: (0.000427) test_compounds: .: (0.000139) test_dblinks_as_hash: .: (0.000143) test_dblinks_as_strings: .: (0.000108) test_entry_id: .: (0.000110) test_enzymes: .: (0.000104) test_kcf: .: (0.000092) test_keggclass: .: (0.000109) test_mass: .: (0.000109) test_name: .: (0.000426) test_orthologs_as_hash: .: (0.000122) test_orthologs_as_strings: .: (0.000091) test_pathways_as_hash: .: (0.000095) test_pathways_as_strings: .: (0.000088) test_reactions: .: (0.000102) test_references: .: (0.000122) test_remark: .: (0.000112) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000389) test_compounds_as_strings: .: (0.000196) test_dblinks_as_hash: .: (0.000148) test_dblinks_as_strings: .: (0.000131) test_description: .: (0.000138) test_diseases_as_hash: .: (0.000151) test_diseases_as_strings: .: (0.000135) test_entry_id: .: (0.000142) test_enzymes_as_strings: .: (0.000124) test_genes_as_hash: .: (0.000127) test_genes_as_strings: .: (0.000124) test_keggclass: .: (0.000139) test_ko_pathway: .: (0.000142) test_modules_as_hash: .: (0.000191) test_modules_as_strings: .: (0.000154) test_name: .: (0.000146) test_new: .: (0.000143) test_organism: .: (0.000136) test_orthologs_as_hash: .: (0.000130) test_orthologs_as_strings: .: (0.000115) test_pathways_as_hash: .: (0.000169) test_pathways_as_strings: .: (0.000141) test_reactions_as_hash: .: (0.000333) test_reactions_as_strings: .: (0.000244) test_references: .: (0.000366) test_rel_pathways_as_hash: .: (0.000244) test_rel_pathways_as_strings: .: (0.000179) Bio::TestBioLITDB: test_author: .: (0.000285) test_entry_id: .: (0.000112) test_field: .: (0.000106) test_journal: .: (0.000100) test_keyword: .: (0.000123) test_reference: .: (0.000235) test_title: .: (0.000135) test_volume: .: (0.000108) Bio::TestBioNBRF: test_aalen: .: (0.000232) test_aaseq: .: (0.000092) test_entry: .: (0.000077) test_length: .: (0.005528) test_nalen: .: (0.000487) test_naseq: .: (0.000133) test_seq: .: (0.000107) test_seq_class: .: (0.000093) test_to_nbrf: .: (0.000116) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000257) test_to_newick_format_leaf: .: (0.000180) test_to_newick_format_leaf_NHX: .: (0.000149) Bio::TestBl2seqReport: test_db_len: .: (0.000553) test_db_num: .: (0.000783) test_new: .: (0.000247) test_undefed_methods: .: (0.000704) test_undefed_methods_for_iteration: .: (0.000650) Bio::TestBl2seqReportConstants: test_rs: .: (0.000173) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000284) test_hits: .: (0.000203) Bio::TestBlast: test_blast_reports_format0: .: (0.004744) test_blast_reports_format0_with_block: .: (0.000893) test_blast_reports_format7: .: (0.043943) test_blast_reports_format7_with_block: .: (0.007277) test_blast_reports_format7_with_parser: .: (0.006789) test_blast_reports_format7_with_parser_with_block: .: (0.009845) test_blast_reports_format8: .: (0.000737) test_blast_reports_format8_with_block: .: (0.000395) test_blast_reports_format8_with_parser: .: (0.000200) test_blast_reports_format8_with_parser_with_block: .: (0.000162) test_blast_reports_xml: .: (0.007367) test_blast_reports_xml_with_block: .: (0.006511) test_blastll: .: (0.000173) test_db: .: (0.000084) test_exec_genomenet: .: (0.000066) test_exec_local: .: (0.000061) test_exec_ncbi: .: (0.000063) test_filter: .: (0.000074) test_format: .: (0.000081) test_make_command_line: .: (0.000274) test_make_command_line_2: .: (0.000205) test_matrix: .: (0.000074) test_new: .: (0.000174) test_new_opt_string: .: (0.000136) test_option: .: (0.000092) test_option_set: .: (0.000132) test_option_set_m0: .: (0.000109) test_options: .: (0.000071) test_output: .: (0.000070) test_parse_result: .: (0.006057) test_parser: .: (0.000160) test_program: .: (0.000089) test_query: .: (0.000077) test_self_local: .: (0.000136) test_self_remote: .: (0.001427) test_server: .: (0.000139) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000276) test_delete: .: (0.000186) test_equal_equal: .: (0.000199) test_get: .: (0.000287) test_make_command_line_options: .: (0.000175) test_normalize!: .: (0.000111) test_parse: .: (0.000126) test_set: .: (0.000324) Bio::TestBlastReport: test_db: .: (0.011096) test_db_len: .: (0.006492) test_db_num: .: (0.006635) test_each_hit: .: (0.009592) test_each_iteration: .: (0.006641) test_eff_space: .: (0.006227) test_entrez_query: .: (0.005943) test_entropy: .: (0.009294) test_expect: .: (0.006473) test_filter: .: (0.006336) test_gap_extend: .: (0.008645) test_gap_open: .: (0.006577) test_hits: .: (0.006347) test_hsp_len: .: (0.005945) test_inclusion: .: (0.008634) test_iterations: .: (0.006421) test_kappa: .: (0.006240) test_lambda: .: (0.008223) test_matrix: .: (0.006424) test_message: .: (0.006276) test_parameters: .: (0.007483) test_pattern: .: (0.007365) test_program: .: (0.006194) test_query_def: .: (0.006278) test_query_id: .: (0.008509) test_query_len: .: (0.006705) test_reference: .: (0.006626) test_sc_match: .: (0.007664) test_sc_mismatch: .: (0.007624) test_statistics: .: (0.006544) test_version: .: (0.006301) Bio::TestBlastReportDefault: test_db: .: (0.000641) test_db_len: .: (0.000448) test_db_num: .: (0.000400) test_each_hit: .: (0.000395) test_each_iteration: .: (0.000343) test_eff_space: .: (0.000445) test_entropy: .: (0.000437) test_expect: .: (0.000417) test_gap_extend: .: (0.000398) test_gap_open: .: (0.000394) test_gapped_entropy: .: (0.000370) test_gapped_kappa: .: (0.000360) test_gapped_lambda: .: (0.000361) test_hits: .: (0.000415) test_iterations: .: (0.000385) test_kappa: .: (0.000375) test_lambda: .: (0.000355) test_matrix: .: (0.000425) test_message: .: (0.000333) test_pattern: .: (0.000327) test_program: .: (0.000362) test_query_def: .: (0.000414) test_query_len: .: (0.000361) test_reference: .: (0.000402) test_sc_match: .: (0.000413) test_sc_mismatch: .: (0.000399) test_version: .: (0.000343) Bio::TestBlastReportHit: test_Hit_accession: .: (0.009684) test_Hit_bit_score: .: (0.006658) test_Hit_definition: .: (0.006436) test_Hit_evalue: .: (0.009021) test_Hit_hit_id: .: (0.006751) test_Hit_hsps: .: (0.006514) test_Hit_identity: .: (0.009038) test_Hit_lap_at: .: (0.006822) test_Hit_len: .: (0.006462) test_Hit_midline: .: (0.007988) test_Hit_num: .: (0.007687) test_Hit_overlap: .: (0.006569) test_Hit_query_def: .: (0.006516) test_Hit_query_end: .: (0.008461) test_Hit_query_id: .: (0.006796) test_Hit_query_len: .: (0.006573) test_Hit_query_seq: .: (0.008708) test_Hit_query_start: .: (0.006965) test_Hit_taeget_def: .: (0.006525) test_Hit_target_end: .: (0.007665) test_Hit_target_id: .: (0.007742) test_Hit_target_len: .: (0.006572) test_Hit_target_seq: .: (0.006379) test_Hit_target_start: .: (0.008530) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001046) test_Hit_definition: .: (0.000537) test_Hit_evalue: .: (0.000496) test_Hit_hsps: .: (0.000413) test_Hit_identity: .: (0.000413) test_Hit_lap_at: .: (0.000674) test_Hit_len: .: (0.000432) test_Hit_midline: .: (0.000517) test_Hit_overlap: .: (0.000401) test_Hit_query_end: .: (0.000461) test_Hit_query_seq: .: (0.000475) test_Hit_query_start: .: (0.000607) test_Hit_taeget_def: .: (0.000373) test_Hit_target_end: .: (0.000494) test_Hit_target_id: .: (0.000412) test_Hit_target_len: .: (0.000367) test_Hit_target_seq: .: (0.000648) test_Hit_target_start: .: (0.000454) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.020172) test_Hit_bit_score: .: (0.019922) test_Hit_definition: .: (0.020452) test_Hit_evalue: .: (0.020340) test_Hit_hit_id: .: (0.019690) test_Hit_hsps: .: (0.019599) test_Hit_identity: .: (0.019682) test_Hit_lap_at: .: (0.019602) test_Hit_len: .: (0.019881) test_Hit_midline: .: (0.019872) test_Hit_num: .: (0.019761) test_Hit_overlap: .: (0.019788) test_Hit_query_def: .: (0.019821) test_Hit_query_end: .: (0.019678) test_Hit_query_id: .: (0.019829) test_Hit_query_len: .: (0.019915) test_Hit_query_seq: .: (0.019787) test_Hit_query_start: .: (0.032428) test_Hit_taeget_def: .: (0.029249) test_Hit_target_end: .: (0.020234) test_Hit_target_id: .: (0.020009) test_Hit_target_len: .: (0.019818) test_Hit_target_seq: .: (0.020033) test_Hit_target_start: .: (0.019825) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.020018) test_Hit_bit_score: .: (0.019791) test_Hit_definition: .: (0.019789) test_Hit_evalue: .: (0.019803) test_Hit_hit_id: .: (0.019801) test_Hit_hsps: .: (0.019801) test_Hit_identity: .: (0.019859) test_Hit_lap_at: .: (0.019746) test_Hit_len: .: (0.019719) test_Hit_midline: .: (0.019652) test_Hit_num: .: (0.019636) test_Hit_overlap: .: (0.019936) test_Hit_query_def: .: (0.019767) test_Hit_query_end: .: (0.019759) test_Hit_query_id: .: (0.019605) test_Hit_query_len: .: (0.019898) test_Hit_query_seq: .: (0.019847) test_Hit_query_start: .: (0.019717) test_Hit_taeget_def: .: (0.019561) test_Hit_target_end: .: (0.019642) test_Hit_target_id: .: (0.037882) test_Hit_target_len: .: (0.037754) test_Hit_target_seq: .: (0.040306) test_Hit_target_start: .: (0.040236) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.017106) test_Hit_bit_score: .: (0.013216) test_Hit_definition: .: (0.012319) test_Hit_evalue: .: (0.018160) test_Hit_hit_id: .: (0.017647) test_Hit_hsps: .: (0.011804) test_Hit_identity: .: (0.017158) test_Hit_lap_at: .: (0.014944) test_Hit_len: .: (0.010596) test_Hit_midline: .: (0.019128) test_Hit_num: .: (0.013331) test_Hit_overlap: .: (0.011433) test_Hit_query_def: .: (0.019055) test_Hit_query_end: .: (0.015056) test_Hit_query_id: .: (0.018468) test_Hit_query_len: .: (0.019800) test_Hit_query_seq: .: (0.013098) test_Hit_query_start: .: (0.010637) test_Hit_taeget_def: .: (0.018110) test_Hit_target_end: .: (0.013354) test_Hit_target_id: .: (0.011366) test_Hit_target_len: .: (0.016015) test_Hit_target_seq: .: (0.011582) test_Hit_target_start: .: (0.013427) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000366) test_Hit_bit_score: .: (0.006048) test_Hit_definition: .: (0.000298) test_Hit_evalue: .: (0.000179) test_Hit_hit_id: .: (0.000166) test_Hit_hsps: .: (0.000145) test_Hit_identity: .: (0.000144) test_Hit_lap_at: .: (0.000158) test_Hit_len: .: (0.000136) test_Hit_midline: .: (0.000137) test_Hit_num: .: (0.000148) test_Hit_overlap: .: (0.000147) test_Hit_query_def: .: (0.000150) test_Hit_query_end: .: (0.000135) test_Hit_query_id: .: (0.000136) test_Hit_query_len: .: (0.000135) test_Hit_query_seq: .: (0.000127) test_Hit_query_start: .: (0.000138) test_Hit_taeget_def: .: (0.000143) test_Hit_target_end: .: (0.000194) test_Hit_target_id: .: (0.000151) test_Hit_target_len: .: (0.000135) test_Hit_target_seq: .: (0.000136) test_Hit_target_start: .: (0.000140) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.017900) test_Hsp_bit_score: .: (0.012900) test_Hsp_density: .: (0.015960) test_Hsp_evalue: .: (0.017442) test_Hsp_gaps: .: (0.014086) test_Hsp_hit_frame: .: (0.015705) test_Hsp_hit_from: .: (0.016593) test_Hsp_hit_to: .: (0.010952) test_Hsp_hseq: .: (0.015699) test_Hsp_identity: .: (0.017339) test_Hsp_midline: .: (0.015223) test_Hsp_mismatch_count: .: (0.010844) test_Hsp_num: .: (0.016913) test_Hsp_pattern_from: .: (0.014971) test_Hsp_pattern_to: .: (0.010731) test_Hsp_percent_identity: .: (0.019103) test_Hsp_positive: .: (0.013364) test_Hsp_qseq: .: (0.015931) test_Hsp_query_frame: .: (0.017344) test_Hsp_query_from: .: (0.012644) test_Hsp_query_to: .: (0.012749) test_Hsp_score: .: (0.018025) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000967) test_Hsp_bit_score: .: (0.000473) test_Hsp_evalue: .: (0.000433) test_Hsp_gaps: .: (0.003885) test_Hsp_hit_frame: .: (0.000616) test_Hsp_hit_from: .: (0.000528) test_Hsp_hit_to: .: (0.000486) test_Hsp_hseq: .: (0.000486) test_Hsp_identity: .: (0.000392) test_Hsp_midline: .: (0.000483) test_Hsp_percent_identity: .: (0.004146) test_Hsp_positive: .: (0.000588) test_Hsp_qseq: .: (0.000546) test_Hsp_query_frame: .: (0.000406) test_Hsp_query_from: .: (0.000467) test_Hsp_query_to: .: (0.000445) test_Hsp_score: .: (0.000528) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.038618) test_Hsp_bit_score: .: (0.043414) test_Hsp_density: .: (0.041761) test_Hsp_evalue: .: (0.040850) test_Hsp_gaps: .: (0.038092) test_Hsp_hit_frame: .: (0.040009) test_Hsp_hit_from: .: (0.040690) test_Hsp_hit_to: .: (0.040706) test_Hsp_hseq: .: (0.042060) test_Hsp_identity: .: (0.028424) test_Hsp_midline: .: (0.019901) test_Hsp_mismatch_count: .: (0.020075) test_Hsp_num: .: (0.020056) test_Hsp_pattern_from: .: (0.020216) test_Hsp_pattern_to: .: (0.020027) test_Hsp_percent_identity: .: (0.019794) test_Hsp_positive: .: (0.019846) test_Hsp_qseq: .: (0.019876) test_Hsp_query_frame: .: (0.019933) test_Hsp_query_from: .: (0.019951) test_Hsp_query_to: .: (0.019967) test_Hsp_score: .: (0.019981) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.020145) test_Hsp_bit_score: .: (0.019809) test_Hsp_density: .: (0.019846) test_Hsp_evalue: .: (0.019689) test_Hsp_gaps: .: (0.019622) test_Hsp_hit_frame: .: (0.019652) test_Hsp_hit_from: .: (0.019800) test_Hsp_hit_to: .: (0.019723) test_Hsp_hseq: .: (0.019651) test_Hsp_identity: .: (0.019751) test_Hsp_midline: .: (0.019851) test_Hsp_mismatch_count: .: (0.019595) test_Hsp_num: .: (0.019878) test_Hsp_pattern_from: .: (0.019971) test_Hsp_pattern_to: .: (0.020294) test_Hsp_percent_identity: .: (0.041779) test_Hsp_positive: .: (0.030470) test_Hsp_qseq: .: (0.020309) test_Hsp_query_frame: .: (0.020348) test_Hsp_query_from: .: (0.020172) test_Hsp_query_to: .: (0.020153) test_Hsp_score: .: (0.021848) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.009240) test_Hsp_bit_score: .: (0.006981) test_Hsp_density: .: (0.006399) test_Hsp_evalue: .: (0.009113) test_Hsp_gaps: .: (0.007113) test_Hsp_hit_frame: .: (0.006468) test_Hsp_hit_from: .: (0.010019) test_Hsp_hit_to: .: (0.007081) test_Hsp_hseq: .: (0.006387) test_Hsp_identity: .: (0.009021) test_Hsp_midline: .: (0.007162) test_Hsp_mismatch_count: .: (0.006566) test_Hsp_num: .: (0.009118) test_Hsp_pattern_from: .: (0.007034) test_Hsp_pattern_to: .: (0.006424) test_Hsp_percent_identity: .: (0.008929) test_Hsp_positive: .: (0.007124) test_Hsp_qseq: .: (0.006513) test_Hsp_query_frame: .: (0.009049) test_Hsp_query_from: .: (0.007154) test_Hsp_query_to: .: (0.006485) test_Hsp_score: .: (0.008937) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000594) test_Hsp_bit_score: .: (0.000223) test_Hsp_density: .: (0.000195) test_Hsp_evalue: .: (0.000188) test_Hsp_gaps: .: (0.000187) test_Hsp_hit_frame: .: (0.000231) test_Hsp_hit_from: .: (0.000188) test_Hsp_hit_to: .: (0.000203) test_Hsp_hseq: .: (0.000185) test_Hsp_identity: .: (0.000177) test_Hsp_midline: .: (0.000179) test_Hsp_mismatch_count: .: (0.000198) test_Hsp_num: .: (0.000184) test_Hsp_pattern_from: .: (0.000173) test_Hsp_pattern_to: .: (0.000173) test_Hsp_percent_identity: .: (0.000199) test_Hsp_positive: .: (0.000192) test_Hsp_qseq: .: (0.000169) test_Hsp_query_frame: .: (0.000169) test_Hsp_query_from: .: (0.000198) test_Hsp_query_to: .: (0.000177) test_Hsp_score: .: (0.000202) Bio::TestBlastReportIteration: test_hits: .: (0.006984) test_message: .: (0.008317) test_num: .: (0.007892) test_statistics: .: (0.006997) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000680) test_message: .: (0.000405) test_num: .: (0.000372) Bio::TestBlastReportIterationMulti: test_each: .: (0.020530) test_hits: .: (0.020688) test_message: .: (0.020989) test_num: .: (0.020503) test_query_def: .: (0.021532) test_query_id: .: (0.020609) test_query_len: .: (0.020899) test_statistics: .: (0.020917) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.020815) test_hits: .: (0.023890) test_message: .: (0.021494) test_num: .: (0.021693) test_query_def: .: (0.021133) test_query_id: .: (0.020260) test_query_len: .: (0.020130) test_statistics: .: (0.020053) Bio::TestBlastReportIterationREXML: test_hits: .: (0.008959) test_message: .: (0.006884) test_num: .: (0.006852) test_statistics: .: (0.008778) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000706) test_message: .: (0.000221) test_num: .: (0.000180) test_statistics: .: (0.000215) Bio::TestBlastReportMulti: test_db: .: (0.020800) test_db_len: .: (0.020332) test_db_num: .: (0.020062) test_each_hit: .: (0.021766) test_each_iteration: .: (0.021277) test_eff_space: .: (0.020511) test_entropy: .: (0.020043) test_expect: .: (0.021883) test_filter: .: (0.020906) test_gap_extend: .: (0.020368) test_gap_open: .: (0.020170) test_hits: .: (0.022129) test_hsp_len: .: (0.021051) test_iterations: .: (0.044986) test_kappa: .: (0.034967) test_lambda: .: (0.050168) test_matrix: .: (0.041502) test_message: .: (0.040831) test_parameters: .: (0.050328) test_pattern: .: (0.042364) test_program: .: (0.022861) test_query_def: .: (0.026372) test_query_id: .: (0.024197) test_query_len: .: (0.025383) test_reference: .: (0.025083) test_reports: .: (0.066448) test_statistics: .: (0.023453) test_version: .: (0.024077) Bio::TestBlastReportMultiREXML: test_db: .: (0.024068) test_db_len: .: (0.024339) test_db_num: .: (0.025247) test_each_hit: .: (0.025155) test_each_iteration: .: (0.023660) test_eff_space: .: (0.024141) test_entropy: .: (0.025228) test_expect: .: (0.023859) test_filter: .: (0.024426) test_gap_extend: .: (0.023707) test_gap_open: .: (0.024039) test_hits: .: (0.024119) test_hsp_len: .: (0.025325) test_iterations: .: (0.024861) test_kappa: .: (0.024102) test_lambda: .: (0.024026) test_matrix: .: (0.023658) test_message: .: (0.025837) test_parameters: .: (0.024965) test_pattern: .: (0.024255) test_program: .: (0.023665) test_query_def: .: (0.026538) test_query_id: .: (0.025035) test_query_len: .: (0.024176) test_reference: .: (0.023137) test_reports: .: (0.026464) test_statistics: .: (0.024146) test_version: .: (0.023817) Bio::TestBlastReportREXML: test_db: .: (0.010734) test_db_len: .: (0.008301) test_db_num: .: (0.009943) test_each_hit: .: (0.007966) test_each_iteration: .: (0.007884) test_eff_space: .: (0.010634) test_entrez_query: .: (0.008336) test_entropy: .: (0.010121) test_expect: .: (0.008595) test_filter: .: (0.009198) test_gap_extend: .: (0.009092) test_gap_open: .: (0.007981) test_hits: .: (0.009750) test_hsp_len: .: (0.008266) test_inclusion: .: (0.009984) test_iterations: .: (0.008373) test_kappa: .: (0.006700) test_lambda: .: (0.010384) test_matrix: .: (0.008254) test_message: .: (0.009924) test_parameters: .: (0.008311) test_pattern: .: (0.009096) test_program: .: (0.009105) test_query_def: .: (0.008208) test_query_id: .: (0.010049) test_query_len: .: (0.008440) test_reference: .: (0.010089) test_sc_match: .: (0.008419) test_sc_mismatch: .: (0.007526) test_statistics: .: (0.010721) test_version: .: (0.007931) Bio::TestBlastReportTabular: test_db: .: (0.000432) test_db_len: .: (0.000207) test_db_num: .: (0.000220) test_each_hit: .: (0.000192) test_each_iteration: .: (0.000121) test_eff_space: .: (0.000099) test_entrez_query: .: (0.000101) test_entropy: .: (0.000073) test_expect: .: (0.000065) test_filter: .: (0.000063) test_gap_extend: .: (0.000063) test_gap_open: .: (0.000069) test_hits: .: (0.000071) test_hsp_len: .: (0.000067) test_inclusion: .: (0.000082) test_iterations: .: (0.000073) test_kappa: .: (0.000063) test_lambda: .: (0.000060) test_matrix: .: (0.000069) test_message: .: (0.000069) test_parameters: .: (0.000069) test_pattern: .: (0.000065) test_program: .: (0.000062) test_query_def: .: (0.000073) test_query_id: .: (0.000064) test_query_len: .: (0.000067) test_reference: .: (0.000061) test_sc_match: .: (0.000063) test_sc_mismatch: .: (0.000061) test_statistics: .: (0.000064) test_version: .: (0.000060) Bio::TestChain: test_aaseq: .: (0.000281) test_addLigand: .: (0.000053) test_addResidue: .: (0.000045) test_atom_seq: .: (0.000051) test_comp: .: (0.000075) test_each: .: (0.000050) test_each_heterogen: .: (0.000051) test_each_residue: .: (0.000049) test_get_heterogen_by_id: .: (0.000048) test_get_residue_by_id: .: (0.000048) test_inspect: .: (0.000068) test_rehash: .: (0.000051) test_rehash_heterogens: .: (0.000280) test_rehash_residues: .: (0.000131) test_square_brace: .: (0.000155) test_to_s: .: (0.000159) Bio::TestChainFinder: test_chains: .: (0.002255) test_each_chain: .: (0.000179) test_find_chain: .: (0.000176) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.006812) test_header: .: (0.000667) test_match_line: .: (0.000789) test_sequence0: .: (0.000596) test_sequence1: .: (0.000740) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.005895) test_header: .: (0.000990) test_match_line: .: (0.000810) test_sequence0: .: (0.000787) test_sequence1: .: (0.000736) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.006395) test_header: .: (0.000658) test_match_line: .: (0.000593) test_sequence0: .: (0.002894) test_sequence1: .: (0.000821) Bio::TestCodonTable: test_Tables: .: (0.000316) test_accessor: .: (0.000164) test_definition: .: (0.000108) test_each: .: (0.000142) test_revtrans: .: (0.000190) test_self_accessor: .: (0.000132) test_self_copy: .: (0.000670) test_set_accessor: .: (0.049544) test_start: .: (0.000195) test_start_codon?: .: (0.000174) test_stop: .: (0.000146) test_stop_codon?: .: (0.000148) test_table: .: (0.000115) Bio::TestCodonTableConstants: test_Definitions: .: (0.000267) test_Starts: .: (0.000169) test_Tables: .: (0.000099) test_stops: .: (0.000160) Bio::TestColorScheme: test_buried: .: (0.001004) Bio::TestCommand: test_command_constants: .: (0.000269) test_escape_shell: .: (0.000183) test_escape_shell_unix: .: (0.000122) test_escape_shell_windows: .: (0.002986) test_make_cgi_params_by_array_of_array: .: (0.000557) test_make_cgi_params_by_array_of_hash: .: (0.000348) test_make_cgi_params_by_array_of_string: .: (0.000196) test_make_cgi_params_by_hash_in_string: .: (0.000427) test_make_cgi_params_by_hash_in_symbol: .: (0.000450) test_make_cgi_params_by_string: .: (0.000198) test_make_command_line: .: (0.001477) test_make_command_line_unix: .: (0.000158) test_make_command_line_windows: .: (0.000137) test_safe_command_line_array: .: (0.000175) test_safe_command_line_array_passthrough: .: (0.000137) Bio::TestContingencyTable: test_lite_example: .: (0.080078) Bio::TestDB: test_entry_id: .: (0.000411) test_exists: .: (0.000172) test_fetch: .: (0.000224) test_get: .: (0.000141) test_open: .: (0.000326) test_tags: .: (0.000132) Bio::TestDataType: test_const_like_method: .: (0.000563) test_pdb_achar: .: (0.000283) test_pdb_atom: .: (0.000242) test_pdb_character: .: (0.000279) test_pdb_date: .: (0.000253) test_pdb_idcode: .: (0.000254) test_pdb_integer: .: (0.000151) test_pdb_list: .: (0.000125) test_pdb_lstring: .: (0.000219) test_pdb_real: .: (0.000200) test_pdb_resudue_name: .: (0.000246) test_pdb_slist: .: (0.000134) test_pdb_string: .: (0.000243) test_pdb_stringrj: .: (0.000125) test_pdb_symop: .: (0.000466) test_specification_list: .: (0.000175) Bio::TestEMBL: test_ac: .: (0.000562) test_accession: .: (0.000347) test_cc: .: (0.000308) test_de: .: (0.000350) test_division: .: (0.000356) test_dr: .: (0.000308) test_dt: .: (0.000310) test_dt_created: .: (0.000485) test_dt_iterator: .: (0.000306) test_dt_updated: .: (0.000308) test_each_cds: .: (0.000481) test_each_gene: .: (0.000424) test_entry: .: (0.000364) test_fh: .: (0.000463) test_ft: .: (0.000459) test_ft_accessor: .: (0.000449) test_ft_iterator: .: (0.000467) test_id_line: .: (0.000345) test_id_line_data_class: .: (0.000329) test_id_line_division: .: (0.000475) test_id_line_entry_name: .: (0.000353) test_id_line_iterator: .: (0.000317) test_id_line_molecule_type: .: (0.000312) test_id_line_sequence_length: .: (0.000334) test_kw: .: (0.000335) test_molecule: .: (0.000372) test_oc: .: (0.000399) test_og: .: (0.000330) test_os: .: (0.000551) test_ref: .: (0.000408) test_references: .: (0.000519) test_seq: .: (0.000560) test_sequence_length: .: (0.000363) test_sq: .: (0.000333) test_sq_get: .: (0.000317) test_sv: .: (0.000330) test_version: .: (0.000520) Bio::TestEMBL89: test_ac: .: (0.000519) test_accession: .: (0.000357) test_cc: .: (0.000281) test_de: .: (0.002848) test_division: .: (0.000806) test_dr: .: (0.000343) test_dt: .: (0.000313) test_dt_created: .: (0.000309) test_dt_iterator: .: (0.000259) test_dt_updated: .: (0.000300) test_each_cds: .: (0.000434) test_each_gene: .: (0.000408) test_entry: .: (0.000379) test_fh: .: (0.000318) test_ft: .: (0.000431) test_ft_accessor: .: (0.000415) test_ft_iterator: .: (0.000420) test_id_line: .: (0.000344) test_id_line_data_class: .: (0.000346) test_id_line_division: .: (0.000321) test_id_line_entry_name: .: (0.000292) test_id_line_iterator: .: (0.000361) test_id_line_molecule_type: .: (0.000315) test_id_line_sequence_length: .: (0.000344) test_id_line_sequence_version: .: (0.000341) test_kw: .: (0.000316) test_molecule: .: (0.000329) test_oc: .: (0.000413) test_og: .: (0.000301) test_os: .: (0.004329) test_ref: .: (0.000882) test_references: .: (0.000604) test_seq: .: (0.000575) test_sequence_length: .: (0.000380) test_sq: .: (0.000363) test_sq_get: .: (0.001107) test_sv: .: (0.000716) test_version: .: (0.000434) Bio::TestEMBLAPI: test_ac: .: (0.000368) test_accessions: .: (0.000192) Bio::TestEMBLCommon: test_ac: .: (0.000314) test_accession: .: (0.000133) test_accessions: .: (0.000135) test_de: .: (0.000080) test_definition: .: (0.000062) test_description: .: (0.000143) test_dr: .: (0.000112) test_keywords: .: (0.000121) test_kw: .: (0.000116) test_oc: .: (0.000063) test_og: .: (0.000055) test_os: .: (0.000041) test_ref: .: (0.000042) test_references: .: (0.000037) Bio::TestEMBLDB: test_fetch: .: (0.000274) test_p_entry2hash: .: (0.000040) Bio::TestEMBLToBioSequence: test_classification: .: (0.002958) test_date_created: .: (0.000617) test_date_modified: .: (0.000488) test_definition: .: (0.000408) test_division: .: (0.000399) test_entry_id: .: (0.000450) test_entry_version: .: (0.000571) test_features: .: (0.000540) test_keywords: .: (0.000411) test_molecule_type: .: (0.000408) test_primary_accession: .: (0.000357) test_references: .: (0.000558) test_release_created: .: (0.000383) test_release_modified: .: (0.000397) test_secondary_accessions: .: (0.000376) test_sequence_version: .: (0.000531) test_species: .: (0.000367) test_topology: .: (0.000384) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002855) test_date_created: .: (0.003173) test_date_modified: .: (0.002408) test_definition: .: (0.002361) test_division: .: (0.007327) test_entry_id: .: (0.003453) test_entry_version: .: (0.002825) test_features: .: (0.002862) test_keywords: .: (0.002669) test_molecule_type: .: (0.002605) test_primary_accession: .: (0.002921) test_references: .: (0.002442) test_release_created: .: (0.002418) test_release_modified: .: (0.007781) test_secondary_accessions: .: (0.003680) test_sequence_version: .: (0.002777) test_species: .: (0.002320) test_topology: .: (0.002301) Bio::TestFasta: test_db: .: (0.000241) test_format: .: (0.000080) test_format_arg_integer: .: (0.000099) test_format_arg_str: .: (0.000090) test_ktup: .: (0.000094) test_matrix: .: (0.000088) test_option: .: (0.000143) test_options: .: (0.000090) test_output: .: (0.000074) test_program: .: (0.000085) test_server: .: (0.000085) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000262) test_accession: .: (0.000119) test_accessions: .: (0.000168) test_description: .: (0.000099) test_descriptions: .: (0.000115) test_entry_id: .: (0.000091) test_get_all_by_type: .: (0.000102) test_gi: .: (0.001764) test_id_strings: .: (0.000187) test_list_ids: .: (0.000110) test_locus: .: (0.000979) test_words: .: (0.000154) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000260) test_accession: .: (0.000725) test_accessions: .: (0.000159) test_description: .: (0.000104) test_descriptions: .: (0.000927) test_emb: .: (0.000289) test_entry_id: .: (0.001079) test_get_all_by_type: .: (0.000122) test_get_emb: .: (0.000111) test_gi: .: (0.001662) test_id_strings: .: (0.000162) test_list_ids: .: (0.000827) test_locus: .: (0.000167) test_words: .: (0.000157) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000780) test_accession: .: (0.000116) test_accessions: .: (0.000157) test_description: .: (0.000996) test_descriptions: .: (0.001037) test_entry_id: .: (0.000104) test_get_all_by_type: .: (0.000096) test_gi: .: (0.000400) test_id_strings: .: (0.000148) test_list_ids: .: (0.000102) test_locus: .: (0.000551) test_sp: .: (0.000120) test_words: .: (0.000138) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000320) test_accession: .: (0.001151) test_accessions: .: (0.000148) test_description: .: (0.001902) test_descriptions: .: (0.000162) test_entry_id: .: (0.000122) test_get_all_by_type: .: (0.000182) test_gi: .: (0.000132) test_id_strings: .: (0.001798) test_list_ids: .: (0.000933) test_locus: .: (0.000190) test_words: .: (0.001048) Bio::TestFastaDeflineSce: test_acc_version: .: (0.001133) test_accession: .: (0.001026) test_accessions: .: (0.000123) test_description: .: (0.000943) test_descriptions: .: (0.000189) test_entry_id: .: (0.000115) test_get_all_by_type: .: (0.001044) test_gi: .: (0.000125) test_id_strings: .: (0.001178) test_list_ids: .: (0.000129) test_locus: .: (0.001047) test_words: .: (0.001102) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000974) test_accession: .: (0.000103) test_accessions: .: (0.000095) test_description: .: (0.001097) test_descriptions: .: (0.000110) test_entry_id: .: (0.000551) test_get_all_by_type: .: (0.000107) test_gi: .: (0.000503) test_id_strings: .: (0.000142) test_list_ids: .: (0.001065) test_locus: .: (0.000115) test_words: .: (0.000117) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.001534) test_accession: .: (0.000167) test_accessions: .: (0.000131) test_description: .: (0.000691) test_descriptions: .: (0.000141) test_entry_id: .: (0.000116) test_get: .: (0.000630) test_get_all_by_type: .: (0.000146) test_id_strings: .: (0.000177) test_list_ids: .: (0.000871) test_locus: .: (0.000860) test_sp: .: (0.000155) test_words: .: (0.001980) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.001259) test_accession: .: (0.000192) test_accessions: .: (0.000918) test_description: .: (0.000947) test_descriptions: .: (0.000948) test_entry_id: .: (0.000165) test_get: .: (0.000186) test_get_all_by_type: .: (0.000124) test_id_strings: .: (0.000227) test_list_ids: .: (0.000144) test_locus: .: (0.000529) test_tr: .: (0.000287) test_words: .: (0.000250) Bio::TestFastaFirstName: test_first_name1: .: (0.000267) test_first_name_multi_identifier: .: (0.000121) test_first_name_single_worded_defintion: .: (0.000117) test_no_definition: .: (0.000113) test_space_before_first_name: .: (0.000115) test_tabbed_defintion: .: (0.000176) Bio::TestFastaFormat: test_aalen: .: (0.000590) test_aaseq: .: (0.000144) test_acc_version: .: (0.000189) test_accession: .: (0.000163) test_accessions: .: (0.000174) test_data: .: (0.000128) test_definition: .: (0.000121) test_entry: .: (0.000154) test_entry_id: .: (0.001648) test_entry_overrun: .: (0.000378) test_first_name: .: (0.000141) test_gi: .: (0.000176) test_identifiers: .: (0.000169) test_length: .: (0.000142) test_query: .: (0.000148) test_seq: .: (0.000131) Bio::TestFastaFormatConst: test_delimiter: .: (0.000228) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000275) test_data: .: (0.000133) test_definition: .: (0.000124) test_entry: .: (0.000139) test_entry_id: .: (0.000141) test_first_name: .: (0.000062) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000193) test_naseq: .: (0.000183) test_naseq_class: .: (0.000118) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000250) Bio::TestFastaInitialize: test_new_1: .: (0.000588) test_option: .: (0.000121) test_option_backward_compatibility: .: (0.000149) Bio::TestFastaNumericFormat: test_arg: .: (0.000275) test_data: .: (0.000174) test_definition: .: (0.000108) test_each: .: (0.000150) test_entry: .: (0.000127) test_entry_id: .: (0.000136) test_length: .: (0.000149) test_to_biosequence: .: (0.000775) Bio::TestFastaQuery: test_query: .: (0.000195) test_self_local: .: (0.000104) test_self_parser: .: (0.000078) test_self_remote: .: (0.000130) Bio::TestFastacmd: test_database: .: (0.000298) test_fastacmd: .: (0.000098) test_methods: .: (0.000122) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000629) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000472) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000411) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000593) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000469) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000417) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000388) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000395) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000552) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000453) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000436) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000399) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000382) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000935) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000767) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000435) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000377) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000407) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.002796) test_error_probabilities_as_sanger: .: (0.001681) test_error_probabilities_as_solexa: .: (0.001898) test_quality_scores_as_illumina: .: (0.000376) test_quality_scores_as_sanger: .: (0.000282) test_quality_scores_as_solexa: .: (0.000299) test_validate_format: .: (0.000442) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000754) test_entry_id: .: (0.000692) test_error_probabilities: .: (0.053391) test_nalen: .: (0.000857) test_naseq: .: (0.000747) test_quality_scores: .: (0.001140) test_quality_string: .: (0.001076) test_roundtrip: .: (0.053653) test_seq: .: (0.000740) test_sequence_string: .: (0.000445) test_to_biosequence: .: (0.047234) test_to_biosequence_and_output: .: (0.002937) test_to_s: .: (0.000756) test_validate_format: .: (0.000805) test_validate_format_with_array: .: (0.000718) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000632) test_mask_20_with_empty_string: .: (0.000533) test_mask_20_with_longer_string: .: (0.000385) test_mask_20_with_x: .: (0.000331) test_mask_60: .: (0.000373) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.002944) test_error_probabilities_as_sanger: .: (0.002231) test_error_probabilities_as_solexa: .: (0.003789) test_quality_scores_as_illumina: .: (0.000482) test_quality_scores_as_sanger: .: (0.000317) test_quality_scores_as_solexa: .: (0.000366) test_validate_format: .: (0.000513) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.002565) test_error_probabilities_as_sanger: .: (0.002135) test_error_probabilities_as_solexa: .: (0.001972) test_quality_scores_as_illumina: .: (0.000458) test_quality_scores_as_sanger: .: (0.000370) test_quality_scores_as_solexa: .: (0.000322) test_validate_format: .: (0.000506) Bio::TestFeature: test_append: .: (0.000415) test_append_nil: .: (0.000123) test_assoc: .: (0.000137) test_each: .: (0.000134) test_feature: .: (0.000102) test_locations: .: (0.000177) test_new: .: (0.000106) test_position: .: (0.000102) test_qualifiers: .: (0.000113) Bio::TestFeatures: test_append: .: (0.000286) test_arg: .: (0.000117) test_each: .: (0.000108) test_features: .: (0.000117) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.001011) test_aaindex2: .: (0.000272) test_blast: .: (0.000242) test_blastxml: .: (0.000691) test_embl: .: (0.000294) test_embl_oldrelease: .: (0.000249) test_fastaformat: .: (0.000384) test_fastanumericformat: .: (0.000158) test_fastq: .: (0.000213) test_genbank: .: (0.000216) test_genpept: .: (0.000242) test_hmmer: .: (0.000242) test_maxml_cluster: .: (0.002274) test_maxml_sequence: .: (0.000153) test_medline: .: (0.000169) test_prosite: .: (0.003445) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002892) test_transfac: .: (0.001379) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000366) test_auto_1arg_filename: .: (0.000487) test_auto_1arg_io: .: (0.000374) test_auto_1arg_io_with_block: .: (0.001048) test_auto_1arg_with_block: .: (0.000538) test_auto_2arg_filename_mode: .: (0.000341) test_auto_2arg_filename_mode_with_block: .: (0.000524) test_auto_3arg: .: (0.000350) test_auto_3arg_with_block: .: (0.000486) test_foreach: .: (0.000417) test_new_2arg_class: .: (0.000202) test_new_2arg_nil: .: (0.000283) test_open_0arg: .: (0.000151) test_open_1arg_class: .: (0.000127) test_open_1arg_filename: .: (0.000306) test_open_1arg_io: .: (0.000299) test_open_1arg_io_with_block: .: (0.000547) test_open_1arg_nil: .: (0.000149) test_open_1arg_with_block: .: (0.000492) test_open_2arg_autodetect: .: (0.000291) test_open_2arg_autodetect_io: .: (0.000281) test_open_2arg_autodetect_io_with_block: .: (0.000466) test_open_2arg_autodetect_with_block: .: (0.000458) test_open_2arg_class: .: (0.000186) test_open_2arg_class_io: .: (0.000184) test_open_2arg_class_io_with_block: .: (0.000416) test_open_2arg_class_with_block: .: (0.000376) test_open_2arg_filename_mode: .: (0.000336) test_open_2arg_filename_mode_with_block: .: (0.000465) test_open_3arg: .: (0.000502) test_open_3arg_with_block: .: (0.000998) test_open_4arg: .: (0.000955) test_to_a: .: (0.000515) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000438) test_close: .: (0.000181) test_dbclass: .: (0.000159) test_dbclass_eq: .: (0.000187) test_dbclass_nil: .: (0.000232) test_each: .: (0.000328) test_each_entry: .: (0.000363) test_ended_pos: .: (0.000276) test_entry_pos_flag: .: (0.000203) test_entry_raw: .: (0.000347) test_eof?: .: (0.002880) test_next_entry: .: (0.000592) test_path: .: (0.000235) test_pos: .: (0.000273) test_raw: .: (0.000310) test_rewind: .: (0.000253) test_start_pos: .: (0.000259) test_start_pos_ended_pos_not_recorded: .: (0.000261) test_to_io: .: (0.000195) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000330) test_simpleformat2: .: (0.000224) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000287) test_eof_false_after_prefetch: .: (0.000698) test_eof_false_first: .: (0.000135) test_eof_true: .: (0.000167) test_getc: .: (0.000136) test_getc_after_prefetch: .: (0.000140) test_gets: .: (0.000141) test_gets_equal_prefetch_gets: .: (0.000144) test_gets_paragraph_mode: .: (0.000192) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000278) test_gets_paragraph_mode_within_buffer: .: (0.000352) test_gets_rs: .: (0.000169) test_gets_rs_equal_prefetch_gets: .: (0.000160) test_gets_rs_within_buffer: .: (0.000264) test_pos: .: (0.000143) test_pos=: .: (0.000141) test_prefetch_buffer: .: (0.000127) test_prefetch_gets: .: (0.000152) test_prefetch_gets_with_arg: .: (0.000359) test_rewind: .: (0.000093) test_skip_spaces: .: (0.000077) test_to_io: .: (0.000077) test_ungetc: .: (0.000062) test_ungetc_after_prefetch: .: (0.000064) test_ungets: .: (0.000076) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000182) test_self_open_file: .: (0.000085) test_self_open_file_with_block: .: (0.052591) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000364) test_parse_file_open_arg_int_perm: .: (0.000138) test_parse_file_open_arg_int_perm_opt: .: (0.000133) test_parse_file_open_arg_integer: .: (0.000123) test_parse_file_open_arg_nil: .: (0.000115) test_parse_file_open_arg_opt: .: (0.000172) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000265) test_parse_file_open_arg_str: .: (0.000148) test_parse_file_open_arg_str_opt: .: (0.000130) test_parse_file_open_arg_str_perm: .: (0.000116) test_parse_file_open_arg_str_perm_opt: .: (0.000134) test_parse_file_open_arg_str_with_enc: .: (0.000120) test_parse_file_open_arg_str_with_ext_enc: .: (0.000108) test_parse_file_open_mode_integer: .: (0.000117) test_parse_file_open_mode_nil: .: (0.000119) test_parse_file_open_mode_str: .: (0.000123) test_parse_file_open_mode_str_with_enc: .: (0.000146) test_parse_file_open_mode_str_with_ext_enc: .: (0.000113) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000326) test_entry: .: (0.000132) test_entry_ended_pos: .: (0.000070) test_entry_pos_flag: .: (0.000067) test_entry_start_pos: .: (0.000046) test_get_entry: .: (0.000099) test_rewind: .: (0.000071) test_skip_leader: .: (0.000065) test_stream: .: (0.000046) test_stream_pos: .: (0.000057) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000319) test_delimiter_overrun: .: (0.000047) test_entry: .: (0.000079) test_entry_ended_pos: .: (0.000053) test_entry_ended_pos_default_nil: .: (0.000048) test_entry_start_pos: .: (0.000048) test_entry_start_pos_default_nil: .: (0.000047) test_get_entry: .: (0.000105) test_get_parsed_entry: .: (0.000117) test_header: .: (0.000041) test_skip_leader: .: (0.000063) test_skip_leader_without_header: .: (0.000065) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000207) test_entry_ended_pos: .: (0.000116) test_entry_start_pos: .: (0.000389) test_flag_to_fetch_header: .: (0.000230) test_get_entry: .: (0.000284) test_get_parsed_entry: .: (0.000248) test_rewind: .: (0.000201) test_skip_leader: .: (0.000129) Bio::TestGCGMsf: test_alignment: .: (0.000893) test_checksum: .: (0.000444) test_compcheck: .: (0.000229) test_date: .: (0.000265) test_description: .: (0.000208) test_entry_id: .: (0.000234) test_gap_length_weight: .: (0.006400) test_gap_weight: .: (0.000371) test_heading: .: (0.000253) test_length: .: (0.000234) test_seq_type: .: (0.000212) test_symbol_comparison_table: .: (0.000222) test_validate_checksum: .: (0.000994) Bio::TestGFF: test_record_class: .: (0.000554) test_records: .: (0.000287) Bio::TestGFF2: test_const_version: .: (0.000484) test_gff_version: .: (0.000395) test_metadata: .: (0.000319) test_metadata_size: .: (0.000305) test_records_size: .: (0.000325) test_to_s: .: (0.000528) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.004162) test_attributes_case2: .: (0.000285) test_attributes_incompatible_backslash_semicolon: .: (0.000261) Bio::TestGFF2MetaData: test_data: .: (0.000216) test_directive: .: (0.000101) test_parse: .: (0.000123) Bio::TestGFF2Record: test_attribute: .: (0.000358) test_attribute_nonexistent: .: (0.000185) test_attributes: .: (0.000167) test_attributes_to_hash: .: (0.000167) test_comment_only?: .: (0.000136) test_delete_attribute: .: (0.000157) test_delete_attribute_multiple: .: (0.000158) test_delete_attribute_multiple2: .: (0.000201) test_delete_attribute_multiple_nil: .: (0.000153) test_delete_attribute_nil: .: (0.000382) test_delete_attribute_nonexistent: .: (0.003676) test_delete_attributes: .: (0.000465) test_delete_attributes_multiple: .: (0.000281) test_delete_attributes_nonexistent: .: (0.000414) test_end: .: (0.000259) test_eqeq: .: (0.000546) test_eqeq_false: .: (0.000475) test_feature: .: (0.000431) test_frame: .: (0.000258) test_get_attribute: .: (0.000435) test_get_attribute_nonexistent: .: (0.000248) test_get_attributes: .: (0.000331) test_get_attributes_nonexistent: .: (0.000236) test_replace_attributes: .: (0.000468) test_replace_attributes_multiple_multiple_over: .: (0.000272) test_replace_attributes_multiple_multiple_same: .: (0.000257) test_replace_attributes_multiple_multiple_two: .: (0.000279) test_replace_attributes_multiple_single: .: (0.000299) test_replace_attributes_nonexistent: .: (0.000322) test_replace_attributes_nonexistent_multiple: .: (0.003661) test_replace_attributes_single_multiple: .: (0.000418) test_score: .: (0.000241) test_self_parse: .: (0.000665) test_seqname: .: (0.000255) test_set_attribute: .: (0.000430) test_set_attribute_multiple: .: (0.000253) test_set_attribute_nonexistent: .: (0.000243) test_sort_attributes_by_tag!: .: (0.000303) test_sort_attributes_by_tag_bang_test2: .: (0.000293) test_sort_attributes_by_tag_bang_with_block: .: (0.000202) test_source: .: (0.000157) test_start: .: (0.000165) test_strand: .: (0.000149) test_to_s: .: (0.000257) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000183) test_comment_eq: .: (0.000042) test_comment_only?: .: (0.000043) test_comment_only_false: .: (0.000041) test_to_s: .: (0.000046) test_to_s_not_empty: .: (0.000083) Bio::TestGFF3: test_const_version: .: (0.000459) test_gff_version: .: (0.000251) test_records: .: (0.000376) test_sequence_regions: .: (0.000261) test_sequences: .: (0.000310) test_to_s: .: (0.008954) Bio::TestGFF3MetaData: test_data: .: (0.000292) test_directive: .: (0.000127) test_parse: .: (0.000144) Bio::TestGFF3Record: test_attributes: .: (0.000369) test_end: .: (0.000189) test_feature: .: (0.000187) test_frame: .: (0.000183) test_id: .: (0.000181) test_score: .: (0.000178) test_seqname: .: (0.000220) test_source: .: (0.000189) test_start: .: (0.000215) test_strand: .: (0.000191) test_to_s: .: (0.006889) test_to_s_attr_order_changed: .: (0.000544) Bio::TestGFF3RecordEscape: test_escape: .: (0.000288) test_escape_attribute: .: (0.000139) test_escape_seqid: .: (0.000136) test_unescape: .: (0.000135) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000343) test_eqeq: .: (0.000203) test_new_from_sequences_na: .: (0.000203) test_new_from_sequences_na_aa: .: (0.000254) test_new_from_sequences_na_aa_boundary_gap: .: (0.000368) test_new_from_sequences_na_aa_example: .: (0.000274) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000263) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000228) test_process_sequences_na: .: (0.000220) test_process_sequences_na_aa: .: (0.000196) test_process_sequences_na_aa_reverse_frameshift: .: (0.000187) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000198) test_process_sequences_na_aa_tooshort: .: (0.000292) test_process_sequences_na_tooshort: .: (0.000233) test_to_s: .: (0.000185) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000305) test_attributes_one: .: (0.000153) test_attributes_with_escaping: .: (0.000149) test_id_multiple: .: (0.000259) test_id_multiple2: .: (0.000541) test_id_replace: .: (0.000223) test_id_set: .: (0.000195) test_initialize_9: .: (0.000130) test_phase: .: (0.000187) test_score: .: (0.000178) test_to_s_void: .: (0.000168) Bio::TestGFF3RecordTarget: test_end: .: (0.000244) test_parse: .: (0.000216) test_start: .: (0.000119) test_strand: .: (0.000111) test_target_id: .: (0.000109) test_to_s: .: (0.016071) Bio::TestGFF3SequenceRegion: test_end: .: (0.000364) test_parse: .: (0.000220) test_seqid: .: (0.000132) test_start: .: (0.000112) test_to_s: .: (0.000187) Bio::TestGFFRecord: test_attributes: .: (0.000323) test_comment: .: (0.000189) test_end: .: (0.000135) test_feature: .: (0.000090) test_frame: .: (0.000073) test_score: .: (0.000064) test_seqname: .: (0.000063) test_source: .: (0.000983) test_start: .: (0.000222) test_strand: .: (0.000203) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000244) Bio::TestGeneAssociation: test_aspect: .: (0.000541) test_assigned_by: .: (0.000121) test_date: .: (0.000080) test_db: .: (0.000061) test_db_object_id: .: (0.000059) test_db_object_name: .: (0.000057) test_db_object_symbol: .: (0.000073) test_db_object_synonym: .: (0.000071) test_db_object_type: .: (0.000067) test_db_reference: .: (0.000075) test_evidence: .: (0.000062) test_goid: .: (0.000073) test_parser: .: (0.004963) test_qualifier: .: (0.000152) test_taxon: .: (0.000126) test_to_str: .: (0.000142) test_with: .: (0.000132) Bio::TestGenscanReport: test_date_run: .: (0.000956) test_gccontent: .: (0.000614) test_genscan_version: .: (0.004112) test_isochore: .: (0.000812) test_length: .: (0.000637) test_matrix: .: (0.000631) test_predictions_size: .: (0.000799) test_query_name: .: (0.004392) test_time: .: (0.000796) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000819) test_donor_score: .: (0.000770) test_exon_type: .: (0.000623) test_exon_type_long: .: (0.000506) test_first: .: (0.000455) test_initiation_score: .: (0.007696) test_last: .: (0.000712) test_number: .: (0.000593) test_p_value: .: (0.000573) test_phase: .: (0.004941) test_range: .: (0.000803) test_score: .: (0.000634) test_strand: .: (0.000629) test_t_score: .: (0.000600) test_termination_score: .: (0.000625) Bio::TestGenscanReportGene: test_aaseq: .: (0.015554) test_naseq: .: (0.000911) test_number: .: (0.000722) test_polyA: .: (0.005969) test_promoter: .: (0.001240) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000968) test_reports_ary_contents: .: (0.000701) Bio::TestHMMERReportConstants: test_rs: .: (0.000271) Bio::TestHMMERReportHit: test_accession: .: (0.007262) test_append_hsp: .: (0.000814) test_bit_score: .: (0.000625) test_definition: .: (0.000627) test_description: .: (0.000619) test_each: .: (0.000652) test_each_hsp: .: (0.000629) test_entry_id: .: (0.000723) test_evalue: .: (0.000543) test_hit: .: (0.005660) test_hit_id: .: (0.000803) test_hsps: .: (0.000650) test_num: .: (0.000525) test_score: .: (0.000475) test_target_def: .: (0.000458) test_target_id: .: (0.000842) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000751) test_each: .: (0.006400) test_each_hit: .: (0.000839) test_histogram: .: (0.000695) test_hits: .: (0.000644) test_hsps: .: (0.000600) test_parameter: .: (0.000774) test_program: .: (0.000628) test_query_info: .: (0.001122) test_statistical_detail: .: (0.005542) test_total_seq_searched: .: (0.000827) test_whole_seq_top_hits: .: (0.000696) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000946) test_histogram: .: (0.000765) test_statistical_detail: .: (0.000727) test_total_seq_searched: .: (0.006853) test_whole_seq_top_hit: .: (0.000978) Bio::TestHMMERReportHsp: test_accession: .: (0.000738) test_bit_score: .: (0.000465) test_csline: .: (0.000445) test_domain: .: (0.000437) test_evalue: .: (0.000724) test_flatseq: .: (0.000574) test_hmm_f: .: (0.000548) test_hmm_t: .: (0.015653) test_hmmseq: .: (0.001037) test_hsp: .: (0.000723) test_midline: .: (0.002723) test_query_frame: .: (0.000710) test_query_from: .: (0.000714) test_query_seq: .: (0.000692) test_query_to: .: (0.000639) test_rfline: .: (0.001453) test_score: .: (0.000666) test_seq_f: .: (0.000611) test_seq_ft: .: (0.000588) test_seq_t: .: (0.000595) test_set_alignment: .: (0.000570) test_targat_to: .: (0.000881) test_target_frame: .: (0.000614) test_target_from: .: (0.000567) test_target_seq: .: (0.000565) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000440) test_find_hetatm: .: (0.000239) test_hetatms: .: (0.000566) Bio::TestHeterogen: test_addAtom: .: (0.000336) test_each: .: (0.000205) test_each_hetatm: .: (0.000185) test_get_residue_id_from_atom: .: (0.000199) test_het_atom: .: (0.000147) test_iCode: .: (0.000147) test_inspect: .: (0.000164) test_resSeq: .: (0.000384) test_sort: .: (0.000199) test_square_bracket: .: (0.000110) test_to_s: .: (0.000158) test_update_resudue_id: .: (0.000086) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000190) test_find_heterogen: .: (0.000061) test_heterogens: .: (0.000078) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000220) test_match_description: .: (0.000078) test_match_evalue: .: (0.000071) test_match_ipr_description: .: (0.000074) test_match_ipr_id: .: (0.000072) test_match_match_end: .: (0.000071) test_match_match_start: .: (0.000089) test_match_method: .: (0.000194) test_matches_size: .: (0.000072) test_query_id: .: (0.000066) test_query_length: .: (0.000065) Bio::TestIprscanRawReport: test_entry_id: .: (0.001365) test_match_accession: .: (0.001958) test_match_crc64: .: (0.001350) test_match_date: .: (0.001338) test_match_description: .: (0.007442) test_match_evalue: .: (0.002495) test_match_go_terms: .: (0.001652) test_match_ipr_description: .: (0.001579) test_match_ipr_id: .: (0.002039) test_match_match_end: .: (0.001376) test_match_match_start: .: (0.001334) test_match_method: .: (0.005729) test_match_query_id: .: (0.002174) test_match_query_length: .: (0.001586) test_match_status: .: (0.001724) test_obj: .: (0.001922) test_query_id: .: (0.001376) test_query_length: .: (0.005557) test_self_reports_in_raw: .: (0.003652) Bio::TestIprscanReport: test_output_raw: .: (0.000741) test_to_raw: .: (0.002648) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.003150) test_match_accession: .: (0.003641) test_match_date: .: (0.001201) test_match_description: .: (0.003210) test_match_evalue: .: (0.001022) test_match_go_terms: .: (0.002503) test_match_ipr_description: .: (0.003622) test_match_ipr_id: .: (0.003404) test_match_match_end: .: (0.002565) test_match_match_start: .: (0.004318) test_match_method: .: (0.004296) test_match_status: .: (0.004698) test_matches_size: .: (0.009482) test_query_id: .: (0.000731) test_query_length: .: (0.000482) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000662) test_to_hash_match?: .: (0.000558) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.002148) Bio::TestKeggCompound: test_comment: .: (0.000776) test_dblinks_as_hash: .: (0.000382) test_dblinks_as_strings: .: (0.000313) test_entry_id: .: (0.000332) test_enzymes: .: (0.000520) test_formula: .: (0.000295) test_kcf: .: (0.000255) test_mass: .: (0.000276) test_name: .: (0.000769) test_names: .: (0.000332) test_pathways_as_hash: .: (0.000460) test_pathways_as_strings: .: (0.000364) test_reactions: .: (0.000526) test_remark: .: (0.000303) test_rpairs: .: (0.000289) Bio::TestKeggEnzyme: test_all_reac: .: (0.000634) test_classes: .: (0.000427) test_cofactors: .: (0.000638) test_comment: .: (0.000454) test_dblinks_as_hash: .: (0.000487) test_dblinks_as_strings: .: (0.000428) test_diseases: .: (0.000466) test_entry: .: (0.000493) test_entry_id: .: (0.000715) test_genes: .: (0.012935) test_genes_as_hash: .: (0.012261) test_genes_as_strings: .: (0.006210) test_inhibitors: .: (0.000593) test_iubmb_reactions: .: (0.000520) test_kegg_reactions: .: (0.000500) test_motifs: .: (0.000430) test_name: .: (0.000520) test_names: .: (0.000504) test_obsolete?: .: (0.000467) test_orthologs_as_hash: .: (0.000559) test_orthologs_as_strings: .: (0.001407) test_pathways_as_hash: .: (0.000619) test_pathways_as_strings: .: (0.000548) test_products: .: (0.000557) test_reaction: .: (0.000549) test_structures: .: (0.000707) test_substrates: .: (0.000511) test_sysname: .: (0.000482) Bio::TestKeggGenesDblinks: test_data: .: (0.000514) test_dblinks_0: .: (0.000161) test_dblinks_1: .: (0.000168) test_dblinks_2: .: (0.000131) Bio::TestKeggGenesStructure: test_data: .: (0.000279) test_ids: .: (0.000188) test_ids_in_array: .: (0.000159) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004613) test_graphics__size: .: (0.003971) test_id: .: (0.004100) test_link: .: (0.003939) test_name: .: (0.003994) test_reaction: .: (0.003948) test_type: .: (0.003989) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.009613) test_graphics__size: .: (0.004609) test_id: .: (0.004347) test_link: .: (0.004407) test_name: .: (0.004517) test_reaction: .: (0.004057) test_type: .: (0.004022) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.004116) test_category: .: (0.008507) test_entry_id: .: (0.004687) test_fgcolor=: .: (0.004298) test_height=: .: (0.004224) test_label=: .: (0.004754) test_shape=: .: (0.004164) test_width=: .: (0.005856) test_x=: .: (0.004151) test_y=: .: (0.007735) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.005076) test_graphics__size: .: (0.004404) test_id: .: (0.004309) test_link: .: (0.004543) test_name: .: (0.004164) test_reaction: .: (0.004023) test_type: .: (0.003964) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000289) test_graphics=: .: (0.000135) test_id=: .: (0.000145) test_link=: .: (0.000159) test_name=: .: (0.000143) test_reaction=: .: (0.000128) test_type=: .: (0.000119) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000277) test_category=: .: (0.000133) test_entry_id=: .: (0.000131) test_fgcolor=: .: (0.000139) test_height=: .: (0.000129) test_label=: .: (0.000165) test_pathway=: .: (0.000115) test_shape=: .: (0.000134) test_width=: .: (0.000136) test_x=: .: (0.000131) test_y=: .: (0.000129) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.009002) test_coords: .: (0.009520) test_fgcolor: .: (0.006261) test_height: .: (0.008053) test_name: .: (0.004500) test_type: .: (0.004172) test_width: .: (0.003926) test_x: .: (0.005191) test_y: .: (0.007235) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.005004) test_coords: .: (0.004255) test_fgcolor: .: (0.004325) test_height: .: (0.004331) test_name: .: (0.004016) test_type: .: (0.004067) test_width: .: (0.004135) test_x: .: (0.007163) test_y: .: (0.004789) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000294) test_coords=: .: (0.000145) test_fgcolor=: .: (0.000139) test_height=: .: (0.000149) test_name=: .: (0.000139) test_type=: .: (0.000069) test_width=: .: (0.000079) test_x=: .: (0.000059) test_y=: .: (0.000051) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.004678) test_entries__size: .: (0.004566) test_image: .: (0.003987) test_link: .: (0.003985) test_name: .: (0.003930) test_number: .: (0.006081) test_org: .: (0.005346) test_reactions=: .: (0.004413) test_reactions__size: .: (0.004159) test_relations=: .: (0.004520) test_relations__size: .: (0.003944) test_title: .: (0.003961) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.009837) test_name: .: (0.009225) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000322) test_initialize_0: .: (0.000127) test_initialize_1: .: (0.000136) test_initialize_2: .: (0.000128) test_name=: .: (0.000141) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.004308) test_name: .: (0.004569) test_products: .: (0.004063) test_substrates: .: (0.004052) test_type: .: (0.004083) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000323) test_name=: .: (0.000177) test_products=: .: (0.000141) test_substraces=: .: (0.000136) test_type=: .: (0.000132) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000261) test_entry_id=: .: (0.000143) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.007442) test_entry2: .: (0.004997) test_name: .: (0.005411) test_type: .: (0.004588) test_value: .: (0.004149) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000306) test_node1=: .: (0.000164) test_node2=: .: (0.000159) test_rel=: .: (0.000159) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000261) test_entry2=: .: (0.000156) test_name=: .: (0.000128) test_type=: .: (0.000114) test_value=: .: (0.000122) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.014823) test_name: .: (0.014367) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000196) test_initialize_0: .: (0.000043) test_initialize_1: .: (0.000041) test_initialize_2: .: (0.000042) test_name=: .: (0.000056) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000124) test_initialize_0: .: (0.000036) test_initialize_1: .: (0.000037) test_initialize_2: .: (0.000148) test_name=: .: (0.000055) Bio::TestKeggModule: test_compounds: .: (0.000543) test_compounds_as_hash: .: (0.000290) test_compounds_as_strings: .: (0.000246) test_definition: .: (0.000232) test_entry_id: .: (0.000202) test_keggclass: .: (0.000199) test_name: .: (0.000202) test_new: .: (0.000199) test_orthologs: .: (0.000265) test_orthologs_as_array: .: (0.000292) test_orthologs_as_hash: .: (0.000267) test_orthologs_as_strings: .: (0.000220) test_pathways: .: (0.000695) test_pathways_as_hash: .: (0.000233) test_pathways_as_strings: .: (0.000179) test_reactions: .: (0.000252) test_reactions_as_hash: .: (0.000231) test_reactions_as_strings: .: (0.000197) Bio::TestKeggOrthology: test_dblinks: .: (0.000524) test_dblinks_as_hash: .: (0.000353) test_dblinks_as_strings: .: (0.000322) test_definition: .: (0.000343) test_entry_id: .: (0.000345) test_genes_as_hash: .: (0.051157) test_genes_as_strings: .: (0.002927) test_keggclass: .: (0.000564) test_keggclasses: .: (0.000432) test_modules: .: (0.000386) test_modules_as_hash: .: (0.000340) test_modules_as_strings: .: (0.000355) test_name: .: (0.000356) test_names: .: (0.000707) test_pathways_as_strings: .: (0.001107) test_pathways_in_keggclass: .: (0.000486) test_references: .: (0.000478) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000367) test_compounds_as_strings: .: (0.000180) test_dblinks_as_hash: .: (0.000174) test_dblinks_as_strings: .: (0.000171) test_description: .: (0.000204) test_diseases_as_hash: .: (0.000176) test_diseases_as_strings: .: (0.000179) test_entry_id: .: (0.000202) test_enzymes_as_strings: .: (0.000174) test_genes_as_hash: .: (0.000175) test_genes_as_strings: .: (0.000172) test_keggclass: .: (0.000190) test_ko_pathway: .: (0.000213) test_modules_as_hash: .: (0.000239) test_modules_as_strings: .: (0.000196) test_name: .: (0.000212) test_organism: .: (0.000190) test_orthologs_as_hash: .: (0.000175) test_orthologs_as_strings: .: (0.000173) test_pathways_as_hash: .: (0.000196) test_pathways_as_strings: .: (0.000188) test_reactions_as_hash: .: (0.000195) test_reactions_as_strings: .: (0.000175) test_references: .: (0.000176) test_rel_pathways_as_hash: .: (0.000211) test_rel_pathways_as_strings: .: (0.000187) Bio::TestKeggReaction: test_definition: .: (0.000392) test_entry_id: .: (0.000227) test_enzymes: .: (0.000224) test_equation: .: (0.000229) test_name: .: (0.000213) test_orthologs_as_hash: .: (0.000235) test_orthologs_as_strings: .: (0.000196) test_pathways_as_hash: .: (0.000209) test_pathways_as_strings: .: (0.000189) test_rpairs_as_hash: .: (0.000220) test_rpairs_as_strings: .: (0.000190) test_rpairs_as_tokens: .: (0.000235) Bio::TestLasergene: test_methods: .: (0.007505) Bio::TestLocations: test_complement: .: (0.000318) test_hat: .: (0.000141) test_normal: .: (0.000129) test_replace_single_base: .: (0.000103) test_should_not_modify_argument: .: (0.000112) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002288) test_locations_to_s: .: (0.000934) Bio::TestMEDLINE: test_authors: .: (0.000597) test_authors_with_last_name_all_caps: .: (0.000119) test_authors_with_suffix: .: (0.000145) Bio::TestMEDLINE_20146148: test_ab: .: (0.001108) test_ad: .: (0.000359) test_au: .: (0.000263) test_authors: .: (0.000272) test_doi: .: (0.000259) test_dp: .: (0.000256) test_ip: .: (0.000286) test_mh: .: (0.000290) test_pages: .: (0.000303) test_pg: .: (0.000259) test_pii: .: (0.000258) test_pmid: .: (0.000269) test_pt: .: (0.000265) test_reference: .: (0.000486) test_self_new: .: (0.003460) test_so: .: (0.000636) test_ta: .: (0.000296) test_ti: .: (0.000317) test_ui: .: (0.000325) test_vi: .: (0.000285) test_year: .: (0.000323) Bio::TestMapSimple: test_attributes: .: (0.000924) Bio::TestMapping: test_add_mapping_as_map: .: (0.000332) test_add_mapping_as_marker: .: (0.000155) test_contains_marker?: .: (0.000129) test_mapped_to?: .: (0.000121) test_mapping_location_comparison: .: (0.000281) test_mappings_as_map_each: .: (0.000126) test_mappings_as_marker_each: .: (0.000193) test_mappings_on: .: (0.000182) test_multiple_mappings_between_same_marker_and_map: .: (0.000274) test_positions_on: .: (0.000173) test_raise_error_kind_of: .: (0.000464) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000365) test_check_options_with_invalid_opts: .: (0.000185) test_check_options_with_valid_opts: .: (0.000156) test_command_to_be_run: .: (0.000174) test_config_defaults: .: (0.000141) test_minimal_config: .: (0.000154) test_more_config: .: (0.000136) test_run: .: (0.000097) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000619) test_report_has_motifs: .: (0.000246) Bio::TestModel: test_addChain: .: (0.000239) test_comp: .: (0.000145) test_each: .: (0.000118) test_each_chain: .: (0.000102) test_inspect: .: (0.000108) test_rehash: .: (0.000101) test_square_brace: .: (0.000110) test_to_s: .: (0.000100) Bio::TestModelFinder: test_find_model: .: (0.000235) Bio::TestMotif: test_creation_and_attributes: .: (0.000215) test_length: .: (0.000086) Bio::TestMyGraph: test_cliquishness: .: (0.000468) Bio::TestNA: test_accessor: .: (0.000171) test_na: .: (0.000081) test_name: .: (0.000094) test_names: .: (0.000078) test_to_re: .: (0.000191) test_weight: .: (0.000104) test_weight_rna: .: (0.000080) Bio::TestNAConstants: test_NAMES: .: (0.000162) test_NAMES_1_to_name: .: (0.000086) test_WEIGHT: .: (0.000099) Bio::TestNATranslate: test_translate: .: (0.000324) test_translate_1: .: (0.000169) test_translate_2: .: (0.000109) test_translate_3: .: (0.000101) test_translate_4: .: (0.000174) test_translate_5: .: (0.000150) test_translate_6: .: (0.000105) Bio::TestNCBIDB: test_fetch: .: (0.000235) test_p_entry2hash: .: (0.000083) test_p_subtag2array: .: (0.000071) test_p_toptag2array: .: (0.000081) Bio::TestNewick: test_reparse: .: (0.000973) test_reparse_before_lazy_parsing: .: (0.000320) test_string_tree: .: (0.000536) Bio::TestNewick2: test_string_tree: .: (0.000547) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000183) test_parse_newick_leaf: .: (0.000184) test_parse_newick_tokenize: .: (0.000263) Bio::TestNexus: test_nexus: .: (0.006207) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000312) test_uncapitalized_letter_Q32725_9POAL: .: (0.000138) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000240) test_load_parameters: .: (0.000124) test_parameters: .: (0.000087) test_set_default_parameters: .: (0.000125) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000568) test_expected_parameters_set_in_control_file: .: (0.000457) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000216) test_new_with_parameters: .: (0.000111) test_new_with_two_argument: .: (0.000122) test_new_without_argument: .: (0.000101) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.005601) test_rates_hundred_and_fiftieth_position: .: (0.000926) test_rates_last_position: .: (0.001454) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.000731) test_tree: .: (0.000534) test_tree_length: .: (0.000481) test_tree_log_likelihood: .: (0.000471) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000443) test_parameters_should_be_loaded_from_control: .: (0.000249) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001295) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000329) test_dN_dS: .: (0.000166) test_kappa: .: (0.000165) test_lnL: .: (0.000167) test_m3_classes: .: (0.000238) test_m3_lnL: .: (0.000154) test_m3_to_s: .: (0.000149) test_m3_tree: .: (0.000206) test_omega: .: (0.000156) test_to_s: .: (0.000156) test_tree: .: (0.000207) test_tree_length: .: (0.000164) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000508) test_p: .: (0.000322) test_position: .: (0.000298) test_probability: .: (0.000319) test_w: .: (0.000495) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000470) test_graph_omega: .: (0.000349) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000306) test_footer: .: (0.000166) test_header: .: (0.000163) test_initialize: .: (0.000202) test_models: .: (0.000189) test_nb_sites: .: (0.001380) test_num_codons: .: (0.000213) test_num_sequences: .: (0.000194) test_significant: .: (0.000205) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000349) test_nb_sites: .: (0.000284) test_significant: .: (0.000182) test_sites: .: (0.000738) Bio::TestPDB: test_accession: .: (0.000965) test_addModel: .: (0.000594) test_authors: .: (0.000524) test_bracket: .: (0.000571) test_classification: .: (0.000553) test_dbref: .: (0.000609) test_definition: .: (0.000523) test_each: .: (0.000560) test_each_model: .: (0.000506) test_entry_id: .: (0.000508) test_helix: .: (0.000574) test_inspect: .: (0.000552) test_jrnl: .: (0.000508) test_keywords: .: (0.000515) test_record: .: (0.000486) test_remark: .: (0.000670) test_seqres: .: (0.000738) test_sheet: .: (0.000707) test_ssbond: .: (0.000542) test_to_s: .: (0.000687) test_turn: .: (0.000533) test_version: .: (0.000525) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000285) test_U12: .: (0.006515) test_U13: .: (0.000248) test_U22: .: (0.000135) test_U23: .: (0.000123) test_U33: .: (0.000127) test_altLoc: .: (0.000155) test_chainID: .: (0.000159) test_charge: .: (0.000119) test_element: .: (0.000128) test_iCode: .: (0.000129) test_name: .: (0.000135) test_resName: .: (0.000128) test_resSeq: .: (0.000124) test_segID: .: (0.000130) test_serial: .: (0.000133) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000275) test_anisou: .: (0.000495) test_chainID: .: (0.000120) test_charge: .: (0.000107) test_comparable: .: (0.000126) test_do_parse: .: (0.000097) test_element: .: (0.000121) test_iCode: .: (0.000100) test_name: .: (0.000098) test_occupancy: .: (0.000137) test_original_data: .: (0.000121) test_record_name: .: (0.000110) test_resName: .: (0.000098) test_resSeq: .: (0.000092) test_residue: .: (0.000094) test_segID: .: (0.000098) test_serial: .: (0.000097) test_sigatm: .: (0.000095) test_tempFactor: .: (0.000122) test_ter: .: (0.000387) test_to_a: .: (0.000114) test_to_s: .: (0.000131) test_x: .: (0.000163) test_xyz: .: (0.000134) test_y: .: (0.000106) test_z: .: (0.000103) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000277) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000227) test_idcode: .: (0.000088) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000240) test_chainID2: .: (0.000106) test_icode1: .: (0.000117) test_icode2: .: (0.000117) test_measure: .: (0.000126) test_modNum: .: (0.000325) test_pep1: .: (0.000165) test_pep2: .: (0.000119) test_seqNum1: .: (0.000097) test_seqNum2: .: (0.000094) test_serNum: .: (0.000090) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000232) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000185) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000230) test_alpha: .: (0.000129) test_b: .: (0.000116) test_beta: .: (0.000098) test_c: .: (0.000142) test_gamma: .: (0.000095) test_sGroup: .: (0.000100) test_z: .: (0.000101) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000264) test_database: .: (0.000337) test_dbAccession: .: (0.000157) test_dbIdCode: .: (0.000129) test_dbseqBegin: .: (0.000126) test_dbseqEnd: .: (0.000120) test_idCode: .: (0.000120) test_idbnsBeg: .: (0.000128) test_insertBegin: .: (0.000125) test_insertEnd: .: (0.000119) test_seqBegin: .: (0.000119) test_seqEnd: .: (0.000132) Bio::TestPDBRecord::TestDefault: test_text: .: (0.002495) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.001174) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.001216) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000231) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.001411) test_depDate: .: (0.000127) test_idCode: .: (0.000104) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.003406) test_hetID: .: (0.000184) test_iCode: .: (0.000227) test_numHetAtoms: .: (0.000118) test_seqNum: .: (0.000113) test_text: .: (0.001223) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000246) test_anisou: .: (0.001418) test_chainID: .: (0.000135) test_charge: .: (0.000089) test_comparable: .: (0.001180) test_do_parse: .: (0.000127) test_element: .: (0.000154) test_iCode: .: (0.001235) test_name: .: (0.000118) test_occupancy: .: (0.001307) test_original_data: .: (0.000140) test_record_name: .: (0.000106) test_resName: .: (0.000099) test_resSeq: .: (0.000167) test_residue: .: (0.000097) test_segID: .: (0.001169) test_serial: .: (0.001255) test_sigatm: .: (0.000147) test_tempFactor: .: (0.001350) test_ter: .: (0.000139) test_to_a: .: (0.000116) test_to_s: .: (0.000140) test_x: .: (0.000154) test_xyz: .: (0.002308) test_y: .: (0.001370) test_z: .: (0.000167) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.001586) test_ChainH: .: (0.000150) test_ICode1: .: (0.001228) test_altLoc1: .: (0.000877) test_altLoc2: .: (0.000170) test_altLocH: .: (0.000716) test_chainID2: .: (0.001153) test_iCode2: .: (0.001293) test_iCodeH: .: (0.000162) test_name1: .: (0.000881) test_name2: .: (0.002910) test_nameH: .: (0.001095) test_resName1: .: (0.000184) test_resName2: .: (0.001351) test_resSeq1: .: (0.002071) test_resSeq2: .: (0.000794) test_resSeqH: .: (0.000690) test_sym1: .: (0.000294) test_sym2: .: (0.000151) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000258) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000285) test_altLoc2: .: (0.000137) test_chainID1: .: (0.000125) test_chainID2: .: (0.000131) test_iCode1: .: (0.000141) test_iCode2: .: (0.000133) test_name1: .: (0.000129) test_name2: .: (0.000129) test_resName1: .: (0.000136) test_resName2: .: (0.000828) test_resSeq1: .: (0.000156) test_resSeq2: .: (0.000135) test_sym1: .: (0.000130) test_sym2: .: (0.000121) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000259) test_numCoord: .: (0.000098) test_numHelix: .: (0.000093) test_numHet: .: (0.000096) test_numRemark: .: (0.000097) test_numSeq: .: (0.000089) test_numSheet: .: (0.000091) test_numSite: .: (0.000097) test_numTer: .: (0.000096) test_numTurn: .: (0.000101) test_numXform: .: (0.000098) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000253) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000251) test_comment: .: (0.000071) test_iCode: .: (0.000060) test_idCode: .: (0.000055) test_resName: .: (0.000070) test_seqNum: .: (0.000059) test_stdRes: .: (0.000054) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000150) test_Mn2: .: (0.000050) test_Mn3: .: (0.000046) test_Vn: .: (0.000045) test_iGiven: .: (0.000049) test_serial: .: (0.000047) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000122) test_Mn2: .: (0.000047) test_Mn3: .: (0.000061) test_Vn: .: (0.000042) test_iGiven: .: (0.000042) test_serial: .: (0.000041) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000123) test_Mn2: .: (0.000046) test_Mn3: .: (0.000043) test_Vn: .: (0.000040) test_iGiven: .: (0.000045) test_serial: .: (0.000039) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000127) test_rIdCode: .: (0.000058) test_repDate: .: (0.000050) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000121) test_On2: .: (0.000047) test_On3: .: (0.000044) test_Tn: .: (0.000178) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000292) test_modId: .: (0.000107) test_modNum: .: (0.000101) test_modType: .: (0.000109) test_record: .: (0.000111) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000196) test_text: .: (0.000094) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000207) test_Sn2: .: (0.000130) test_Sn3: .: (0.000088) test_Un: .: (0.000085) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000188) test_Sn2: .: (0.000091) test_Sn3: .: (0.000089) test_Un: .: (0.000081) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000381) test_Sn2: .: (0.000102) test_Sn3: .: (0.000090) test_Un: .: (0.000086) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000231) test_conflict: .: (0.000124) test_database: .: (0.000110) test_dbIdCode: .: (0.000106) test_dbRes: .: (0.000109) test_dbSeq: .: (0.000110) test_iCode: .: (0.000113) test_idCode: .: (0.000167) test_resName: .: (0.000114) test_seqNum: .: (0.000114) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000227) test_numRes: .: (0.000110) test_resName: .: (0.000136) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000262) test_curChainId: .: (0.000140) test_curICode: .: (0.000126) test_curResName: .: (0.000226) test_curResSeq: .: (0.000134) test_endChainID: .: (0.000128) test_endICode: .: (0.000121) test_endResName: .: (0.000123) test_endSeqNum: .: (0.000191) test_initChainID: .: (0.000168) test_initICode: .: (0.000139) test_initResName: .: (0.000142) test_initSeqNum: .: (0.000136) test_numStrands: .: (0.000130) test_prevAtom: .: (0.000147) test_prevChainId: .: (0.000139) test_prevICode: .: (0.000122) test_prevResName: .: (0.000120) test_prevResSeq: .: (0.000181) test_sense: .: (0.000135) test_sheetID: .: (0.000132) test_strand: .: (0.000124) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000255) test_chainID: .: (0.000124) test_charge: .: (0.000120) test_element: .: (0.000114) test_iCode: .: (0.000108) test_name: .: (0.000109) test_resName: .: (0.000112) test_resSeq: .: (0.000108) test_segID: .: (0.000118) test_serial: .: (0.000116) test_sigOcc: .: (0.000119) test_sigTemp: .: (0.000113) test_sigX: .: (0.000107) test_sigY: .: (0.000110) test_sigZ: .: (0.000175) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000289) test_SigmaU12: .: (0.000120) test_SigmaU13: .: (0.000117) test_SigmaU22: .: (0.000110) test_SigmaU23: .: (0.000139) test_SigmaU33: .: (0.000111) test_altLoc: .: (0.000106) test_chainID: .: (0.000104) test_charge: .: (0.000108) test_element: .: (0.000107) test_iCode: .: (0.000110) test_name: .: (0.000114) test_resName: .: (0.000107) test_resSeq: .: (0.000124) test_segID: .: (0.000113) test_serial: .: (0.000105) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000259) test_chainID2: .: (0.000190) test_chainID3: .: (0.000131) test_chainID4: .: (0.000117) test_iCode1: .: (0.000137) test_iCode2: .: (0.000120) test_iCode3: .: (0.000115) test_iCode4: .: (0.000116) test_numRes: .: (0.000136) test_resName1: .: (0.000112) test_resName2: .: (0.000113) test_resName3: .: (0.000143) test_resName4: .: (0.000114) test_seq1: .: (0.000124) test_seq2: .: (0.000140) test_seq3: .: (0.000123) test_seq4: .: (0.000112) test_seqNum: .: (0.000114) test_siteID: .: (0.000127) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000248) test_altLoc2: .: (0.000111) test_atom1: .: (0.000105) test_atom2: .: (0.000222) test_chainID1: .: (0.000122) test_chainID2: .: (0.000126) test_iCode1: .: (0.000121) test_iCode2: .: (0.000107) test_resName1: .: (0.000102) test_resName2: .: (0.000124) test_resSeq1: .: (0.000100) test_resSeq2: .: (0.000112) test_sym1: .: (0.000106) test_sym2: .: (0.000099) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000249) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000202) test_sIdCode: .: (0.000107) test_sprsdeDate: .: (0.000100) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000204) test_iCode: .: (0.000104) test_resName: .: (0.000105) test_resSeq: .: (0.000098) test_serial: .: (0.000113) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000188) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000217) test_t1: .: (0.000123) test_t2: .: (0.000106) test_t3: .: (0.000094) test_text: .: (0.000744) Bio::TestPROSITE: test_ac: .: (0.000968) test_cc: .: (0.000815) test_de: .: (0.000845) test_division: .: (0.000840) test_dr: .: (0.016753) test_dt: .: (0.000890) test_false_neg: .: (0.000913) test_false_pos: .: (0.000896) test_false_positive_sequences: .: (0.000867) test_list_falsenegative: .: (0.020242) test_list_falsepositive: .: (0.014144) test_list_potentialhit: .: (0.015407) test_list_truepositive: .: (0.013748) test_list_unknown: .: (0.011935) test_list_xref: .: (0.014627) test_ma: .: (0.001070) test_max_repeat: .: (0.000862) test_name: .: (0.000847) test_nr: .: (0.000889) test_pa: .: (0.000819) test_pa2re: .: (0.001019) test_partial: .: (0.000849) test_pdb_xref: .: (0.000952) test_pdoc_xref: .: (0.000949) test_positive: .: (0.001004) test_positive_hits: .: (0.003134) test_positive_sequences: .: (0.001738) test_release: .: (0.001664) test_ru: .: (0.000883) test_self_pa2re: .: (0.001138) test_site: .: (0.001407) test_skip_flag: .: (0.001061) test_swissprot_release_number: .: (0.001098) test_swissprot_release_sequences: .: (0.001079) test_taxon_range: .: (0.001006) test_total: .: (0.002900) test_total_hits: .: (0.001134) test_total_sequences: .: (0.001435) test_unknown: .: (0.000985) test_unknown_hits: .: (0.001161) test_unknown_sequences: .: (0.001251) Bio::TestPROSITEConst: test_delimiter: .: (0.000192) test_tagsize: .: (0.000041) Bio::TestPTS1: test_function_set: .: (0.000143) test_function_set_number_1: .: (0.000053) test_function_set_number_2: .: (0.000046) test_function_set_number_3: .: (0.000048) test_function_show: .: (0.000043) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000105) Bio::TestPTS1New: test_fungi: .: (0.000427) test_general: .: (0.000161) test_metazoa: .: (0.000134) Bio::TestQualifier: test_qualifier: .: (0.000252) test_value: .: (0.000155) Bio::TestREBASE: test_methods: .: (0.000698) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000826) test_bit_score: .: (0.000580) test_evalue: .: (0.000536) test_gaps: .: (0.000569) test_hit_from: .: (0.000608) test_hit_to: .: (0.000539) test_hseq: .: (0.000546) test_identity: .: (0.000511) test_midline: .: (0.000562) test_percent_identity: .: (0.000593) test_positive: .: (0.000575) test_qseq: .: (0.000522) test_query_from: .: (0.000564) test_query_to: .: (0.000516) test_score: .: (0.000498) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000628) test_hits_size: .: (0.001040) test_iterations_size: .: (0.000977) test_program: .: (0.000464) test_query_def: .: (0.000989) test_query_len: .: (0.000984) test_version: .: (0.000458) test_version_date: .: (0.003307) test_version_number: .: (0.000630) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000868) test_definition: .: (0.000636) test_evalue: .: (0.000573) test_hsps_size: .: (0.000473) test_identity: .: (0.000446) test_lap_at: .: (0.001008) test_len: .: (0.000612) test_midline: .: (0.000450) test_overlap: .: (0.000730) test_query_end: .: (0.000619) test_query_seq: .: (0.000609) test_query_start: .: (0.000558) test_target_def: .: (0.000565) test_target_end: .: (0.000606) test_target_len: .: (0.000680) test_target_seq: .: (0.000564) test_target_start: .: (0.000538) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000467) test_get_entry: .: (0.000428) test_rewind: .: (0.000146) test_skip_leader: .: (0.000243) Bio::TestReference: test_abstract: .: (0.000256) test_affiliations: .: (0.000110) test_authors: .: (0.000113) test_format_bibitem: .: (0.000156) test_format_bibtex: .: (0.000265) test_format_bibtex_with_arguments: .: (0.000193) test_format_cell: .: (0.000142) test_format_current: .: (0.000125) test_format_endnote: .: (0.000151) test_format_general: .: (0.000136) test_format_genome_biol: .: (0.000130) test_format_genome_res: .: (0.000131) test_format_nar: .: (0.000121) test_format_nature: .: (0.000132) test_format_rd: .: (0.000141) test_format_science: .: (0.000239) test_format_trends: .: (0.000123) test_issue: .: (0.000105) test_journal: .: (0.000108) test_mesh: .: (0.000114) test_pages: .: (0.000105) test_pubmed: .: (0.000093) test_pubmed_url: .: (0.000104) test_url: .: (0.000114) test_volume: .: (0.000115) test_year: .: (0.000103) Bio::TestReference_noURL: test_format_endnote: .: (0.000314) test_url: .: (0.000111) Bio::TestReferences: test_append: .: (0.000919) test_each: .: (0.000139) Bio::TestRelation: test_comparison_operator: .: (0.000251) test_uniq: .: (0.000145) Bio::TestResidue: test_addAtom: .: (0.000362) test_each: .: (0.000219) test_each_atom: .: (0.000179) test_get_residue_id_from_atom: .: (0.000193) test_het_atom: .: (0.000163) test_iCode: .: (0.000158) test_inspect: .: (0.000203) test_resSeq: .: (0.000149) test_sort: .: (0.000215) test_square_bracket: .: (0.000182) test_to_s: .: (0.000212) test_update_resudue_id: .: (0.000150) Bio::TestResidueFinder: test_each_residue: .: (0.000309) test_find_residue: .: (0.000148) test_residues: .: (0.000190) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.217167) test_cut_from_bio_sequence_na: .: (0.036326) test_cut_without_permutations: .: (0.017883) test_view_ranges: .: (0.014239) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001001) test_cuts_after_remove_incomplete_cuts: .: (0.000528) test_strands_for_display: .: (0.001739) test_strands_for_display_current: .: (0.000601) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.003624) test_fragments_for_display_1: .: (0.000661) test_fragments_for_display_10: .: (0.000564) test_fragments_for_display_2: .: (0.001046) test_fragments_for_display_3: .: (0.000877) test_fragments_for_display_4: .: (0.000953) test_fragments_for_display_5: .: (0.000472) test_fragments_for_display_6: .: (0.000461) test_fragments_for_display_7: .: (0.000702) test_fragments_for_display_8: .: (0.000457) test_fragments_for_display_9: .: (0.000438) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000464) test_obj_3: .: (0.000229) test_obj_7: .: (0.000191) test_obj_z: .: (0.000377) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000364) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000262) test_bracket_eq: .: (0.000201) test_concat: .: (0.000140) test_delete: .: (0.000142) test_dup: .: (0.000176) test_each: .: (0.000151) test_eqeq: .: (0.000146) test_eqeq_false: .: (0.000156) test_eqeq_other: .: (0.000114) test_eqeq_self: .: (0.000360) test_include?: .: (0.000131) test_internal_data: .: (0.000156) test_internal_data_eq: .: (0.000137) test_length: .: (0.000112) test_ltlt: .: (0.000163) test_ltlt_larger: .: (0.000132) test_ltlt_middle: .: (0.000125) test_plus: .: (0.000156) test_plus_error: .: (0.000174) test_push: .: (0.000137) test_reverse_each: .: (0.000165) test_self_bracket: .: (0.000115) test_self_new: .: (0.000134) test_size: .: (0.000127) test_sort!: .: (0.000118) test_to_a: .: (0.000152) test_uniq!: .: (0.000126) test_unshift: .: (0.000184) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003474) test_complement: .: (0.003033) test_complement_with_cut_symbols: .: (0.014978) test_cut_locations: .: (0.021714) test_cut_locations_in_enzyme_notation: .: (0.017772) test_primary: .: (0.005604) test_primary_with_cut_symbols: .: (0.003534) test_to_re: .: (0.003293) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000939) test_align_with_cuts: .: (0.000917) test_argument_error: .: (0.000890) test_ds: .: (0.000887) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000485) test_complement: .: (0.000188) test_contents: .: (0.000161) test_primary: .: (0.000145) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000307) test_complement: .: (0.000107) test_contents: .: (0.000093) test_primary: .: (0.000342) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000177) test_contents: .: (0.000069) test_primary: .: (0.000080) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000175) test_complement_to_array_index: .: (0.000129) test_complement_to_array_index_class: .: (0.000341) test_contents: .: (0.000171) test_primary: .: (0.000182) test_primary_to_array_index: .: (0.000203) test_primary_to_array_index_class: .: (0.000190) test_to_array_index: .: (0.000553) test_to_array_index_class: .: (0.000311) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000403) test_rebase: .: (0.000162) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000744) test_creation_with_no_cuts: .: (0.000622) test_cut_locations: .: (0.000365) test_cut_locations_in_enzyme_notation: .: (0.000346) test_orientation: .: (0.000331) test_pattern: .: (0.000524) test_pattern_palindromic?: .: (0.000414) test_stripped: .: (0.000361) test_to_re: .: (0.002065) test_with_cut_symbols: .: (0.000428) test_with_spaces: .: (0.000382) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000744) test_creation_with_no_cuts: .: (0.000436) test_cut_locations: .: (0.000409) test_cut_locations_in_enzyme_notation: .: (0.000419) test_orientation: .: (0.000373) test_pattern: .: (0.000348) test_pattern_palindromic?: .: (0.000447) test_stripped: .: (0.000346) test_to_re: .: (0.000362) test_with_cut_symbols: .: (0.000388) test_with_spaces: .: (0.000371) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000490) test_initialize_with_pattern: .: (0.000279) test_max: .: (0.000136) test_min: .: (0.000135) test_to_array_index: .: (0.000162) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000221) test_bracket_eq: .: (0.000124) test_concat: .: (0.000079) test_delete: .: (0.000055) test_dup: .: (0.000085) test_each: .: (0.000081) test_eqeq: .: (0.000053) test_eqeq_false: .: (0.000047) test_eqeq_other: .: (0.000043) test_eqeq_self: .: (0.000040) test_include?: .: (0.000049) test_internal_data_hash: .: (0.000044) test_internal_data_hash_eq: .: (0.000071) test_length: .: (0.000042) test_ltlt: .: (0.000047) test_ltlt_noeffect: .: (0.000048) test_plus: .: (0.000048) test_plus_error: .: (0.000090) test_private_push_element: .: (0.000051) test_private_push_element_intermediate: .: (0.000048) test_private_push_element_last: .: (0.000046) test_private_push_element_noeffect: .: (0.000044) test_private_sorted_keys: .: (0.000043) test_private_unshift_element: .: (0.000048) test_private_unshift_element_first: .: (0.000053) test_private_unshift_element_intermediate: .: (0.000048) test_private_unshift_element_noeffect: .: (0.000047) test_push: .: (0.000050) test_reverse_each: .: (0.000086) test_self_bracket: .: (0.000041) test_self_new: .: (0.000064) test_size: .: (0.000039) test_sort!: .: (0.000040) test_to_a: .: (0.000039) test_uniq!: .: (0.000036) test_unshift: .: (0.000053) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000188) test_left_padding: .: (0.000077) test_right_padding: .: (0.000069) test_strip_padding: .: (0.000076) Bio::TestSOFT: test_dataset: .: (0.009787) test_series: .: (0.005013) Bio::TestSOSUIReport: test_entry_id: .: (0.000396) test_prediction: .: (0.000207) test_tmh: .: (0.000193) test_tmhs: .: (0.000219) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000264) test_rs: .: (0.000164) Bio::TestSOSUITMH: test_grade: .: (0.000322) test_range: .: (0.000163) test_sequence: .: (0.000150) Bio::TestSampleGraph: test_bellman_ford: .: (0.000419) test_bfs_shortest_path: .: (0.000196) test_breadth_first_search: .: (0.000169) test_depth_first_search: .: (0.000270) test_dijkstra: .: (0.000212) test_dump_list: .: (0.000410) test_dump_matrix: .: (0.000335) test_extract_subgraph_by_label: .: (0.000217) test_extract_subgraph_by_list: .: (0.000183) test_extract_subgraph_retains_disconnected_nodes: .: (0.000145) test_small_world_aka_node_degree_histogram: .: (0.000146) test_to_matrix: .: (0.000291) test_to_matrix_fixed_index: .: (0.000225) test_undirected_cliquishness: .: (0.000231) Bio::TestScf_version_2: test_complement: .: (0.004622) test_seq: .: (0.004352) test_to_biosequence: .: (0.004375) Bio::TestScf_version_3: test_complement: .: (0.012814) test_seq: .: (0.013292) test_to_biosequence: .: (0.013138) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000326) test_AA_new_sequence_all_legal_symbols: .: (0.000163) test_AA_new_sequence_removes_whitespace: .: (0.000138) test_AA_new_sequence_upcases_symbols: .: (0.000146) test_DNA_new_blank_sequence: .: (0.000139) test_DNA_new_sequence_downcases_symbols: .: (0.000112) test_DNA_new_sequence_removes_whitespace: .: (0.000110) test_NA_randomize_with_counts: .: (0.000637) test_NA_randomize_with_counts_and_block: .: (0.001407) test_RNA_new_sequence: .: (0.000147) test_ambiguous_dna_sequence_complement: .: (0.000116) test_ambiguous_rna_sequence_complement: .: (0.000106) test_amino_acid_codes: .: (0.000145) test_amino_acid_molecular_weight: .: (0.000226) test_amino_acid_names: .: (0.000152) test_amino_acid_randomize_can_be_chained: .: (0.001341) test_amino_acid_randomize_has_same_composition: .: (0.000719) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000421) test_dna_composition: .: (0.000143) test_dna_gc_percent: .: (0.000175) test_dna_molecular_weight: .: (0.000298) test_dna_pikachu: .: (0.000155) test_dna_sequence_complement: .: (0.000157) test_dna_sequence_translate: .: (0.000609) test_dna_to_re: .: (0.000424) test_element_reference_operator_with_one_argument: .: (0.000141) test_element_reference_operator_with_two_arguments: .: (0.000131) test_invalid_nucleic_acid_illegal_bases: .: (0.000153) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000190) test_nucleic_acid_names: .: (0.000165) test_randomize_dna_can_be_chained: .: (0.000315) test_randomize_dna_retains_composition: .: (0.000258) test_randomize_dna_with_block: .: (0.000442) test_rna_composition: .: (0.000141) test_rna_gc_percent: .: (0.000145) test_rna_molecular_weight: .: (0.000193) test_rna_pikachu: .: (0.000128) test_rna_sequence_complement: .: (0.000115) test_rna_sequence_translate: .: (0.000386) test_rna_to_re: .: (0.000239) test_total: .: (0.000175) test_two_consecutive_dna_randomizations_not_equal: .: (0.000261) test_valid_dna_sequence_illegal_bases: .: (0.000163) Bio::TestSequenceAA: test_codes: .: (0.000397) test_molecular_weight: .: (0.000187) test_names: .: (0.000133) test_to_re: .: (0.000176) test_to_s: .: (0.000104) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000291) Bio::TestSequenceAANew: test_new: .: (0.000180) test_new_n: .: (0.000108) test_new_r: .: (0.000106) test_new_t: .: (0.000102) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000229) test_concat: .: (0.000105) test_push: .: (0.000098) test_seq: .: (0.000150) test_splicing: .: (0.000206) test_sum: .: (0.000107) test_to_s: .: (0.000119) test_to_str: .: (0.000098) test_total: .: (0.000108) test_window_search: .: (0.000189) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000202) test_normalize_A: .: (0.000103) test_normalize_a: .: (0.000101) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000916) test_randomize_with_block: .: (0.002703) test_randomize_with_hash: .: (0.001012) test_randomize_with_hash_block: .: (0.002962) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:325:in `test_randomize_equiprobability' =============================================================================== : (0.001060) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:331:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.000875) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000286) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000124) test_subseq_returns_subsequence: .: (0.000105) test_to_s_returns_self_as_string: .: (0.000116) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000235) test_window_search_with_width_3_step_two_with_residual: .: (0.000141) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000261) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000325) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000324) test_na_self_randomize: .: (0.000195) Bio::TestSequenceDBLink: test_database: .: (0.000202) test_id: .: (0.000094) test_secondary_ids: .: (0.000093) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000209) test_parse_uniprot_DR_line: .: (0.000136) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000578) test_output_width_35: .: (0.000280) test_output_width_nil: .: (0.000251) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000480) test_output_after_adding_sequence: .: (0.000259) test_output_after_truncating_sequence: .: (0.000180) test_output_from_error_probabilities: .: (0.001969) test_output_width45: .: (0.000303) test_output_with_converting_score_phred2solexa: .: (0.000443) test_output_with_converting_score_solexa2phred: .: (0.000257) test_output_with_default_score: .: (0.000191) Bio::TestSequenceMasker: test_mask: .: (0.000269) test_mask_with_enumerator: .: (0.000145) test_mask_with_enumerator_empty_mask_char: .: (0.000138) test_mask_with_enumerator_excess: .: (0.000323) test_mask_with_enumerator_longer_mask_char: .: (0.000129) test_mask_with_enumerator_shorter: .: (0.000169) test_mask_with_error_probability: .: (0.000178) test_mask_with_quality_score: .: (0.000132) Bio::TestSequenceNA: test_at_content: .: (0.000365) test_at_skew: .: (0.000203) test_codon_usage: .: (0.000136) test_complement: .: (0.000114) test_dna: .: (0.000138) test_dna!: .: (0.000119) test_forward_complement: .: (0.000141) test_gc_content: .: (0.000201) test_gc_percent: .: (0.000161) test_gc_skew: .: (0.000257) test_iliegal_bases: .: (0.000131) test_molecular_weight: .: (0.000230) test_names: .: (0.000238) test_reverse_complement: .: (0.000160) test_rna: .: (0.000108) test_rna!: .: (0.000119) test_splicing: .: (0.000210) test_to_re: .: (0.000185) test_to_s: .: (0.000110) Bio::TestSequenceNACommon: test_composition: .: (0.000265) test_concat: .: (0.000110) test_push: .: (0.000108) test_seq: .: (0.000173) test_splicing: .: (0.000217) test_sum: .: (0.000109) test_to_s: .: (0.000092) test_to_str: .: (0.000093) test_total: .: (0.000105) test_window_search: .: (0.000273) Bio::TestSequenceNANew: test_new: .: (0.000253) test_new_n: .: (0.000120) test_new_r: .: (0.000096) test_new_t: .: (0.000131) Bio::TestSequenceNATranslation: test_translate: .: (0.000461) test_translate_0: .: (0.000656) test_translate_1: .: (0.000212) test_translate_2: .: (0.000192) test_translate_3: .: (0.000234) test_translate_4: .: (0.000221) test_translate_5: .: (0.000324) test_translate_6: .: (0.000223) test_translate_7: .: (0.000356) test_translate_given_codon_table: .: (0.034649) test_translate_n1: .: (0.000574) test_translate_n2: .: (0.000458) test_translate_n3: .: (0.000432) test_translate_unknown_o: .: (0.000288) test_translate_unknown_x: .: (0.000340) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000347) test_convert_scores_from_phred_to_solexa: .: (0.000345) test_convert_scores_from_solexa_to_phred: .: (0.000161) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000228) test_convert_scores_from_phred: .: (0.000109) test_convert_scores_from_phred_to_solexa: .: (0.000305) test_convert_scores_from_solexa: .: (0.000149) test_convert_scores_from_solexa_to_phred: .: (0.000171) test_convert_scores_to_phred: .: (0.000113) test_convert_scores_to_solexa: .: (0.000499) test_p2q: .: (0.000164) test_phred_p2q: .: (0.000131) test_phred_q2p: .: (0.001539) test_q2p: .: (0.001684) test_quality_score_type: .: (0.000080) test_self_convert_scores_to_solexa: .: (0.000357) test_self_p2q: .: (0.000102) test_self_q2p: .: (0.001313) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000258) test_convert_scores_from_phred: .: (0.000223) test_convert_scores_from_phred_to_solexa: .: (0.000227) test_convert_scores_from_solexa: .: (0.000041) test_convert_scores_from_solexa_to_phred: .: (0.000079) test_convert_scores_to_phred: .: (0.000092) test_convert_scores_to_solexa: .: (0.000038) test_p2q: .: (0.000112) test_q2p: .: (0.002414) test_quality_score_type: .: (0.000131) test_self_convert_scores_to_phred: .: (0.000180) test_self_p2q: .: (0.000180) test_self_q2p: .: (0.001359) test_solexa_p2q: .: (0.000199) test_solexa_q2p: .: (0.001434) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000336) test_center: .: (0.000128) test_chomp: .: (0.000177) test_chop: .: (0.000157) test_delete: .: (0.000118) test_delete_prefix: .: (0.000113) test_delete_suffix: .: (0.000111) test_downcase: .: (0.000140) test_each_char: .: (0.000183) test_each_char_enum: .: (0.000288) test_each_grapheme_cluster: .: (0.000858) test_each_grapheme_cluster_enum: .: (0.000214) test_each_line: .: (0.000194) test_each_line_enum: .: (0.000151) test_gsub: .: (0.000144) test_gsub_with_block: .: (0.000373) test_ljust: .: (0.000125) test_lstrip: .: (0.000133) test_multiply: .: (0.000126) test_next: .: (0.000123) test_reverse: .: (0.000119) test_rjust: .: (0.000129) test_rstrip: .: (0.000147) test_slice: .: (0.000144) test_slice2: .: (0.000130) test_split: .: (0.000155) test_squeeze: .: (0.000126) test_strip: .: (0.000113) test_sub: .: (0.000140) test_sub_with_block: .: (0.000501) test_succ: .: (0.000154) test_swapcase: .: (0.000160) test_tr: .: (0.000151) test_tr_s: .: (0.000143) test_upcase: .: (0.000128) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000312) test_partition_nomatch: .: (0.000152) test_partition_sep_TSeq: .: (0.000146) test_partition_sep_regexp: .: (0.000154) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000280) test_rpartition_nomatch: .: (0.000778) test_rpartition_sep_TSeq: .: (0.000153) test_rpartition_sep_regexp: .: (0.000144) Bio::TestShRNA: test_blocK_it: .: (0.026745) test_blocK_it_: .: (0.021801) test_blocK_it_BLOCK_IT: .: (0.020978) test_blocK_it_BLOCK_iT: .: (0.020438) test_blocK_it_piGene: .: (0.023509) test_bottom_strand: .: (0.021320) test_bottom_strand_class: .: (0.020217) test_bottom_strand_nil: .: (0.019959) test_design: .: (0.021164) test_design_BLOCK_IT: .: (0.020833) test_report: .: (0.020794) test_report_before_design: .: (0.020972) test_top_strand: .: (0.020137) test_top_strand_class: .: (0.021144) test_top_strand_nil: .: (0.020283) Bio::TestShRNANew: test_new: .: (0.000715) Bio::TestSiRNA: test_antisense_size: .: (0.000265) test_design: .: (0.022066) test_design_reynolds: .: (0.051561) test_design_uitei: .: (0.039842) test_max_gc_percent: .: (0.000195) test_min_gc_percent: .: (0.000159) test_reynolds: .: (0.057109) test_reynolds?: .: (0.000233) test_uitei: .: (0.049786) test_uitei?: .: (0.003441) Bio::TestSiRNANew: test_new: .: (0.001289) Bio::TestSiRNAPair: test_antisense: .: (0.049175) test_gc_percent: .: (0.048279) test_report: .: (0.043570) test_rule: .: (0.043424) test_sense: .: (0.044478) test_start: .: (0.046073) test_stop: .: (0.045781) test_target: .: (0.042492) Bio::TestSiRNAPairNew: test_new: .: (0.004189) Bio::TestSim4Report: test_all_hits: .: (0.000866) test_each: .: (0.000426) test_each_hit: .: (0.000281) test_hits: .: (0.000290) test_num_hits: .: (0.000242) test_query_def: .: (0.000209) test_query_id: .: (0.000193) test_query_len: .: (0.000210) test_seq1: .: (0.000253) Bio::TestSim4Report2: test_all_hits: .: (0.007131) test_each: .: (0.000404) test_each_hit: .: (0.000249) test_hits: .: (0.000237) test_num_hits: .: (0.000354) test_query_def: .: (0.000201) test_query_id: .: (0.000192) test_query_len: .: (0.000198) test_seq1: .: (0.000254) Bio::TestSim4Report4: test_all_hits: .: (0.000378) test_each: .: (0.000289) test_each_hit: .: (0.000237) test_hits: .: (0.000290) test_num_hits: .: (0.000236) test_query_def: .: (0.000218) test_query_id: .: (0.000207) test_query_len: .: (0.000195) test_seq1: .: (0.000250) Bio::TestSim4ReportHit: test_align: .: (0.000404) test_complement?: .: (0.000200) test_definition: .: (0.000194) test_each: .: (0.000532) test_exons: .: (0.003568) test_hit_id: .: (0.000928) test_hsps: .: (0.000452) test_introns: .: (0.000394) test_len: .: (0.000242) test_query_def: .: (0.000240) test_query_id: .: (0.000202) test_query_len: .: (0.000191) test_segmentpairs: .: (0.004162) test_seq1: .: (0.000373) test_seq2: .: (0.000256) test_target_def: .: (0.000197) test_target_id: .: (0.000182) test_target_len: .: (0.000192) Bio::TestSim4ReportHit2: test_align: .: (0.000419) test_complement?: .: (0.000206) test_definition: .: (0.000191) test_each: .: (0.000324) test_exons: .: (0.000325) test_hit_id: .: (0.000194) test_hsps: .: (0.000308) test_introns: .: (0.003208) test_len: .: (0.000363) test_query_def: .: (0.000230) test_query_id: .: (0.000185) test_query_len: .: (0.000175) test_segmentpairs: .: (0.000272) test_seq1: .: (0.000147) test_seq2: .: (0.000145) test_target_def: .: (0.000091) test_target_id: .: (0.000084) test_target_len: .: (0.000079) Bio::TestSim4ReportHit4: test_align: .: (0.000311) test_complement?: .: (0.000109) test_definition: .: (0.000092) test_each: .: (0.000268) test_exons: .: (0.000242) test_hit_id: .: (0.000100) test_hsps: .: (0.004700) test_introns: .: (0.000481) test_len: .: (0.000254) test_query_def: .: (0.000233) test_query_id: .: (0.000240) test_query_len: .: (0.000230) test_segmentpairs: .: (0.000406) test_seq1: .: (0.000238) test_seq2: .: (0.005662) test_target_def: .: (0.000563) test_target_id: .: (0.000218) test_target_len: .: (0.005508) Bio::TestSim4ReportSegment: test_from: .: (0.000355) test_self_new: .: (0.000163) test_seq: .: (0.000112) test_to: .: (0.000102) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000499) test_direction: .: (0.000302) test_hit_from: .: (0.000286) test_hit_to: .: (0.000282) test_hseq: .: (0.000313) test_midline: .: (0.001049) test_percent_identity: .: (0.000595) test_qseq: .: (0.000324) test_query_from: .: (0.000280) test_query_to: .: (0.000558) test_seq1: .: (0.000471) test_seq2: .: (0.000410) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000454) test_direction: .: (0.000585) test_hit_from: .: (0.000305) test_hit_to: .: (0.000284) test_hseq: .: (0.000300) test_midline: .: (0.000290) test_percent_identity: .: (0.000263) test_qseq: .: (0.000268) test_query_from: .: (0.000292) test_query_to: .: (0.000270) test_seq1: .: (0.005337) test_seq2: .: (0.000553) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000950) test_direction: .: (0.000416) test_hit_from: .: (0.000399) test_hit_to: .: (0.000388) test_hseq: .: (0.000369) test_midline: .: (0.000355) test_percent_identity: .: (0.000325) test_qseq: .: (0.000536) test_query_from: .: (0.006061) test_query_to: .: (0.000588) test_seq1: .: (0.000373) test_seq2: .: (0.000268) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000360) test_direction: .: (0.000225) test_hit_from: .: (0.000512) test_hit_to: .: (0.000385) test_hseq: .: (0.000334) test_midline: .: (0.000331) test_percent_identity: .: (0.000331) test_qseq: .: (0.000314) test_query_from: .: (0.001071) test_query_to: .: (0.000400) test_seq1: .: (0.000511) test_seq2: .: (0.000403) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000695) test_direction: .: (0.000411) test_hit_from: .: (0.000371) test_hit_to: .: (0.000350) test_hseq: .: (0.000315) test_midline: .: (0.004899) test_percent_identity: .: (0.000511) test_qseq: .: (0.000385) test_query_from: .: (0.000324) test_query_to: .: (0.000302) test_seq1: .: (0.000346) test_seq2: .: (0.000348) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000424) test_direction: .: (0.000334) test_hit_from: .: (0.000302) test_hit_to: .: (0.000259) test_hseq: .: (0.000241) test_midline: .: (0.000237) test_percent_identity: .: (0.000236) test_qseq: .: (0.000588) test_query_from: .: (0.000338) test_query_to: .: (0.000278) test_seq1: .: (0.000331) test_seq2: .: (0.000288) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000426) test_direction: .: (0.000307) test_hit_from: .: (0.000269) test_hit_to: .: (0.007965) test_hseq: .: (0.000825) test_midline: .: (0.000352) test_percent_identity: .: (0.000318) test_qseq: .: (0.000221) test_query_from: .: (0.000170) test_query_to: .: (0.000167) test_seq1: .: (0.000205) test_seq2: .: (0.000190) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000183) test_entry_id: .: (0.000161) test_filename: .: (0.000118) test_len: .: (0.000113) test_self_new: .: (0.000144) test_self_parse: .: (0.000150) Bio::TestTMHMMReport: test_entry_id: .: (0.000618) test_exp_aas_in_tmhs: .: (0.000390) test_exp_first_60aa: .: (0.000351) test_helix: .: (0.000374) test_predicted_tmhs: .: (0.000319) test_query_len: .: (0.000296) test_tmhs: .: (0.000668) test_to_s: .: (0.000387) test_total_prob_of_N_in: .: (0.000292) Bio::TestTMHMMReport_reports: test_reports: .: (0.000271) Bio::TestTMHMMTMH: test_entry_id: .: (0.000391) test_pos: .: (0.001648) test_range: .: (0.000301) test_status: .: (0.000325) test_version: .: (0.000301) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000375) test_cutoff: .: (0.000262) test_entry_id: .: (0.000206) test_length: .: (0.000237) test_loc: .: (0.000210) test_name: .: (0.000179) test_networks: .: (0.000183) test_prediction: .: (0.000204) test_query_len: .: (0.000215) test_query_sequences: .: (0.000200) test_rc: .: (0.000193) test_version: .: (0.000198) Bio::TestTargetPReportConst: test_delimiter: .: (0.000251) test_rs: .: (0.000105) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000196) test_togows_access_wait: .: (2.005542) Bio::TestTogoWSREST: test_debug: .: (0.000610) test_debug_default: .: (0.000275) test_internal_http: .: (0.000211) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000224) test_entry: .: (0.000066) test_entry_database_list: .: (0.000046) test_new: .: (0.000138) test_new_with_uri_object: .: (0.000119) test_new_with_uri_string: .: (0.000098) test_retrieve: .: (0.000040) test_search: .: (0.000039) test_search_database_list: .: (0.000039) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000225) test_prepare_return_value: .: (0.000119) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.004700) Bio::TestTree: test_get_edge_distance: .: (0.000306) test_get_edge_distance_string: .: (0.000157) test_get_node_name: .: (0.000119) test_initialize: .: (0.000334) test_options: .: (0.000145) test_root: .: (0.000113) test_root=: .: (0.000124) Bio::TestTree2: test_add_edge: .: (0.000417) test_add_node: .: (0.006097) test_adjacency_matrix: .: (0.000512) test_adjacency_matrix_with_block: .: (0.000232) test_adjacent_nodes: .: (0.000258) test_adjacent_nodes_nonexistent: .: (0.000199) test_ancestors: .: (0.000209) test_children: .: (0.000127) test_clear: .: (0.009677) test_clear_node: .: (0.000380) test_clear_node_nonexistent: .: (0.000576) test_collect_edge!: .: (0.000314) test_collect_node!: .: (0.000265) test_concat: .: (0.000264) test_descendents: .: (0.000197) test_distance_matrix: .: (0.000426) test_each_edge: .: (0.000225) test_each_node: .: (0.000248) test_each_out_edge: .: (0.000974) test_each_out_edge_chimpanzee: .: (0.000188) test_each_out_edge_human: .: (0.000179) test_each_out_edge_mammals: .: (0.000204) test_each_out_edge_nonexistent: .: (0.000172) test_each_out_edge_primates: .: (0.005665) test_each_out_edge_rat: .: (0.000334) test_each_out_edge_rodents: .: (0.000279) test_edges: .: (0.000213) test_get_edge: .: (0.000604) test_get_edge_indirect: .: (0.000202) test_get_edge_merged: .: (0.000185) test_get_edge_nonexistent: .: (0.000162) test_get_node_bootstrap: .: (0.000178) test_get_node_bootstrap_string=: .: (0.000166) test_get_node_by_name: .: (0.000232) test_get_node_by_name_noexistent: .: (0.000172) test_include?: .: (0.000199) test_include_nonexistent: .: (0.000192) test_insert_node: .: (0.000242) test_leaves: .: (0.000197) test_leaves_noargs: .: (0.000167) test_lowest_common_ancestor: .: (0.000184) test_nodes: .: (0.000168) test_number_of_edges: .: (0.000341) test_number_of_nodes: .: (0.000166) test_out_degree: .: (0.000191) test_out_degree_nonexistent: .: (0.004751) test_out_edges: .: (0.000511) test_out_edges_mammals: .: (0.000260) test_out_edges_nonexistent: .: (0.000180) test_out_edges_primates: .: (0.000221) test_out_edges_rodents: .: (0.000214) test_parent: .: (0.000197) test_path: .: (0.000168) test_remove_edge: .: (0.000177) test_remove_edge_if: .: (0.000343) test_remove_edge_if_nothing_removed: .: (0.000220) test_remove_edge_nonexistent: .: (0.000263) test_remove_node: .: (0.000172) test_remove_node_if: .: (0.000097) test_remove_node_if_false: .: (0.000116) test_remove_node_nonexistent: .: (0.000160) test_remove_nonsense_nodes: .: (0.000134) test_subtree: .: (0.000154) test_subtree_with_all_paths: .: (0.000197) test_total_distance: .: (0.000096) Bio::TestTreeEdge: test_distance: .: (0.000209) test_distance=: .: (0.000069) test_distance_string: .: (0.000040) test_distance_string=: .: (0.000059) test_initialize: .: (0.000064) test_inspect: .: (0.000042) test_to_s: .: (0.000040) Bio::TestTreeNode: test_bootstrap: .: (0.000108) test_bootstrap=: .: (0.000064) test_bootstrap_string: .: (0.000036) test_bootstrap_string=: .: (0.000074) test_initialize: .: (0.000058) test_inspect: .: (0.000060) test_name: .: (0.000043) test_to_s: .: (0.000036) Bio::TestUniProt: test_gene_name: .: (0.008164) Bio::TestUniProtKB: test_ac: .: (0.004815) test_accession: .: (0.007972) test_cc: .: (0.011139) test_cc_alternative_products: .: (0.046090) test_cc_database: .: (0.005015) test_cc_mass_spectrometry: .: (0.003873) test_de: .: (0.003900) test_dr: .: (0.005965) test_dr_with_key: .: (0.004880) test_dr_with_key_empty: .: (0.004529) test_dt: .: (0.004475) test_dt_annotation: .: (0.003423) test_dt_created: .: (0.002589) test_dt_sequence: .: (0.002196) test_entry: .: (0.002057) test_ft: .: (0.009343) test_gene_name: .: (0.003009) test_gene_names: .: (0.002319) test_gn: .: (0.002733) test_gn_old_parser: .: (0.002030) test_gn_uniprot_parser: .: (0.002130) test_id_line: .: (0.004693) test_id_line_data_class: .: (0.003457) test_id_line_entry_name: .: (0.002557) test_id_line_molecule_type: .: (0.002064) test_id_line_sequence_length: .: (0.002626) test_kw: .: (0.001944) test_molecule: .: (0.001877) test_oc: .: (0.005482) test_og_1: .: (0.003038) test_og_2: .: (0.002383) test_og_3: .: (0.002264) test_og_4: .: (0.002623) test_og_5: .: (0.002091) test_og_6: .: (0.004208) test_os: .: (0.003526) test_os_access: .: (0.002495) test_os_access2: .: (0.002355) test_ox: .: (0.002763) test_protein_name: .: (0.002046) test_ref: .: (0.008422) test_seq: .: (0.002896) test_sequence_length: .: (0.002238) test_sq: .: (0.002630) test_sq_crc64: .: (0.002045) test_sq_len: .: (0.004119) test_sq_mw: .: (0.003529) test_synonyms: .: (0.002936) Bio::TestUniProtKB_CC: test_allergen: .: (0.000463) test_alternative_products_access_as_hash: .: (0.000315) test_alternative_products_ai: .: (0.000333) test_alternative_products_apu: .: (0.000705) test_alternative_products_as: .: (0.000383) test_alternative_products_rf: .: (0.000127) test_biophysicochemical_properties: .: (0.000456) test_biotechnology: .: (0.000263) test_catalytic_activity: .: (0.000206) test_caution: .: (0.000264) test_cofactor: .: (0.000227) test_developmental_stage: .: (0.000232) test_disease: .: (0.000309) test_domain: .: (0.000318) test_enzyme_regulation: .: (0.000258) test_function: .: (0.000246) test_induction: .: (0.000199) test_interaction: .: (0.000280) test_mass_spectrometry: .: (0.000304) test_miscellaneous: .: (0.000205) test_pathway: .: (0.000232) test_pharmaceutical: .: (0.000233) test_polymorphism: .: (0.000285) test_ptm: .: (0.000205) test_rna_editing: .: (0.000292) test_similarity: .: (0.000217) test_subcellular_location: .: (0.000258) test_subunit: .: (0.000191) test_tissue_specificity: .: (0.000228) test_toxic_dose: .: (0.000188) test_web_resource: .: (0.000280) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000449) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000452) test_protein_name: .: (0.000942) test_synonyms: .: (0.000368) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000282) test_entry: .: (0.000142) test_entry_id: .: (0.000143) test_entry_name: .: (0.000140) test_id_line: .: (0.000147) test_molecule: .: (0.000148) test_sequence_length: .: (0.000141) Bio::TestUniProtKB_P03589: test_ac: .: (0.000560) test_accession: .: (0.000413) test_cc: .: (0.000563) test_cc_alternative_products: .: (0.000506) test_cc_database: .: (0.000500) test_cc_mass_spectrometry: .: (0.000536) test_de: .: (0.000416) test_dr: .: (0.000571) test_dr_with_key: .: (0.000580) test_dr_with_key_empty: .: (0.000576) test_dt: .: (0.000389) test_dt_annotation: .: (0.000360) test_dt_created: .: (0.000330) test_dt_sequence: .: (0.000353) test_entry: .: (0.000365) test_ft: .: (0.000561) test_gene_name: .: (0.000454) test_gene_names: .: (0.000397) test_gn: .: (0.000369) test_gn_old_parser: .: (0.000413) test_gn_uniprot_parser: .: (0.000404) test_id_line: .: (0.000357) test_id_line_data_class: .: (0.000350) test_id_line_entry_name: .: (0.000370) test_id_line_sequence_length: .: (0.003206) test_kw: .: (0.000558) test_oc: .: (0.000492) test_oh: .: (0.000720) test_os: .: (0.000436) test_os_access: .: (0.000416) test_os_access2: .: (0.001479) test_ox: .: (0.000502) test_protein_name: .: (0.000461) test_protein_name_after_calling_de: .: (0.000448) test_ref: .: (0.000455) test_seq: .: (0.001143) test_sequence_length: .: (0.000437) test_sq: .: (0.000469) test_sq_crc64: .: (0.000451) test_sq_len: .: (0.000460) test_sq_mw: .: (0.000432) test_synonyms: .: (0.000531) Bio::TestUniProtKB_P28907: test_ac: .: (0.001182) test_accession: .: (0.001243) test_cc: .: (0.001413) test_cc_alternative_products: .: (0.001739) test_cc_database: .: (0.002190) test_cc_mass_spectrometry: .: (0.001362) test_de: .: (0.000921) test_dr: .: (0.005490) test_dr_with_key: .: (0.003327) test_dr_with_key_empty: .: (0.004024) test_dt: .: (0.001056) test_dt_annotation: .: (0.000953) test_dt_created: .: (0.000967) test_dt_sequence: .: (0.004056) test_entry: .: (0.001199) test_ft: .: (0.003206) test_gene_name: .: (0.001344) test_gene_names: .: (0.001221) test_gn: .: (0.001204) test_gn_old_parser: .: (0.001081) test_gn_uniprot_parser: .: (0.001052) test_id_line: .: (0.000950) test_id_line_data_class: .: (0.001498) test_id_line_entry_name: .: (0.000875) test_id_line_sequence_length: .: (0.000858) test_kw: .: (0.001061) test_oc: .: (0.000980) test_os: .: (0.000884) test_os_access: .: (0.000970) test_os_access2: .: (0.000996) test_ox: .: (0.003947) test_protein_name: .: (0.001894) test_protein_name_after_calling_de: .: (0.001438) test_ref: .: (0.002025) test_seq: .: (0.001377) test_sequence_length: .: (0.000964) test_sq: .: (0.001094) test_sq_crc64: .: (0.001104) test_sq_len: .: (0.001603) test_sq_mw: .: (0.000953) test_synonyms: .: (0.001027) test_synonyms_after_calling_de: .: (0.001024) Bio::TestUniProtKB_P49144: test_ac: .: (0.000700) test_accession: .: (0.000517) test_cc: .: (0.000893) test_cc_alternative_products: .: (0.000875) test_cc_database: .: (0.000845) test_cc_mass_spectrometry: .: (0.003634) test_de: .: (0.000668) test_dr: .: (0.001075) test_dr_with_key: .: (0.001817) test_dr_with_key_empty: .: (0.001127) test_dt: .: (0.000625) test_dt_annotation: .: (0.001129) test_dt_created: .: (0.000669) test_dt_sequence: .: (0.000595) test_entry: .: (0.000607) test_ft: .: (0.001523) test_gene_name: .: (0.000599) test_gene_names: .: (0.000713) test_gn: .: (0.001269) test_gn_old_parser: .: (0.000588) test_gn_uniprot_parser: .: (0.000541) test_id_line: .: (0.000464) test_id_line_data_class: .: (0.000444) test_id_line_entry_name: .: (0.000427) test_id_line_sequence_length: .: (0.000491) test_kw: .: (0.000607) test_oc: .: (0.000558) test_os: .: (0.000501) test_os_access: .: (0.000495) test_os_access2: .: (0.000521) test_ox: .: (0.000493) test_protein_name: .: (0.000575) test_protein_name_after_calling_de: .: (0.000611) test_ref: .: (0.000672) test_seq: .: (0.000645) test_sequence_length: .: (0.003230) test_sq: .: (0.000881) test_sq_crc64: .: (0.000633) test_sq_len: .: (0.000715) test_sq_mw: .: (0.001430) test_synonyms: .: (0.000706) test_synonyms_after_calling_de: .: (0.000674) Bio::TestUniProtKB_Ref: test_RA: .: (0.000517) test_RC: .: (0.000431) test_RG: .: (0.000289) test_RL: .: (0.000257) test_RN: .: (0.000248) test_RP: .: (0.000268) test_RT: .: (0.000252) test_RX: .: (0.000259) test_ref: .: (0.000263) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000583) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000523) test_alternative_products_with_ft: .: (0.000653) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000374) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000314) test_RL_lines: .: (0.000177) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000560) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000283) test_RG_line: .: (0.000187) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000472) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000320) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000237) test_RL_line: .: (0.000171) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000680) test_RP_line: .: (0.000265) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000177) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000317) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000273) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000222) test_CC_interaction_isoform: .: (0.000197) test_CC_interaction_no_gene_name: .: (0.000234) test_CC_interaction_self_association: .: (0.000280) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000343) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000350) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000368) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000300) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000298) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000292) test_DT_line: .: (0.000224) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.003142) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000751) test_CC_web_resource: .: (0.000126) test_FT_VER_SEQ: .: (0.000239) test_OH_line_exception: .: (0.000283) test_OH_lines: .: (0.000308) Bio::TestUtils: test_centreOfGravity: .: (0.000481) test_dihedral_angle: .: (0.000421) test_distance: .: (0.000327) test_geometricCentre: .: (0.000306) test_rad2deg: .: (0.000192) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000330) test_dijkstra_on_weighted_graph: .: (0.000174) Finished in 12.490327617 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 315.52 tests/s, 1729.42 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-2.0.6' 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_2.0.6-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.6-1_arm64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.6-1_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/515837 and its subdirectories I: Current time: Mon Sep 29 00:43:56 -12 2025 I: pbuilder-time-stamp: 1759149836 Mon Sep 29 12:43:58 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Mon Sep 29 12:43:58 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Mon Sep 29 12:44:58 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Mon Sep 29 12:44:59 UTC 2025 I: ruby-bio_2.0.6-1_arm64.changes: Format: 1.8 Date: Fri, 26 Sep 2025 16:59:33 +0530 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Ruby Team Changed-By: Nilesh Patra Description: ruby-bio - Ruby tools for computational molecular biology Closes: 1116111 Changes: ruby-bio (2.0.6-1) unstable; urgency=medium . * Team Upload. . [ Lucas Nussbaum ] * debian/gbp.conf: Add for DEP-14 * debian/gbp.conf: remove trailing empty lines * debian/.gitattributes: remove * debian/salsa-ci.yml: use team-specific include . [ Nilesh Patra ] * New upstream version 2.0.6 * Change Recommends from blast2 => ncbi-blast+-legacy Closes: #1116111 * Bump Standards-Version to 4.7.2 (no changes needed) * Drop myself from uploaders Checksums-Sha1: 68b9d38780c52e4778cb2da4df127794d40c30cb 705580 ruby-bio_2.0.6-1_all.deb fb12cd641b65f2f8bfbab13cf6446f8bb578d58c 7488 ruby-bio_2.0.6-1_arm64.buildinfo Checksums-Sha256: 11173dfaa9e46e2e4888606f2e352d1c63c63f5edf863c011dae91ece002230c 705580 ruby-bio_2.0.6-1_all.deb b3002f5c28f05302e419e7a539c56ec06a23c905e79f6752884e603fc3621416 7488 ruby-bio_2.0.6-1_arm64.buildinfo Files: 828bb6ced0347bf22572590ac7cb273f 705580 ruby optional ruby-bio_2.0.6-1_all.deb e1bfa2ec98f216a1b65c0eafb797f5b5 7488 ruby optional ruby-bio_2.0.6-1_arm64.buildinfo Mon Sep 29 12:45:00 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_11-126025.service; invocation ID: cba1cfb78bba403a93af948c1a74ecff # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/ruby-bio_2.0.6-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/ruby-bio_2.0.6-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/ruby-bio_2.0.6-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/b1/ruby-bio_2.0.6-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/b2/ruby-bio_2.0.6-1_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/SUCCESS Service runtime: 219ms CPU time consumed: 170ms Memory peak: 18M (swap: 0B) Mon Sep 29 12:45:00 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Mon Sep 29 12:45:00 UTC 2025 I: ruby-bio from forky built successfully and reproducibly on arm64. Mon Sep 29 12:45:01 UTC 2025 I: Removing signed ruby-bio_2.0.6-1_arm64.buildinfo.asc files: removed './b1/ruby-bio_2.0.6-1_arm64.buildinfo.asc' removed './b2/ruby-bio_2.0.6-1_arm64.buildinfo.asc'