Fri May 31 22:30:43 UTC 2024 I: starting to build ruby-bio/trixie/amd64 on jenkins on '2024-05-31 22:30' Fri May 31 22:30:43 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_16/22454/console.log Fri May 31 22:30:43 UTC 2024 I: Downloading source for trixie/ruby-bio=2.0.5-1 --2024-05-31 22:30:43-- http://deb.debian.org/debian/pool/main/r/ruby-bio/ruby-bio_2.0.5-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2108 (2.1K) [text/prs.lines.tag] Saving to: ‘ruby-bio_2.0.5-1.dsc’ 0K .. 100% 285M=0s 2024-05-31 22:30:43 (285 MB/s) - ‘ruby-bio_2.0.5-1.dsc’ saved [2108/2108] Fri May 31 22:30:43 UTC 2024 I: ruby-bio_2.0.5-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.5-1 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Nilesh Patra Homepage: https://bioruby.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-bio Vcs-Git: https://salsa.debian.org/ruby-team/ruby-bio.git Testsuite: autopkgtest-pkg-ruby Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Package-List: ruby-bio deb ruby optional arch=all Checksums-Sha1: c5eafc8420a966903759ca1971b56b977d5c19b7 1403239 ruby-bio_2.0.5.orig.tar.gz f481b14185f8a52163cead283563fa8287e4e32f 14388 ruby-bio_2.0.5-1.debian.tar.xz Checksums-Sha256: 9f66cc728e61a0608cba24ccbee03a5c4fd08e8b6a51cd65b608e6a1d6389b1d 1403239 ruby-bio_2.0.5.orig.tar.gz e012d4a27cd47da374f43f35c775f541b645badbb2feeda94836f628534a5086 14388 ruby-bio_2.0.5-1.debian.tar.xz Files: 76215231a9bb1d93a22a0eba24647886 1403239 ruby-bio_2.0.5.orig.tar.gz 9d2401ccde190177cc92465890847141 14388 ruby-bio_2.0.5-1.debian.tar.xz Ruby-Versions: all -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE/t7ByzN7z1CfQ8IkORS1MvTfvpkFAmXkefUACgkQORS1MvTf vpmcDhAAnrwI3Wbj3eGvkYew5UH6Rgau+ritM1SzyzaMftoOhT/RmN96MlWK8I0t BIPwqtsz8QxIcgNtMVqV6TsDz3Cwgkv2ffudm9z6jvnYyJar83HHOnot7hSTWdgU FhxDIpCHnn3G+FHd8KNCfLwlizy/TWhIHVM355FL7wuw3ddzEQmsidn2s+lf44Qj f6dOhvjRspWshnnCUUzcGLpv5a+m2aVZDdjGangK3qjOI30TfoVKwfp7ZwXr2A7H WlNEgz04WE4s1O1dXjfU9l1YWpZ+4qRSr6EpAYpOJS/9uBsLgbj36VE4GHraCHxJ V9YDjfiwdiXARaJ1T2RuvVfbGwOtcM90r44jIyaJrcMJQIy2krKEg8v7t7yVgEHV hEfz5J7JIli77uqPxA37WaD10GzUykY65TKvLhvt27ZheMbS4k8JZ5zS+OfZC8F/ lhk7TSimAOS3mVAbkNEy3cPX3ue7J5H8h0VhOPSDpNAkFyoIV2V6bcnuBccGHjX8 v68T8yJLKMtxJkh9VMlcHtgI9Zg2VK93qZ7rEC0FKXlRzjqYscbD43rqevJumbeG ZFiKNbCngp/cWxNFrTLKEP9eqt8+22In+7qq6aFDqUMjcTB5Yo8MrHtRLNtN/BJa Xvnzdh2UtKaG9vYNrB1AaknU7Knq6sInvVdenAePLpdqCrA4+bY= =z+Qe -----END PGP SIGNATURE----- Fri May 31 22:30:43 UTC 2024 I: Checking whether the package is not for us Fri May 31 22:30:43 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri May 31 22:30:43 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri May 31 22:31:53 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 3 16:53:46 -12 2025 I: pbuilder-time-stamp: 1751604826 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ruby-bio_2.0.5-1.dsc] I: copying [./ruby-bio_2.0.5.orig.tar.gz] I: copying [./ruby-bio_2.0.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 3 13:24:05 2024 gpgv: using RSA key FEDEC1CB337BCF509F43C2243914B532F4DFBE99 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.5-1.dsc: no acceptable signature found dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.5 dpkg-source: info: unpacking ruby-bio_2.0.5.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable_tests_using_chi2.patch dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3150131/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4fc604c9fcd24bdf9a5b8d0efd0a55bf' 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='3150131' 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.gRDLdcBv/pbuilderrc_3OAR --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/b1 --logfile b1/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 29 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3150131/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: amd64 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 ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libb-hooks-op-check-perl{a} libbsd0{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap-2.5-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} 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 dput dput-ng dupload equivs fonts-lato libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc strace unzip wget zip 0 packages upgraded, 134 newly installed, 0 to remove and 0 not upgraded. Need to get 48.7 MB of archives. After unpacking 171 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.1-2 [94.2 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.40-3 [950 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.40-3 [847 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 64 http://deb.debian.org/debian trixie/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 95 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 devscripts all 2.23.7 [1068 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 docbook all 4.5-11 [126 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 docbook-to-man amd64 1:2.0.0-46 [73.3 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 123 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 125 http://deb.debian.org/debian trixie/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 gem2deb-test-runner amd64 2.2.3 [17.8 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 ruby3.1-dev amd64 3.1.2-8.3 [1001 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 ruby-all-dev amd64 1:3.1+nmu1 [5672 B] Get: 131 http://deb.debian.org/debian trixie/main amd64 gem2deb amd64 2.2.3 [47.8 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 ruby-libxml amd64 3.2.4-2+b2 [83.5 kB] Fetched 48.7 MB in 7s (7427 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21007 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. 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Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.1-2_amd64.deb ... Unpacking bsdextrautils (2.40.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... 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Preparing to unpack .../038-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnpth0t64:amd64. Preparing to unpack .../039-libnpth0t64_1.6-3.1_amd64.deb ... Unpacking libnpth0t64:amd64 (1.6-3.1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../040-dirmngr_2.2.40-3_amd64.deb ... Unpacking dirmngr (2.2.40-3) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../041-gnupg-l10n_2.2.40-3_all.deb ... Unpacking gnupg-l10n (2.2.40-3) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../042-gnupg-utils_2.2.40-3_amd64.deb ... Unpacking gnupg-utils (2.2.40-3) ... Selecting previously unselected package gpg. Preparing to unpack .../043-gpg_2.2.40-3_amd64.deb ... Unpacking gpg (2.2.40-3) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../044-pinentry-curses_1.2.1-3+b2_amd64.deb ... Unpacking pinentry-curses (1.2.1-3+b2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../045-gpg-agent_2.2.40-3_amd64.deb ... Unpacking gpg-agent (2.2.40-3) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../046-gpg-wks-client_2.2.40-3_amd64.deb ... Unpacking gpg-wks-client (2.2.40-3) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../047-gpg-wks-server_2.2.40-3_amd64.deb ... Unpacking gpg-wks-server (2.2.40-3) ... Selecting previously unselected package gpgsm. Preparing to unpack .../048-gpgsm_2.2.40-3_amd64.deb ... Unpacking gpgsm (2.2.40-3) ... Selecting previously unselected package gnupg. Preparing to unpack .../049-gnupg_2.2.40-3_all.deb ... Unpacking gnupg (2.2.40-3) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../050-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../051-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../052-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../053-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../054-libio-pty-perl_1%3a1.20-1+b1_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1+b1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../055-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../056-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../057-libclass-xsaccessor-perl_1.19-4+b3_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b3) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../058-libb-hooks-op-check-perl_0.22-3+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../059-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../060-libdevel-callchecker-perl_0.009-1_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.009-1) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../061-libparams-classify-perl_0.015-2+b3_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../062-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../063-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../064-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../065-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. 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Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../078-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../079-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../080-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../081-perl-openssl-defaults_7+b2_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:amd64. Preparing to unpack .../082-libnet-ssleay-perl_1.94-1+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.94-1+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../083-libio-socket-ssl-perl_2.085-1_all.deb ... Unpacking libio-socket-ssl-perl (2.085-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../084-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 .../085-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 .../086-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../087-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../088-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../089-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../090-wdiff_1.2.2-6_amd64.deb ... Unpacking wdiff (1.2.2-6) ... Selecting previously unselected package devscripts. Preparing to unpack .../091-devscripts_2.23.7_all.deb ... Unpacking devscripts (2.23.7) ... Selecting previously unselected package xml-core. Preparing to unpack .../092-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../093-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../094-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../095-libosp5_1.5.2-15_amd64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../096-opensp_1.5.2-15_amd64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../097-docbook-to-man_1%3a2.0.0-46_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-46) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../098-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../099-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../100-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../101-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../102-ruby-sdbm_1.0.0-5+b4_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../103-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../104-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../105-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../106-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../107-libruby3.1t64_3.1.2-8.3_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../108-ruby3.1_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../109-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../110-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../111-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../112-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../113-gem2deb-test-runner_2.2.3_amd64.deb ... Unpacking gem2deb-test-runner (2.2.3) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../114-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../115-libgmp-dev_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package ruby3.1-dev:amd64. Preparing to unpack .../116-ruby3.1-dev_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1-dev:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby-all-dev:amd64. Preparing to unpack .../117-ruby-all-dev_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:3.1+nmu1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../118-gem2deb_2.2.3_amd64.deb ... Unpacking gem2deb (2.2.3) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../119-ruby-rd_0.6.38-4.1_all.deb ... Unpacking ruby-rd (0.6.38-4.1) ... Selecting previously unselected package rdtool. Preparing to unpack .../120-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:amd64. Preparing to unpack .../121-ruby-libxml_3.2.4-2+b2_amd64.deb ... Unpacking ruby-libxml:amd64 (3.2.4-2+b2) ... Setting up libksba8:amd64 (1.6.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:amd64 (1.6-3.1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-2) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-3) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libosp5 (1.5.2-15) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jul 4 04:54:21 UTC 2025. Universal Time is now: Fri Jul 4 04:54:21 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gpg-wks-server (2.2.40-3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up gnupg (2.2.40-3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.0.6-3) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1-dev:amd64 (3.1.2-8.3) ... Setting up ruby-libxml:amd64 (3.2.4-2+b2) ... Setting up gem2deb-test-runner (2.2.3) ... Setting up ruby-all-dev:amd64 (1:3.1+nmu1) ... Setting up gem2deb (2.2.3) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-46) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lucas Nussbaum dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.5.gemspec /usr/bin/ruby3.1 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.1 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.1.0:/var/lib/gems/3.1.0:/usr/local/lib/ruby/gems/3.1.0:/usr/lib/ruby/gems/3.1.0:/usr/lib/x86_64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/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/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000411) test_dbs: .: (0.000195) test_go_ids: .: (0.000198) test_go_terms: .: (0.000305) test_parser: .: (0.000350) test_set_date: .: (0.000188) test_set_desc: .: (0.000183) test_to_str: .: (0.000216) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000660) test_mktmpdir_without_block: .: (0.000515) test_remove_entry_secure: .: (0.000357) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.002649) test_call_command_fork: .: (0.000226) test_call_command_open3: .: (0.002041) test_call_command_popen: .: (0.001928) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.001880) test_call_command_fork: .: (0.000164) test_call_command_open3: .: (0.001926) test_call_command_popen: .: (0.001738) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.001798) test_call_command_fork: .: (0.000171) test_call_command_open3: .: (0.001733) test_call_command_popen: .: (0.001860) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.001712) test_call_command_fork_chdir: .: (0.000325) test_call_command_popen_chdir: .: (0.001470) test_query_command_chdir: .: (0.001449) test_query_command_fork_chdir: .: (0.007791) test_query_command_popen_chdir: .: (0.001553) Bio::FuncTestCommandQuery: test_query_command: .: (0.005950) test_query_command_fork: .: (0.001194) test_query_command_open3: .: (0.005342) test_query_command_popen: .: (0.005144) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000720) test_initialize: .: (0.000436) test_path: .: (0.000291) test_path_after_close: .: (0.000895) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.008997) test_output_fasta: .: (0.005095) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000242) test_accession: .: (0.000112) test_accessions: .: (0.000173) test_comment: .: (0.000091) test_common_name: .: (0.000121) test_definition: .: (0.000109) test_features: .: (0.000222) test_gi: .: (0.000104) test_keywords: .: (0.000096) test_locus: .: (0.000064) test_nid: .: (0.000103) test_organism: .: (0.000117) test_origin: .: (0.000086) test_references: .: (0.000461) test_segment: .: (0.000106) test_source: .: (0.000179) test_taxonomy: .: (0.000107) test_version: .: (0.000101) test_versions: .: (0.000097) Bio::TestAA: test_13: .: (0.000136) test_1n: .: (0.000056) test_name2one: .: (0.000253) test_name2three: .: (0.000170) test_one2name: .: (0.000125) test_one2three: .: (0.000127) test_three2name: .: (0.000129) test_three2one: .: (0.000159) test_to_1_1: .: (0.000131) test_to_1_3: .: (0.000162) test_to_1_name: .: (0.000165) test_to_3_1: .: (0.000131) test_to_3_3: .: (0.000113) test_to_3_name: .: (0.000142) test_to_re: .: (0.000173) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000249) Bio::TestAAindex: test_api: .: (0.000154) test_auto_aax1: .: (0.000482) test_auto_aax2: .: (0.000253) Bio::TestAAindex1: test_author: .: (0.000301) test_comment: .: (0.000224) test_correlation_coefficient: .: (0.000345) test_dblinks: .: (0.000200) test_definition: .: (0.000198) test_entry_id: .: (0.000190) test_index: .: (0.000253) test_journal: .: (0.000480) test_title: .: (0.000293) Bio::TestAAindex2: test_access_A_R: .: (0.000714) test_access_R_A: .: (0.000490) test_author: .: (0.000375) test_cols: .: (0.000242) test_comment: .: (0.000244) test_dblinks: .: (0.000219) test_definition: .: (0.000226) test_entry_id: .: (0.000230) test_journal: .: (0.000258) test_matrix: .: (0.000542) test_matrix_1_2: .: (0.000527) test_matrix_2_2: .: (0.003993) test_matrix_A_R: .: (0.000576) test_matrix_R_A: .: (0.000840) test_matrix_determinant: .: (0.002644) test_matrix_rank: .: (0.002732) test_matrix_transpose: .: (0.000708) test_rows: .: (0.000210) test_title: .: (0.000249) Bio::TestAAindexConstant: test_delimiter: .: (0.000179) test_tagsize: .: (0.000090) Bio::TestAbif: test_complement: .: (0.008580) test_seq: .: (0.007412) test_to_biosequence: .: (0.008098) Bio::TestActsLikeMap: test_mixin: .: (0.000254) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000270) Bio::TestActsLikeMarker: test_mixin: .: (0.000305) Bio::TestAlignment: test_add_seq_no_key: .: (0.000287) test_add_seq_using_seq_with_aaseq_method: .: (0.000167) test_add_seq_using_seq_with_definition_method: .: (0.000159) test_add_seq_using_seq_with_entry_id_method: .: (0.000148) test_add_seq_using_seq_with_naseq_method: .: (0.000142) test_add_seq_using_seq_with_seq_method: .: (0.000162) test_consensus_iupac_gap_modes: .: (0.000374) test_consensus_iupac_missing_char: .: (0.000229) test_consensus_iupac_missing_char_option: .: (0.000475) test_consensus_iupac_no_gaps: .: (0.000234) test_consensus_iupac_of_ambiguous_bases: .: (0.000290) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.003928) test_consensus_opt_gap_mode: .: (0.000814) test_consensus_opt_missing_char: .: (0.000228) test_consensus_string_no_gaps: .: (0.000220) test_consensus_threshold_four_sequences: .: (0.000295) test_consensus_threshold_two_sequences: .: (0.000331) test_convert_match: .: (0.000422) test_convert_unmatch: .: (0.000197) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000162) test_convert_unmatch_different_match_char: .: (0.000177) test_convert_unmatch_multiple_sequences: .: (0.000242) test_default_gap_char: .: (0.000125) test_default_gap_regexp_matches_default_gap_char: .: (0.000130) test_default_missing_char: .: (0.000155) test_each_site_equal_length: .: (0.000181) test_each_site_unequal_length: .: (0.000164) test_equals: .: (0.000241) test_match_line_protein: .: (0.000409) test_normalizebang_extends_sequences_with_gaps: .: (0.000168) test_seq_length_is_max_seq_length: .: (0.000160) test_seq_length_when_one_sequence: .: (0.000125) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000124) test_seqclass_when_seqclass_set: .: (0.000144) test_seqclass_when_sequence_used: .: (0.000136) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000146) test_set_and_get_gap_char: .: (0.000130) test_store_cannot_override_key: .: (0.000412) test_store_with_default_keys_and_user_defined_keys: .: (0.000175) test_store_with_nil_key_uses_next_number_for_key: .: (0.000149) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000292) test_alignment_concat: .: (0.000156) test_alignment_length: .: (0.000190) test_alignment_lstrip!: .: (0.000212) test_alignment_lstrip_nil: .: (0.000185) test_alignment_normalize!: .: (0.000176) test_alignment_rstrip!: .: (0.000244) test_alignment_rstrip_nil: .: (0.000160) test_alignment_site: .: (0.000219) test_alignment_slice: .: (0.000130) test_alignment_strip!: .: (0.000233) test_alignment_strip_nil: .: (0.000170) test_alignment_subseq: .: (0.000190) test_alignment_window: .: (0.000151) test_collect_each_site: .: (0.000176) test_consensus_each_site_default: .: (0.000204) test_consensus_each_site_gap_mode_1: .: (0.002753) test_consensus_each_site_gap_mode_minus1: .: (0.000197) test_consensus_iupac: .: (0.000419) test_consensus_string_default: .: (0.000228) test_consensus_string_half: .: (0.000208) test_convert_match: .: (0.000188) test_convert_unmatch: .: (0.000171) test_each_seq: .: (0.000162) test_each_site: .: (0.000247) test_each_site_step: .: (0.000198) test_each_window: .: (0.000239) test_match_line: .: (0.000717) test_match_line_amino: .: (0.001184) test_match_line_nuc: .: (0.000201) test_private_alignment_site: .: (0.000165) test_remove_all_gaps!: .: (0.000144) test_seqclass: .: (0.000145) test_seqclass=: .: (0.000163) test_seqclass_default: .: (0.000129) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.003076) test_determine_seq_method: .: (0.001367) test_entries: .: (0.000328) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000312) test_avoid_same_name_numbering: .: (0.000201) test_clustal_have_same_name_true: .: (0.000181) test_have_same_name_false: .: (0.000157) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000301) test_gap_char_default: .: (0.000147) test_gap_char_never_nil: .: (0.000150) test_gap_regexp: .: (0.000303) test_gap_regexp=: .: (0.000155) test_gap_regexp_never_nil: .: (0.000145) test_get_all_property_default: .: (0.000127) test_get_all_property_nodefault: .: (0.000147) test_is_gap_default_false: .: (0.000148) test_is_gap_default_true: .: (0.000144) test_is_gap_nodefault_false: .: (0.000156) test_is_gap_nodefault_true: .: (0.000141) test_missing_char=: .: (0.000136) test_missing_char_default: .: (0.000147) test_missing_char_never_nil: .: (0.000164) test_seqclass=: .: (0.000155) test_seqclass_default: .: (0.000148) test_seqclass_never_nil: .: (0.000128) test_set_all_property: .: (0.000267) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000524) test_consensus_string_50percent: .: (0.000166) test_consensus_string_50percent_nil: .: (0.000153) test_consensus_string_default: .: (0.000155) test_consensus_string_default_nil: .: (0.000152) test_has_gap_false: .: (0.000193) test_has_gap_true: .: (0.000127) test_match_line_amino_100percent: .: (0.000192) test_match_line_amino_missing: .: (0.000260) test_match_line_amino_strong: .: (0.000294) test_match_line_amino_weak: .: (0.000199) test_match_line_nuc_100percent: .: (0.000190) test_match_line_nuc_missing: .: (0.000153) test_remove_gaps!: .: (0.000131) test_remove_gaps_bang_not_removed: .: (0.000137) Bio::TestAtomFinder: test_atoms: .: (0.041283) test_each_atom: .: (0.010705) test_find_atom: .: (0.000256) Bio::TestBioFastaDefline: test_acc_version: .: (0.000442) test_accession: .: (0.000418) test_accessions: .: (0.000356) test_description: .: (0.000611) test_descriptions: .: (0.000288) test_entry_id: .: (0.000266) test_get: .: (0.000360) test_get_all_by_type: .: (0.000524) test_get_by_type: .: (0.000275) test_gi: .: (0.000263) test_id_strings: .: (0.000514) test_locus: .: (0.000726) test_method_missing: .: (0.000328) test_to_s: .: (0.000410) test_words: .: (0.001070) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000751) test_goid2term: .: (0.000387) test_parse_goids: .: (0.000354) Bio::TestBioGenBank: test_basecount: .: (0.000776) test_circular: .: (0.000388) test_classification: .: (0.000331) test_date: .: (0.000261) test_date_modified: .: (0.000715) test_division: .: (0.000285) test_each_cds_feature: .: (0.000661) test_each_cds_qualifiers: .: (0.000712) test_each_gene: .: (0.000839) test_entry_id: .: (0.000311) test_length: .: (0.000245) test_locus_circular: .: (0.000309) test_locus_class: .: (0.000298) test_locus_date: .: (0.000293) test_locus_division: .: (0.000273) test_locus_entry_id: .: (0.000271) test_locus_length: .: (0.000347) test_locus_natype: .: (0.000600) test_locus_strand: .: (0.000340) test_natype: .: (0.000257) test_seq: .: (0.000317) test_seq_len: .: (0.000371) test_strand: .: (0.000291) test_strandedness: .: (0.000240) test_to_biosequence: .: (0.001825) Bio::TestBioGenPept: test_circular: .: (0.000382) test_date: .: (0.000494) test_dbsource: .: (0.000230) test_division: .: (0.000215) test_entry_id: .: (0.000234) test_length: .: (0.000226) test_locus: .: (0.000268) test_seq: .: (0.000316) test_seq_len: .: (0.000295) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000381) test_aaseq: .: (0.000543) test_chromosome: .: (0.000288) test_codon_usage: .: (0.000342) test_cu_list: .: (0.000237) test_dblinks_as_hash: .: (0.000263) test_dblinks_as_strings: .: (0.000219) test_definition: .: (0.000297) test_division: .: (0.000266) test_eclinks: .: (0.000325) test_entry: .: (0.000309) test_entry_id: .: (0.000262) test_gbposition: .: (0.000291) test_gene: .: (0.000302) test_genes: .: (0.000283) test_keggclass: .: (0.000274) test_keggclasses: .: (0.000319) test_locations: .: (0.000360) test_motifs_as_hash: .: (0.000536) test_motifs_as_strings: .: (0.000254) test_name: .: (0.000251) test_names_as_array: .: (0.000272) test_new: .: (0.000256) test_ntlen: .: (0.000319) test_ntseq: .: (0.000349) test_organism: .: (0.000277) test_orthologs_as_hash: .: (0.000286) test_orthologs_as_strings: .: (0.000303) test_pathway: .: (0.000269) test_pathway_after_pathways_as_strings: .: (0.000336) test_pathway_before_pathways_as_strings: .: (0.000348) test_pathways_as_hash: .: (0.000296) test_pathways_as_strings: .: (0.000249) test_position: .: (0.000372) test_structure: .: (0.000302) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001177) test_comment: .: (0.000402) test_data_source: .: (0.000385) test_definition: .: (0.000414) test_disease: .: (0.000433) test_entry_id: .: (0.000386) test_lineage: .: (0.000500) test_nalen: .: (0.000427) test_name: .: (0.000386) test_new: .: (0.000367) test_num_gene: .: (0.000403) test_num_rna: .: (0.000397) test_original_databases: .: (0.000395) test_original_db: .: (0.000370) test_plasmids: .: (0.000376) test_references: .: (0.002208) test_statistics: .: (0.000468) test_taxid: .: (0.000487) test_taxonomy: .: (0.000410) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000463) test_comment: .: (0.000348) test_data_source: .: (0.000275) test_definition: .: (0.000325) test_disease: .: (0.000303) test_entry_id: .: (0.000299) test_lineage: .: (0.000347) test_nalen: .: (0.000276) test_name: .: (0.000250) test_new: .: (0.000262) test_num_gene: .: (0.000309) test_num_rna: .: (0.000255) test_original_databases: .: (0.000329) test_original_db: .: (0.000266) test_plasmids: .: (0.000364) test_references: .: (0.000388) test_statistics: .: (0.000258) test_taxid: .: (0.000351) test_taxonomy: .: (0.000327) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000419) test_compounds_as_strings: .: (0.000266) test_dblinks_as_hash: .: (0.000271) test_dblinks_as_strings: .: (0.000226) test_description: .: (0.000299) test_diseases_as_hash: .: (0.000211) test_diseases_as_strings: .: (0.000244) test_entry_id: .: (0.000225) test_enzymes_as_strings: .: (0.000279) test_genes_as_hash: .: (0.000244) test_genes_as_strings: .: (0.000287) test_keggclass: .: (0.000279) test_ko_pathway: .: (0.000312) test_modules_as_hash: .: (0.000291) test_modules_as_strings: .: (0.000274) test_name: .: (0.000243) test_new: .: (0.000283) test_organism: .: (0.000254) test_orthologs_as_hash: .: (0.000281) test_orthologs_as_strings: .: (0.000253) test_pathways_as_hash: .: (0.000287) test_pathways_as_strings: .: (0.000234) test_reactions_as_hash: .: (0.000250) test_reactions_as_strings: .: (0.000237) test_references: .: (0.000265) test_rel_pathways_as_hash: .: (0.000268) test_rel_pathways_as_strings: .: (0.000300) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000607) test_compounds_as_strings: .: (0.000364) test_dblinks_as_hash: .: (0.000269) test_dblinks_as_strings: .: (0.000308) test_description: .: (0.000296) test_diseases_as_hash: .: (0.000346) test_diseases_as_strings: .: (0.000281) test_entry_id: .: (0.000380) test_enzymes_as_strings: .: (0.000286) test_genes_as_hash: .: (0.000371) test_genes_as_strings: .: (0.000295) test_keggclass: .: (0.000278) test_ko_pathway: .: (0.000239) test_modules_as_hash: .: (0.000287) test_modules_as_strings: .: (0.000255) test_name: .: (0.000228) test_new: .: (0.000203) test_organism: .: (0.000170) test_orthologs_as_hash: .: (0.000219) test_orthologs_as_strings: .: (0.000160) test_pathways_as_hash: .: (0.000331) test_pathways_as_strings: .: (0.000220) test_reactions_as_hash: .: (0.000278) test_reactions_as_strings: .: (0.000214) test_references: .: (0.000287) test_rel_pathways_as_hash: .: (0.000310) test_rel_pathways_as_strings: .: (0.000254) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000406) test_compounds_as_strings: .: (0.000250) test_dblinks_as_hash: .: (0.000212) test_dblinks_as_strings: .: (0.000197) test_description: .: (0.000271) test_diseases_as_hash: .: (0.000183) test_diseases_as_strings: .: (0.000262) test_entry_id: .: (0.000244) test_enzymes_as_strings: .: (0.000250) test_genes_as_hash: .: (0.000217) test_genes_as_strings: .: (0.000272) test_keggclass: .: (0.000251) test_ko_pathway: .: (0.000295) test_modules_as_hash: .: (0.000244) test_modules_as_strings: .: (0.000246) test_name: .: (0.000252) test_new: .: (0.000226) test_organism: .: (0.000255) test_orthologs_as_hash: .: (0.000322) test_orthologs_as_strings: .: (0.000276) test_pathways_as_hash: .: (0.000258) test_pathways_as_strings: .: (0.000262) test_reactions_as_hash: .: (0.000258) test_reactions_as_strings: .: (0.000231) test_references: .: (0.000240) test_rel_pathways_as_hash: .: (0.000225) test_rel_pathways_as_strings: .: (0.000291) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000380) test_compounds_as_strings: .: (0.000295) test_dblinks_as_hash: .: (0.000306) test_dblinks_as_strings: .: (0.000308) test_description: .: (0.000501) test_diseases_as_hash: .: (0.000294) test_diseases_as_strings: .: (0.000281) test_entry_id: .: (0.000325) test_enzymes_as_strings: .: (0.000281) test_genes_as_hash: .: (0.000262) test_genes_as_strings: .: (0.000254) test_keggclass: .: (0.000357) test_ko_pathway: .: (0.000282) test_modules_as_hash: .: (0.000349) test_modules_as_strings: .: (0.000342) test_name: .: (0.000342) test_new: .: (0.000304) test_organism: .: (0.000348) test_orthologs_as_hash: .: (0.000311) test_orthologs_as_strings: .: (0.000325) test_pathways_as_hash: .: (0.000265) test_pathways_as_strings: .: (0.000298) test_reactions_as_hash: .: (0.000250) test_reactions_as_strings: .: (0.000262) test_references: .: (0.000707) test_rel_pathways_as_hash: .: (0.000303) test_rel_pathways_as_strings: .: (0.000261) Bio::TestBioKeggDRUG: test_activity: .: (0.000526) test_comment: .: (0.000317) test_dblinks_as_hash: .: (0.000362) test_dblinks_as_strings: .: (0.000297) test_entry_id: .: (0.000262) test_formula: .: (0.000286) test_kcf: .: (0.000298) test_mass: .: (0.000284) test_name: .: (0.000377) test_names: .: (0.000285) test_pathways_as_hash: .: (0.000351) test_pathways_as_strings: .: (0.000286) test_products: .: (0.000277) test_remark: .: (0.000305) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000373) test_composition: .: (0.000302) test_compounds: .: (0.000247) test_dblinks_as_hash: .: (0.000464) test_dblinks_as_strings: .: (0.000270) test_entry_id: .: (0.000278) test_enzymes: .: (0.000313) test_kcf: .: (0.000231) test_keggclass: .: (0.000289) test_mass: .: (0.000257) test_name: .: (0.000290) test_orthologs_as_hash: .: (0.000344) test_orthologs_as_strings: .: (0.000272) test_pathways_as_hash: .: (0.000293) test_pathways_as_strings: .: (0.000288) test_reactions: .: (0.000303) test_references: .: (0.000338) test_remark: .: (0.000311) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000377) test_composition: .: (0.000231) test_compounds: .: (0.000286) test_dblinks_as_hash: .: (0.000274) test_dblinks_as_strings: .: (0.000300) test_entry_id: .: (0.000282) test_enzymes: .: (0.000314) test_kcf: .: (0.000251) test_keggclass: .: (0.000330) test_mass: .: (0.000277) test_name: .: (0.000311) test_orthologs_as_hash: .: (0.000264) test_orthologs_as_strings: .: (0.000284) test_pathways_as_hash: .: (0.000264) test_pathways_as_strings: .: (0.000300) test_reactions: .: (0.000275) test_references: .: (0.000276) test_remark: .: (0.000268) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000590) test_compounds_as_strings: .: (0.000366) test_dblinks_as_hash: .: (0.000301) test_dblinks_as_strings: .: (0.000324) test_description: .: (0.000282) test_diseases_as_hash: .: (0.000319) test_diseases_as_strings: .: (0.000342) test_entry_id: .: (0.000285) test_enzymes_as_strings: .: (0.000369) test_genes_as_hash: .: (0.000329) test_genes_as_strings: .: (0.000331) test_keggclass: .: (0.000349) test_ko_pathway: .: (0.000302) test_modules_as_hash: .: (0.000366) test_modules_as_strings: .: (0.000282) test_name: .: (0.000257) test_new: .: (0.000313) test_organism: .: (0.000265) test_orthologs_as_hash: .: (0.000313) test_orthologs_as_strings: .: (0.000272) test_pathways_as_hash: .: (0.000393) test_pathways_as_strings: .: (0.000317) test_reactions_as_hash: .: (0.004713) test_reactions_as_strings: .: (0.000417) test_references: .: (0.000490) test_rel_pathways_as_hash: .: (0.000399) test_rel_pathways_as_strings: .: (0.000596) Bio::TestBioLITDB: test_author: .: (0.000363) test_entry_id: .: (0.000225) test_field: .: (0.000247) test_journal: .: (0.000219) test_keyword: .: (0.000246) test_reference: .: (0.000362) test_title: .: (0.000255) test_volume: .: (0.000449) Bio::TestBioNBRF: test_aalen: .: (0.000322) test_aaseq: .: (0.000204) test_entry: .: (0.000197) test_length: .: (0.000191) test_nalen: .: (0.000246) test_naseq: .: (0.000262) test_seq: .: (0.000224) test_seq_class: .: (0.000207) test_to_nbrf: .: (0.000236) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000703) test_to_newick_format_leaf: .: (0.000373) test_to_newick_format_leaf_NHX: .: (0.000253) Bio::TestBl2seqReport: test_db_len: .: (0.000711) test_db_num: .: (0.000485) test_new: .: (0.000309) test_undefed_methods: .: (0.001183) test_undefed_methods_for_iteration: .: (0.000968) Bio::TestBl2seqReportConstants: test_rs: .: (0.000239) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000421) test_hits: .: (0.000347) Bio::TestBlast: test_blast_reports_format0: .: (0.005277) test_blast_reports_format0_with_block: .: (0.000714) test_blast_reports_format7: .: (0.010780) test_blast_reports_format7_with_block: .: (0.009576) test_blast_reports_format7_with_parser: .: (0.009466) test_blast_reports_format7_with_parser_with_block: .: (0.015439) test_blast_reports_format8: .: (0.000552) test_blast_reports_format8_with_block: .: (0.002663) test_blast_reports_format8_with_parser: .: (0.000279) test_blast_reports_format8_with_parser_with_block: .: (0.002112) test_blast_reports_xml: .: (0.039244) test_blast_reports_xml_with_block: .: (0.010365) test_blastll: .: (0.000220) test_db: .: (0.000177) test_exec_genomenet: .: (0.000386) test_exec_local: .: (0.000181) test_exec_ncbi: .: (0.000160) test_filter: .: (0.000176) test_format: .: (0.000212) test_make_command_line: .: (0.000461) test_make_command_line_2: .: (0.000347) test_matrix: .: (0.000178) test_new: .: (0.000469) test_new_opt_string: .: (0.000252) test_option: .: (0.000205) test_option_set: .: (0.000261) test_option_set_m0: .: (0.000246) test_options: .: (0.000216) test_output: .: (0.000193) test_parse_result: .: (0.009707) test_parser: .: (0.000209) test_program: .: (0.000191) test_query: .: (0.000190) test_self_local: .: (0.000268) test_self_remote: .: (0.001666) test_server: .: (0.000221) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000349) test_delete: .: (0.000296) test_equal_equal: .: (0.000325) test_get: .: (0.000323) test_make_command_line_options: .: (0.000273) test_normalize!: .: (0.000205) test_parse: .: (0.000239) test_set: .: (0.000479) Bio::TestBlastReport: test_db: .: (0.009745) test_db_len: .: (0.009134) test_db_num: .: (0.010656) test_each_hit: .: (0.009541) test_each_iteration: .: (0.009427) test_eff_space: .: (0.009080) test_entrez_query: .: (0.009016) test_entropy: .: (0.008774) test_expect: .: (0.009905) test_filter: .: (0.009262) test_gap_extend: .: (0.009141) test_gap_open: .: (0.008997) test_hits: .: (0.008837) test_hsp_len: .: (0.008876) test_inclusion: .: (0.010221) test_iterations: .: (0.009275) test_kappa: .: (0.009221) test_lambda: .: (0.008929) test_matrix: .: (0.008776) test_message: .: (0.008831) test_parameters: .: (0.009978) test_pattern: .: (0.009111) test_program: .: (0.008950) test_query_def: .: (0.008893) test_query_id: .: (0.008703) test_query_len: .: (0.008866) test_reference: .: (0.010061) test_sc_match: .: (0.009315) test_sc_mismatch: .: (0.008882) test_statistics: .: (0.008991) test_version: .: (0.008830) Bio::TestBlastReportDefault: test_db: .: (0.000566) test_db_len: .: (0.000411) test_db_num: .: (0.000384) test_each_hit: .: (0.000395) test_each_iteration: .: (0.000469) test_eff_space: .: (0.000463) test_entropy: .: (0.000419) test_expect: .: (0.000438) test_gap_extend: .: (0.000427) test_gap_open: .: (0.000430) test_gapped_entropy: .: (0.000382) test_gapped_kappa: .: (0.000382) test_gapped_lambda: .: (0.000460) test_hits: .: (0.000386) test_iterations: .: (0.000413) test_kappa: .: (0.000415) test_lambda: .: (0.000411) test_matrix: .: (0.000454) test_message: .: (0.000383) test_pattern: .: (0.000402) test_program: .: (0.000399) test_query_def: .: (0.000496) test_query_len: .: (0.000428) test_reference: .: (0.000445) test_sc_match: .: (0.000454) test_sc_mismatch: .: (0.000451) test_version: .: (0.000383) Bio::TestBlastReportHit: test_Hit_accession: .: (0.010816) test_Hit_bit_score: .: (0.009217) test_Hit_definition: .: (0.009091) test_Hit_evalue: .: (0.009015) test_Hit_hit_id: .: (0.008834) test_Hit_hsps: .: (0.009122) test_Hit_identity: .: (0.010190) test_Hit_lap_at: .: (0.009131) test_Hit_len: .: (0.009021) test_Hit_midline: .: (0.009154) test_Hit_num: .: (0.008788) test_Hit_overlap: .: (0.008918) test_Hit_query_def: .: (0.010267) test_Hit_query_end: .: (0.009129) test_Hit_query_id: .: (0.008984) test_Hit_query_len: .: (0.008892) test_Hit_query_seq: .: (0.009011) test_Hit_query_start: .: (0.009525) test_Hit_taeget_def: .: (0.009213) test_Hit_target_end: .: (0.009307) test_Hit_target_id: .: (0.008926) test_Hit_target_len: .: (0.009101) test_Hit_target_seq: .: (0.008917) test_Hit_target_start: .: (0.010157) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000603) test_Hit_definition: .: (0.000402) test_Hit_evalue: .: (0.000393) test_Hit_hsps: .: (0.000404) test_Hit_identity: .: (0.000393) test_Hit_lap_at: .: (0.000604) test_Hit_len: .: (0.000390) test_Hit_midline: .: (0.000500) test_Hit_overlap: .: (0.000387) test_Hit_query_end: .: (0.000485) test_Hit_query_seq: .: (0.000515) test_Hit_query_start: .: (0.000615) test_Hit_taeget_def: .: (0.000382) test_Hit_target_end: .: (0.000490) test_Hit_target_id: .: (0.000415) test_Hit_target_len: .: (0.000423) test_Hit_target_seq: .: (0.000515) test_Hit_target_start: .: (0.000662) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.026544) test_Hit_bit_score: .: (0.028334) test_Hit_definition: .: (0.026029) test_Hit_evalue: .: (0.027925) test_Hit_hit_id: .: (0.026058) test_Hit_hsps: .: (0.027452) test_Hit_identity: .: (0.026339) test_Hit_lap_at: .: (0.026228) test_Hit_len: .: (0.027523) test_Hit_midline: .: (0.026380) test_Hit_num: .: (0.027118) test_Hit_overlap: .: (0.025553) test_Hit_query_def: .: (0.027723) test_Hit_query_end: .: (0.026397) test_Hit_query_id: .: (0.027356) test_Hit_query_len: .: (0.026366) test_Hit_query_seq: .: (0.026116) test_Hit_query_start: .: (0.027417) test_Hit_taeget_def: .: (0.026205) test_Hit_target_end: .: (0.028036) test_Hit_target_id: .: (0.026418) test_Hit_target_len: .: (0.027676) test_Hit_target_seq: .: (0.026450) test_Hit_target_start: .: (0.026534) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.027173) test_Hit_bit_score: .: (0.026500) test_Hit_definition: .: (0.027815) test_Hit_evalue: .: (0.025968) test_Hit_hit_id: .: (0.027900) test_Hit_hsps: .: (0.026079) test_Hit_identity: .: (0.027152) test_Hit_lap_at: .: (0.026254) test_Hit_len: .: (0.025439) test_Hit_midline: .: (0.027467) test_Hit_num: .: (0.026196) test_Hit_overlap: .: (0.027911) test_Hit_query_def: .: (0.025959) test_Hit_query_end: .: (0.027305) test_Hit_query_id: .: (0.026864) test_Hit_query_len: .: (0.026841) test_Hit_query_seq: .: (0.026653) test_Hit_query_start: .: (0.025647) test_Hit_taeget_def: .: (0.026710) test_Hit_target_end: .: (0.025385) test_Hit_target_id: .: (0.026167) test_Hit_target_len: .: (0.025308) test_Hit_target_seq: .: (0.026331) test_Hit_target_start: .: (0.025983) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.009304) test_Hit_bit_score: .: (0.008724) test_Hit_definition: .: (0.008810) test_Hit_evalue: .: (0.008826) test_Hit_hit_id: .: (0.008703) test_Hit_hsps: .: (0.010099) test_Hit_identity: .: (0.009106) test_Hit_lap_at: .: (0.008765) test_Hit_len: .: (0.008942) test_Hit_midline: .: (0.008897) test_Hit_num: .: (0.009543) test_Hit_overlap: .: (0.009028) test_Hit_query_def: .: (0.008971) test_Hit_query_end: .: (0.009017) test_Hit_query_id: .: (0.009399) test_Hit_query_len: .: (0.009495) test_Hit_query_seq: .: (0.010796) test_Hit_query_start: .: (0.009630) test_Hit_taeget_def: .: (0.009540) test_Hit_target_end: .: (0.009454) test_Hit_target_id: .: (0.009586) test_Hit_target_len: .: (0.010939) test_Hit_target_seq: .: (0.009794) test_Hit_target_start: .: (0.009374) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000409) test_Hit_bit_score: .: (0.000191) test_Hit_definition: .: (0.000181) test_Hit_evalue: .: (0.000206) test_Hit_hit_id: .: (0.000191) test_Hit_hsps: .: (0.000196) test_Hit_identity: .: (0.000200) test_Hit_lap_at: .: (0.000219) test_Hit_len: .: (0.000198) test_Hit_midline: .: (0.000198) test_Hit_num: .: (0.000214) test_Hit_overlap: .: (0.000351) test_Hit_query_def: .: (0.000218) test_Hit_query_end: .: (0.000183) test_Hit_query_id: .: (0.000205) test_Hit_query_len: .: (0.000181) test_Hit_query_seq: .: (0.000193) test_Hit_query_start: .: (0.000200) test_Hit_taeget_def: .: (0.000202) test_Hit_target_end: .: (0.000200) test_Hit_target_id: .: (0.000198) test_Hit_target_len: .: (0.000196) test_Hit_target_seq: .: (0.000257) test_Hit_target_start: .: (0.000233) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.010107) test_Hsp_bit_score: .: (0.008970) test_Hsp_density: .: (0.010407) test_Hsp_evalue: .: (0.009712) test_Hsp_gaps: .: (0.009965) test_Hsp_hit_frame: .: (0.009270) test_Hsp_hit_from: .: (0.009072) test_Hsp_hit_to: .: (0.008967) test_Hsp_hseq: .: (0.010228) test_Hsp_identity: .: (0.010365) test_Hsp_midline: .: (0.009266) test_Hsp_mismatch_count: .: (0.009197) test_Hsp_num: .: (0.009180) test_Hsp_pattern_from: .: (0.009847) test_Hsp_pattern_to: .: (0.009757) test_Hsp_percent_identity: .: (0.009433) test_Hsp_positive: .: (0.009274) test_Hsp_qseq: .: (0.009039) test_Hsp_query_frame: .: (0.009179) test_Hsp_query_from: .: (0.010514) test_Hsp_query_to: .: (0.009812) test_Hsp_score: .: (0.009230) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000567) test_Hsp_bit_score: .: (0.000400) test_Hsp_evalue: .: (0.000374) test_Hsp_gaps: .: (0.000374) test_Hsp_hit_frame: .: (0.000363) test_Hsp_hit_from: .: (0.000476) test_Hsp_hit_to: .: (0.000559) test_Hsp_hseq: .: (0.000482) test_Hsp_identity: .: (0.000360) test_Hsp_midline: .: (0.000468) test_Hsp_percent_identity: .: (0.000360) test_Hsp_positive: .: (0.000385) test_Hsp_qseq: .: (0.000590) test_Hsp_query_frame: .: (0.000388) test_Hsp_query_from: .: (0.000454) test_Hsp_query_to: .: (0.000452) test_Hsp_score: .: (0.000376) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.027500) test_Hsp_bit_score: .: (0.026268) test_Hsp_density: .: (0.027617) test_Hsp_evalue: .: (0.026537) test_Hsp_gaps: .: (0.067332) test_Hsp_hit_frame: .: (0.026375) test_Hsp_hit_from: .: (0.026378) test_Hsp_hit_to: .: (0.024649) test_Hsp_hseq: .: (0.025941) test_Hsp_identity: .: (0.024590) test_Hsp_midline: .: (0.025678) test_Hsp_mismatch_count: .: (0.025321) test_Hsp_num: .: (0.025444) test_Hsp_pattern_from: .: (0.025303) test_Hsp_pattern_to: .: (0.025670) test_Hsp_percent_identity: .: (0.025864) test_Hsp_positive: .: (0.024984) test_Hsp_qseq: .: (0.025977) test_Hsp_query_frame: .: (0.025062) test_Hsp_query_from: .: (0.026104) test_Hsp_query_to: .: (0.024890) test_Hsp_score: .: (0.026089) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.024897) test_Hsp_bit_score: .: (0.026230) test_Hsp_density: .: (0.025335) test_Hsp_evalue: .: (0.027497) test_Hsp_gaps: .: (0.025578) test_Hsp_hit_frame: .: (0.027104) test_Hsp_hit_from: .: (0.025711) test_Hsp_hit_to: .: (0.027149) test_Hsp_hseq: .: (0.025198) test_Hsp_identity: .: (0.026073) test_Hsp_midline: .: (0.025488) test_Hsp_mismatch_count: .: (0.025797) test_Hsp_num: .: (0.025482) test_Hsp_pattern_from: .: (0.025423) test_Hsp_pattern_to: .: (0.026061) test_Hsp_percent_identity: .: (0.025469) test_Hsp_positive: .: (0.026622) test_Hsp_qseq: .: (0.025537) test_Hsp_query_frame: .: (0.026632) test_Hsp_query_from: .: (0.025049) test_Hsp_query_to: .: (0.026380) test_Hsp_score: .: (0.025613) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.010182) test_Hsp_bit_score: .: (0.009229) test_Hsp_density: .: (0.009098) test_Hsp_evalue: .: (0.009042) test_Hsp_gaps: .: (0.008723) test_Hsp_hit_frame: .: (0.008946) test_Hsp_hit_from: .: (0.010133) test_Hsp_hit_to: .: (0.009501) test_Hsp_hseq: .: (0.009022) test_Hsp_identity: .: (0.009054) test_Hsp_midline: .: (0.009079) test_Hsp_mismatch_count: .: (0.008846) test_Hsp_num: .: (0.010202) test_Hsp_pattern_from: .: (0.009267) test_Hsp_pattern_to: .: (0.009211) test_Hsp_percent_identity: .: (0.008976) test_Hsp_positive: .: (0.008967) test_Hsp_qseq: .: (0.009164) test_Hsp_query_frame: .: (0.009990) test_Hsp_query_from: .: (0.009435) test_Hsp_query_to: .: (0.009054) test_Hsp_score: .: (0.008875) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000354) test_Hsp_bit_score: .: (0.000181) test_Hsp_density: .: (0.000178) test_Hsp_evalue: .: (0.000344) test_Hsp_gaps: .: (0.000247) test_Hsp_hit_frame: .: (0.000176) test_Hsp_hit_from: .: (0.000170) test_Hsp_hit_to: .: (0.000180) test_Hsp_hseq: .: (0.000189) test_Hsp_identity: .: (0.000400) test_Hsp_midline: .: (0.000218) test_Hsp_mismatch_count: .: (0.000193) test_Hsp_num: .: (0.000192) test_Hsp_pattern_from: .: (0.000186) test_Hsp_pattern_to: .: (0.000190) test_Hsp_percent_identity: .: (0.000200) test_Hsp_positive: .: (0.000201) test_Hsp_qseq: .: (0.000201) test_Hsp_query_frame: .: (0.000192) test_Hsp_query_from: .: (0.000179) test_Hsp_query_to: .: (0.000177) test_Hsp_score: .: (0.000291) Bio::TestBlastReportIteration: test_hits: .: (0.010297) test_message: .: (0.009081) test_num: .: (0.010620) test_statistics: .: (0.009322) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000540) test_message: .: (0.000340) test_num: .: (0.000356) Bio::TestBlastReportIterationMulti: test_each: .: (0.025986) test_hits: .: (0.026144) test_message: .: (0.024716) test_num: .: (0.025845) test_query_def: .: (0.024823) test_query_id: .: (0.025780) test_query_len: .: (0.024713) test_statistics: .: (0.025794) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.025496) test_hits: .: (0.025186) test_message: .: (0.025591) test_num: .: (0.025106) test_query_def: .: (0.026292) test_query_id: .: (0.025478) test_query_len: .: (0.026704) test_statistics: .: (0.025839) Bio::TestBlastReportIterationREXML: test_hits: .: (0.009538) test_message: .: (0.010067) test_num: .: (0.009172) test_statistics: .: (0.009016) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000323) test_message: .: (0.000166) test_num: .: (0.000188) test_statistics: .: (0.000177) Bio::TestBlastReportMulti: test_db: .: (0.027409) test_db_len: .: (0.027033) test_db_num: .: (0.027674) test_each_hit: .: (0.026315) test_each_iteration: .: (0.027775) test_eff_space: .: (0.026069) test_entropy: .: (0.028376) test_expect: .: (0.026279) test_filter: .: (0.027763) test_gap_extend: .: (0.026115) test_gap_open: .: (0.027005) test_hits: .: (0.026063) test_hsp_len: .: (0.025914) test_iterations: .: (0.027141) test_kappa: .: (0.025817) test_lambda: .: (0.026304) test_matrix: .: (0.025091) test_message: .: (0.026133) test_parameters: .: (0.025082) test_pattern: .: (0.025898) test_program: .: (0.025576) test_query_def: .: (0.025227) test_query_id: .: (0.026006) test_query_len: .: (0.024963) test_reference: .: (0.026114) test_reports: .: (0.024802) test_statistics: .: (0.026335) test_version: .: (0.024996) Bio::TestBlastReportMultiREXML: test_db: .: (0.026269) test_db_len: .: (0.025760) test_db_num: .: (0.025193) test_each_hit: .: (0.026022) test_each_iteration: .: (0.024974) test_eff_space: .: (0.026085) test_entropy: .: (0.024993) test_expect: .: (0.026050) test_filter: .: (0.025856) test_gap_extend: .: (0.025260) test_gap_open: .: (0.026146) test_hits: .: (0.025255) test_hsp_len: .: (0.026126) test_iterations: .: (0.024923) test_kappa: .: (0.026153) test_lambda: .: (0.025695) test_matrix: .: (0.025289) test_message: .: (0.027092) test_parameters: .: (0.027131) test_pattern: .: (0.027755) test_program: .: (0.025563) test_query_def: .: (0.026189) test_query_id: .: (0.026000) test_query_len: .: (0.025149) test_reference: .: (0.026305) test_reports: .: (0.025234) test_statistics: .: (0.030901) test_version: .: (0.026002) Bio::TestBlastReportREXML: test_db: .: (0.009262) test_db_len: .: (0.008698) test_db_num: .: (0.008874) test_each_hit: .: (0.008669) test_each_iteration: .: (0.008583) test_eff_space: .: (0.009640) test_entrez_query: .: (0.008996) test_entropy: .: (0.008712) test_expect: .: (0.008794) test_filter: .: (0.008699) test_gap_extend: .: (0.009407) test_gap_open: .: (0.008834) test_hits: .: (0.008742) test_hsp_len: .: (0.009736) test_inclusion: .: (0.008689) test_iterations: .: (0.009384) test_kappa: .: (0.009022) test_lambda: .: (0.009483) test_matrix: .: (0.008688) test_message: .: (0.008773) test_parameters: .: (0.008832) test_pattern: .: (0.009453) test_program: .: (0.009666) test_query_def: .: (0.009871) test_query_id: .: (0.008686) test_query_len: .: (0.008899) test_reference: .: (0.009647) test_sc_match: .: (0.018809) test_sc_mismatch: .: (0.009151) test_statistics: .: (0.008793) test_version: .: (0.008776) Bio::TestBlastReportTabular: test_db: .: (0.000319) test_db_len: .: (0.000168) test_db_num: .: (0.000201) test_each_hit: .: (0.000175) test_each_iteration: .: (0.000189) test_eff_space: .: (0.000189) test_entrez_query: .: (0.000186) test_entropy: .: (0.000180) test_expect: .: (0.000176) test_filter: .: (0.000176) test_gap_extend: .: (0.000176) test_gap_open: .: (0.000176) test_hits: .: (0.000184) test_hsp_len: .: (0.000178) test_inclusion: .: (0.000179) test_iterations: .: (0.000177) test_kappa: .: (0.000259) test_lambda: .: (0.000179) test_matrix: .: (0.000160) test_message: .: (0.000164) test_parameters: .: (0.000169) test_pattern: .: (0.000194) test_program: .: (0.000183) test_query_def: .: (0.000187) test_query_id: .: (0.000182) test_query_len: .: (0.000173) test_reference: .: (0.000171) test_sc_match: .: (0.000170) test_sc_mismatch: .: (0.000186) test_statistics: .: (0.000247) test_version: .: (0.000269) Bio::TestChain: test_aaseq: .: (0.000406) test_addLigand: .: (0.000187) test_addResidue: .: (0.000183) test_atom_seq: .: (0.000199) test_comp: .: (0.000195) test_each: .: (0.000155) test_each_heterogen: .: (0.000197) test_each_residue: .: (0.000215) test_get_heterogen_by_id: .: (0.000188) test_get_residue_by_id: .: (0.000181) test_inspect: .: (0.000217) test_rehash: .: (0.000202) test_rehash_heterogens: .: (0.000320) test_rehash_residues: .: (0.000132) test_square_brace: .: (0.000167) test_to_s: .: (0.000149) Bio::TestChainFinder: test_chains: .: (0.000248) test_each_chain: .: (0.000172) test_find_chain: .: (0.000142) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.007831) test_header: .: (0.000496) test_match_line: .: (0.000553) test_sequence0: .: (0.000467) test_sequence1: .: (0.000423) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.005776) test_header: .: (0.000749) test_match_line: .: (0.000639) test_sequence0: .: (0.000546) test_sequence1: .: (0.000650) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.007074) test_header: .: (0.000552) test_match_line: .: (0.000407) test_sequence0: .: (0.000486) test_sequence1: .: (0.000419) Bio::TestCodonTable: test_Tables: .: (0.000197) test_accessor: .: (0.000139) test_definition: .: (0.000113) test_each: .: (0.000129) test_revtrans: .: (0.000292) test_self_accessor: .: (0.000110) test_self_copy: .: (0.000635) test_set_accessor: .: (0.100643) test_start: .: (0.000130) test_start_codon?: .: (0.000118) test_stop: .: (0.000132) test_stop_codon?: .: (0.000124) test_table: .: (0.000107) Bio::TestCodonTableConstants: test_Definitions: .: (0.000206) test_Starts: .: (0.000134) test_Tables: .: (0.000105) test_stops: .: (0.000122) Bio::TestColorScheme: test_buried: .: (0.000830) Bio::TestCommand: test_command_constants: .: (0.000304) test_escape_shell: .: (0.000143) test_escape_shell_unix: .: (0.000128) test_escape_shell_windows: .: (0.000131) test_make_cgi_params_by_array_of_array: .: (0.000271) test_make_cgi_params_by_array_of_hash: .: (0.000306) test_make_cgi_params_by_array_of_string: .: (0.000160) test_make_cgi_params_by_hash_in_string: .: (0.000403) test_make_cgi_params_by_hash_in_symbol: .: (0.000321) test_make_cgi_params_by_string: .: (0.000162) test_make_command_line: .: (0.000130) test_make_command_line_unix: .: (0.000125) test_make_command_line_windows: .: (0.000136) test_safe_command_line_array: .: (0.000148) test_safe_command_line_array_passthrough: .: (0.000137) Bio::TestContingencyTable: test_lite_example: .: (0.108783) Bio::TestDB: test_entry_id: .: (0.000230) test_exists: .: (0.000129) test_fetch: .: (0.000161) test_get: .: (0.000121) test_open: .: (0.000117) test_tags: .: (0.000120) Bio::TestDataType: test_const_like_method: .: (0.000626) test_pdb_achar: .: (0.000220) test_pdb_atom: .: (0.000225) test_pdb_character: .: (0.000205) test_pdb_date: .: (0.000209) test_pdb_idcode: .: (0.000219) test_pdb_integer: .: (0.000122) test_pdb_list: .: (0.000132) test_pdb_lstring: .: (0.000222) test_pdb_real: .: (0.000389) test_pdb_resudue_name: .: (0.000307) test_pdb_slist: .: (0.000140) test_pdb_string: .: (0.000240) test_pdb_stringrj: .: (0.000403) test_pdb_symop: .: (0.000356) test_specification_list: .: (0.000172) Bio::TestEMBL: test_ac: .: (0.000536) test_accession: .: (0.000338) test_cc: .: (0.000287) test_de: .: (0.000445) test_division: .: (0.000345) test_dr: .: (0.000312) test_dt: .: (0.000294) test_dt_created: .: (0.000284) test_dt_iterator: .: (0.000411) test_dt_updated: .: (0.000276) test_each_cds: .: (0.000440) test_each_gene: .: (0.000426) test_entry: .: (0.000443) test_fh: .: (0.000303) test_ft: .: (0.000400) test_ft_accessor: .: (0.000423) test_ft_iterator: .: (0.000514) test_id_line: .: (0.000304) test_id_line_data_class: .: (0.000312) test_id_line_division: .: (0.000314) test_id_line_entry_name: .: (0.000415) test_id_line_iterator: .: (0.000313) test_id_line_molecule_type: .: (0.000332) test_id_line_sequence_length: .: (0.000309) test_kw: .: (0.000306) test_molecule: .: (0.000383) test_oc: .: (0.000340) test_og: .: (0.000277) test_os: .: (0.000351) test_ref: .: (0.000471) test_references: .: (0.000497) test_seq: .: (0.000479) test_sequence_length: .: (0.000304) test_sq: .: (0.000378) test_sq_get: .: (0.000321) test_sv: .: (0.000283) test_version: .: (0.000286) Bio::TestEMBL89: test_ac: .: (0.000495) test_accession: .: (0.000292) test_cc: .: (0.000257) test_de: .: (0.000317) test_division: .: (0.000303) test_dr: .: (0.000349) test_dt: .: (0.000272) test_dt_created: .: (0.000268) test_dt_iterator: .: (0.000264) test_dt_updated: .: (0.000291) test_each_cds: .: (0.000468) test_each_gene: .: (0.000367) test_entry: .: (0.000316) test_fh: .: (0.000272) test_ft: .: (0.000499) test_ft_accessor: .: (0.000374) test_ft_iterator: .: (0.000390) test_id_line: .: (0.000301) test_id_line_data_class: .: (0.000406) test_id_line_division: .: (0.000328) test_id_line_entry_name: .: (0.000333) test_id_line_iterator: .: (0.000303) test_id_line_molecule_type: .: (0.000403) test_id_line_sequence_length: .: (0.000300) test_id_line_sequence_version: .: (0.000302) test_kw: .: (0.000301) test_molecule: .: (0.000420) test_oc: .: (0.000378) test_og: .: (0.000256) test_os: .: (0.000342) test_ref: .: (0.000352) test_references: .: (0.000489) test_seq: .: (0.002320) test_sequence_length: .: (0.000369) test_sq: .: (0.000308) test_sq_get: .: (0.000314) test_sv: .: (0.000437) test_version: .: (0.000317) Bio::TestEMBLAPI: test_ac: .: (0.000288) test_accessions: .: (0.000220) Bio::TestEMBLCommon: test_ac: .: (0.000198) test_accession: .: (0.000132) test_accessions: .: (0.000121) test_de: .: (0.000135) test_definition: .: (0.000121) test_description: .: (0.000231) test_dr: .: (0.000132) test_keywords: .: (0.000119) test_kw: .: (0.000132) test_oc: .: (0.000125) test_og: .: (0.000125) test_os: .: (0.000131) test_ref: .: (0.000124) test_references: .: (0.000123) Bio::TestEMBLDB: test_fetch: .: (0.000298) test_p_entry2hash: .: (0.000129) Bio::TestEMBLToBioSequence: test_classification: .: (0.002582) test_date_created: .: (0.000567) test_date_modified: .: (0.000414) test_definition: .: (0.000341) test_division: .: (0.000343) test_entry_id: .: (0.000405) test_entry_version: .: (0.000331) test_features: .: (0.000426) test_keywords: .: (0.000445) test_molecule_type: .: (0.000345) test_primary_accession: .: (0.000321) test_references: .: (0.000479) test_release_created: .: (0.000382) test_release_modified: .: (0.000347) test_secondary_accessions: .: (0.000347) test_sequence_version: .: (0.000417) test_species: .: (0.000321) test_topology: .: (0.000335) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002148) test_date_created: .: (0.001991) test_date_modified: .: (0.001956) test_definition: .: (0.001927) test_division: .: (0.001917) test_entry_id: .: (0.001842) test_entry_version: .: (0.002012) test_features: .: (0.002221) test_keywords: .: (0.002235) test_molecule_type: .: (0.002115) test_primary_accession: .: (0.002278) test_references: .: (0.002308) test_release_created: .: (0.001999) test_release_modified: .: (0.002171) test_secondary_accessions: .: (0.002073) test_sequence_version: .: (0.002130) test_species: .: (0.001987) test_topology: .: (0.002184) Bio::TestFasta: test_db: .: (0.000214) test_format: .: (0.000117) test_format_arg_integer: .: (0.000143) test_format_arg_str: .: (0.000129) test_ktup: .: (0.000136) test_matrix: .: (0.000267) test_option: .: (0.000157) test_options: .: (0.000132) test_output: .: (0.000118) test_program: .: (0.000118) test_server: .: (0.000130) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000270) test_accession: .: (0.000166) test_accessions: .: (0.000167) test_description: .: (0.000146) test_descriptions: .: (0.000148) test_entry_id: .: (0.002509) test_get_all_by_type: .: (0.000147) test_gi: .: (0.000141) test_id_strings: .: (0.000188) test_list_ids: .: (0.000147) test_locus: .: (0.000155) test_words: .: (0.000195) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000276) test_accession: .: (0.000157) test_accessions: .: (0.000174) test_description: .: (0.000145) test_descriptions: .: (0.000154) test_emb: .: (0.000186) test_entry_id: .: (0.000167) test_get_all_by_type: .: (0.000164) test_get_emb: .: (0.000184) test_gi: .: (0.000163) test_id_strings: .: (0.000211) test_list_ids: .: (0.000174) test_locus: .: (0.000164) test_words: .: (0.000213) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000266) test_accession: .: (0.000168) test_accessions: .: (0.000160) test_description: .: (0.000147) test_descriptions: .: (0.000340) test_entry_id: .: (0.000135) test_get_all_by_type: .: (0.000136) test_gi: .: (0.000145) test_id_strings: .: (0.000174) test_list_ids: .: (0.000155) test_locus: .: (0.000155) test_sp: .: (0.000160) test_words: .: (0.000203) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000261) test_accession: .: (0.000183) test_accessions: .: (0.000193) test_description: .: (0.000468) test_descriptions: .: (0.000170) test_entry_id: .: (0.000167) test_get_all_by_type: .: (0.000169) test_gi: .: (0.000178) test_id_strings: .: (0.000279) test_list_ids: .: (0.000174) test_locus: .: (0.000169) test_words: .: (0.000445) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000294) test_accession: .: (0.000197) test_accessions: .: (0.000154) test_description: .: (0.000152) test_descriptions: .: (0.000157) test_entry_id: .: (0.000164) test_get_all_by_type: .: (0.000172) test_gi: .: (0.000167) test_id_strings: .: (0.000259) test_list_ids: .: (0.000188) test_locus: .: (0.000182) test_words: .: (0.000267) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000255) test_accession: .: (0.000139) test_accessions: .: (0.000138) test_description: .: (0.000133) test_descriptions: .: (0.000130) test_entry_id: .: (0.000128) test_get_all_by_type: .: (0.000129) test_gi: .: (0.000129) test_id_strings: .: (0.000160) test_list_ids: .: (0.000128) test_locus: .: (0.000130) test_words: .: (0.000159) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000387) test_accession: .: (0.000146) test_accessions: .: (0.000158) test_description: .: (0.000132) test_descriptions: .: (0.000140) test_entry_id: .: (0.000142) test_get: .: (0.000153) test_get_all_by_type: .: (0.000144) test_id_strings: .: (0.000223) test_list_ids: .: (0.000156) test_locus: .: (0.000145) test_sp: .: (0.000154) test_words: .: (0.000228) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000368) test_accession: .: (0.000088) test_accessions: .: (0.000077) test_description: .: (0.000085) test_descriptions: .: (0.000082) test_entry_id: .: (0.000132) test_get: .: (0.000137) test_get_all_by_type: .: (0.000134) test_id_strings: .: (0.000217) test_list_ids: .: (0.000146) test_locus: .: (0.000145) test_tr: .: (0.000160) test_words: .: (0.000260) Bio::TestFastaFirstName: test_first_name1: .: (0.000403) test_first_name_multi_identifier: .: (0.000136) test_first_name_single_worded_defintion: .: (0.000129) test_no_definition: .: (0.000126) test_space_before_first_name: .: (0.000131) test_tabbed_defintion: .: (0.000135) Bio::TestFastaFormat: test_aalen: .: (0.000299) test_aaseq: .: (0.000159) test_acc_version: .: (0.000170) test_accession: .: (0.000176) test_accessions: .: (0.000183) test_data: .: (0.000144) test_definition: .: (0.000139) test_entry: .: (0.000143) test_entry_id: .: (0.000376) test_entry_overrun: .: (0.000131) test_first_name: .: (0.000134) test_gi: .: (0.000169) test_identifiers: .: (0.000175) test_length: .: (0.000155) test_query: .: (0.000164) test_seq: .: (0.000171) Bio::TestFastaFormatConst: test_delimiter: .: (0.000239) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000302) test_data: .: (0.000134) test_definition: .: (0.000146) test_entry: .: (0.000134) test_entry_id: .: (0.000318) test_first_name: .: (0.000155) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000216) test_naseq: .: (0.000134) test_naseq_class: .: (0.000139) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000253) Bio::TestFastaInitialize: test_new_1: .: (0.000455) test_option: .: (0.000134) test_option_backward_compatibility: .: (0.000143) Bio::TestFastaNumericFormat: test_arg: .: (0.000421) test_data: .: (0.000152) test_definition: .: (0.000121) test_each: .: (0.000150) test_entry: .: (0.000144) test_entry_id: .: (0.000134) test_length: .: (0.000167) test_to_biosequence: .: (0.000712) Bio::TestFastaQuery: test_query: .: (0.000208) test_self_local: .: (0.000119) test_self_parser: .: (0.000093) test_self_remote: .: (0.000270) Bio::TestFastacmd: test_database: .: (0.000204) test_fastacmd: .: (0.000114) test_methods: .: (0.000120) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000548) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000403) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000446) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000441) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000437) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000427) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000467) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000323) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000316) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000311) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000466) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000398) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000385) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000899) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000896) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000439) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000399) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000528) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.003562) test_error_probabilities_as_sanger: .: (0.003546) test_error_probabilities_as_solexa: .: (0.003599) test_quality_scores_as_illumina: .: (0.000458) test_quality_scores_as_sanger: .: (0.000296) test_quality_scores_as_solexa: .: (0.000325) test_validate_format: .: (0.000483) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000918) test_entry_id: .: (0.000804) test_error_probabilities: .: (0.124469) test_nalen: .: (0.000954) test_naseq: .: (0.000701) test_quality_scores: .: (0.001486) test_quality_string: .: (0.000762) test_roundtrip: .: (0.089662) test_seq: .: (0.000847) test_sequence_string: .: (0.000628) test_to_biosequence: .: (0.082623) test_to_biosequence_and_output: .: (0.003822) test_to_s: .: (0.000812) test_validate_format: .: (0.000661) test_validate_format_with_array: .: (0.000811) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000499) test_mask_20_with_empty_string: .: (0.000343) test_mask_20_with_longer_string: .: (0.000377) test_mask_20_with_x: .: (0.000336) test_mask_60: .: (0.000516) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.005714) test_error_probabilities_as_sanger: .: (0.004416) test_error_probabilities_as_solexa: .: (0.004654) test_quality_scores_as_illumina: .: (0.000361) test_quality_scores_as_sanger: .: (0.000292) test_quality_scores_as_solexa: .: (0.000362) test_validate_format: .: (0.000648) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.003403) test_error_probabilities_as_sanger: .: (0.003417) test_error_probabilities_as_solexa: .: (0.003312) test_quality_scores_as_illumina: .: (0.000367) test_quality_scores_as_sanger: .: (0.000337) test_quality_scores_as_solexa: .: (0.000273) test_validate_format: .: (0.000491) Bio::TestFeature: test_append: .: (0.000340) test_append_nil: .: (0.000137) test_assoc: .: (0.000151) test_each: .: (0.000142) test_feature: .: (0.000128) test_locations: .: (0.000191) test_new: .: (0.000120) test_position: .: (0.000116) test_qualifiers: .: (0.000115) Bio::TestFeatures: test_append: .: (0.000303) test_arg: .: (0.000126) test_each: .: (0.000126) test_features: .: (0.000147) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000925) test_aaindex2: .: (0.000270) test_blast: .: (0.000238) test_blastxml: .: (0.000695) test_embl: .: (0.000278) test_embl_oldrelease: .: (0.000257) test_fastaformat: .: (0.000408) test_fastanumericformat: .: (0.000167) test_fastq: .: (0.000197) test_genbank: .: (0.000233) test_genpept: .: (0.000268) test_hmmer: .: (0.000258) test_maxml_cluster: .: (0.002434) test_maxml_sequence: .: (0.000153) test_medline: .: (0.000180) test_prosite: .: (0.003546) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003109) test_transfac: .: (0.001182) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000257) test_auto_1arg_filename: .: (0.000356) test_auto_1arg_io: .: (0.000331) test_auto_1arg_io_with_block: .: (0.000833) test_auto_1arg_with_block: .: (0.000509) test_auto_2arg_filename_mode: .: (0.000307) test_auto_2arg_filename_mode_with_block: .: (0.000485) test_auto_3arg: .: (0.000359) test_auto_3arg_with_block: .: (0.000478) test_foreach: .: (0.000436) test_new_2arg_class: .: (0.000191) test_new_2arg_nil: .: (0.000304) test_open_0arg: .: (0.000147) test_open_1arg_class: .: (0.000145) test_open_1arg_filename: .: (0.000399) test_open_1arg_io: .: (0.000290) test_open_1arg_io_with_block: .: (0.000494) test_open_1arg_nil: .: (0.000144) test_open_1arg_with_block: .: (0.000501) test_open_2arg_autodetect: .: (0.000344) test_open_2arg_autodetect_io: .: (0.000291) test_open_2arg_autodetect_io_with_block: .: (0.000511) test_open_2arg_autodetect_with_block: .: (0.000482) test_open_2arg_class: .: (0.000206) test_open_2arg_class_io: .: (0.000233) test_open_2arg_class_io_with_block: .: (0.000399) test_open_2arg_class_with_block: .: (0.000405) test_open_2arg_filename_mode: .: (0.000313) test_open_2arg_filename_mode_with_block: .: (0.000532) test_open_3arg: .: (0.000539) test_open_3arg_with_block: .: (0.002773) test_open_4arg: .: (0.001215) test_to_a: .: (0.000447) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000376) test_close: .: (0.000174) test_dbclass: .: (0.000323) test_dbclass_eq: .: (0.000212) test_dbclass_nil: .: (0.000216) test_each: .: (0.000298) test_each_entry: .: (0.000360) test_ended_pos: .: (0.000280) test_entry_pos_flag: .: (0.000178) test_entry_raw: .: (0.000309) test_eof?: .: (0.000268) test_next_entry: .: (0.000514) test_path: .: (0.000173) test_pos: .: (0.000233) test_raw: .: (0.000317) test_rewind: .: (0.000246) test_start_pos: .: (0.000275) test_start_pos_ended_pos_not_recorded: .: (0.000258) test_to_io: .: (0.000184) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000458) test_simpleformat2: .: (0.000232) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000223) test_eof_false_after_prefetch: .: (0.000195) test_eof_false_first: .: (0.000140) test_eof_true: .: (0.000227) test_getc: .: (0.000153) test_getc_after_prefetch: .: (0.000149) test_gets: .: (0.000153) test_gets_equal_prefetch_gets: .: (0.000170) test_gets_paragraph_mode: .: (0.000215) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000323) test_gets_paragraph_mode_within_buffer: .: (0.000423) test_gets_rs: .: (0.000172) test_gets_rs_equal_prefetch_gets: .: (0.000179) test_gets_rs_within_buffer: .: (0.000268) test_pos: .: (0.000160) test_pos=: .: (0.000154) test_prefetch_buffer: .: (0.000143) test_prefetch_gets: .: (0.000158) test_prefetch_gets_with_arg: .: (0.000182) test_rewind: .: (0.000155) test_skip_spaces: .: (0.000163) test_to_io: .: (0.000176) test_ungetc: .: (0.000166) test_ungetc_after_prefetch: .: (0.000173) test_ungets: .: (0.000327) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000229) test_self_open_file: .: (0.000158) test_self_open_file_with_block: .: (0.000197) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000241) test_parse_file_open_arg_int_perm: .: (0.000133) test_parse_file_open_arg_int_perm_opt: .: (0.000130) test_parse_file_open_arg_integer: .: (0.000124) test_parse_file_open_arg_nil: .: (0.000118) test_parse_file_open_arg_opt: .: (0.000159) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000145) test_parse_file_open_arg_str: .: (0.000165) test_parse_file_open_arg_str_opt: .: (0.000152) test_parse_file_open_arg_str_perm: .: (0.000140) test_parse_file_open_arg_str_perm_opt: .: (0.000145) test_parse_file_open_arg_str_with_enc: .: (0.000179) test_parse_file_open_arg_str_with_ext_enc: .: (0.000142) test_parse_file_open_mode_integer: .: (0.000120) test_parse_file_open_mode_nil: .: (0.000130) test_parse_file_open_mode_str: .: (0.000134) test_parse_file_open_mode_str_with_enc: .: (0.000138) test_parse_file_open_mode_str_with_ext_enc: .: (0.000137) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000252) test_entry: .: (0.000145) test_entry_ended_pos: .: (0.000135) test_entry_pos_flag: .: (0.000146) test_entry_start_pos: .: (0.000130) test_get_entry: .: (0.000183) test_rewind: .: (0.000162) test_skip_leader: .: (0.000158) test_stream: .: (0.000127) test_stream_pos: .: (0.000281) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000222) test_delimiter_overrun: .: (0.000118) test_entry: .: (0.000148) test_entry_ended_pos: .: (0.000167) test_entry_ended_pos_default_nil: .: (0.000155) test_entry_start_pos: .: (0.000158) test_entry_start_pos_default_nil: .: (0.000149) test_get_entry: .: (0.000247) test_get_parsed_entry: .: (0.000269) test_header: .: (0.000131) test_skip_leader: .: (0.000166) test_skip_leader_without_header: .: (0.000278) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000296) test_entry_ended_pos: .: (0.000209) test_entry_start_pos: .: (0.000228) test_flag_to_fetch_header: .: (0.000199) test_get_entry: .: (0.000251) test_get_parsed_entry: .: (0.000406) test_rewind: .: (0.000206) test_skip_leader: .: (0.000191) Bio::TestGCGMsf: test_alignment: .: (0.000792) test_checksum: .: (0.000336) test_compcheck: .: (0.000209) test_date: .: (0.000236) test_description: .: (0.000208) test_entry_id: .: (0.000220) test_gap_length_weight: .: (0.000264) test_gap_weight: .: (0.000418) test_heading: .: (0.000236) test_length: .: (0.000202) test_seq_type: .: (0.000212) test_symbol_comparison_table: .: (0.000231) test_validate_checksum: .: (0.001405) Bio::TestGFF: test_record_class: .: (0.000393) test_records: .: (0.000272) Bio::TestGFF2: test_const_version: .: (0.000459) test_gff_version: .: (0.000432) test_metadata: .: (0.000376) test_metadata_size: .: (0.000317) test_records_size: .: (0.000439) test_to_s: .: (0.000510) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000229) test_attributes_case2: .: (0.000367) test_attributes_incompatible_backslash_semicolon: .: (0.000238) Bio::TestGFF2MetaData: test_data: .: (0.000205) test_directive: .: (0.000109) test_parse: .: (0.000131) Bio::TestGFF2Record: test_attribute: .: (0.000347) test_attribute_nonexistent: .: (0.000217) test_attributes: .: (0.000267) test_attributes_to_hash: .: (0.000280) test_comment_only?: .: (0.000242) test_delete_attribute: .: (0.000313) test_delete_attribute_multiple: .: (0.000248) test_delete_attribute_multiple2: .: (0.000294) test_delete_attribute_multiple_nil: .: (0.000340) test_delete_attribute_nil: .: (0.000234) test_delete_attribute_nonexistent: .: (0.000261) test_delete_attributes: .: (0.000249) test_delete_attributes_multiple: .: (0.000290) test_delete_attributes_nonexistent: .: (0.000271) test_end: .: (0.000364) test_eqeq: .: (0.000474) test_eqeq_false: .: (0.000413) test_feature: .: (0.000354) test_frame: .: (0.000217) test_get_attribute: .: (0.000284) test_get_attribute_nonexistent: .: (0.000230) test_get_attributes: .: (0.000317) test_get_attributes_nonexistent: .: (0.000221) test_replace_attributes: .: (0.000280) test_replace_attributes_multiple_multiple_over: .: (0.000255) test_replace_attributes_multiple_multiple_same: .: (0.000245) test_replace_attributes_multiple_multiple_two: .: (0.000247) test_replace_attributes_multiple_single: .: (0.000294) test_replace_attributes_nonexistent: .: (0.000275) test_replace_attributes_nonexistent_multiple: .: (0.000355) test_replace_attributes_single_multiple: .: (0.000243) test_score: .: (0.000254) test_self_parse: .: (0.000436) test_seqname: .: (0.000326) test_set_attribute: .: (0.000236) test_set_attribute_multiple: .: (0.000271) test_set_attribute_nonexistent: .: (0.000244) test_sort_attributes_by_tag!: .: (0.000316) test_sort_attributes_by_tag_bang_test2: .: (0.000397) test_sort_attributes_by_tag_bang_with_block: .: (0.000276) test_source: .: (0.000241) test_start: .: (0.000219) test_strand: .: (0.000228) test_to_s: .: (0.000341) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000235) test_comment_eq: .: (0.000129) test_comment_only?: .: (0.000129) test_comment_only_false: .: (0.000130) test_to_s: .: (0.000142) test_to_s_not_empty: .: (0.000195) Bio::TestGFF3: test_const_version: .: (0.000623) test_gff_version: .: (0.000537) test_records: .: (0.000534) test_sequence_regions: .: (0.000520) test_sequences: .: (0.000449) test_to_s: .: (0.000898) Bio::TestGFF3MetaData: test_data: .: (0.000207) test_directive: .: (0.000109) test_parse: .: (0.000137) Bio::TestGFF3Record: test_attributes: .: (0.000359) test_end: .: (0.000251) test_feature: .: (0.000231) test_frame: .: (0.000222) test_id: .: (0.000243) test_score: .: (0.000257) test_seqname: .: (0.000260) test_source: .: (0.000401) test_start: .: (0.000226) test_strand: .: (0.000201) test_to_s: .: (0.000311) test_to_s_attr_order_changed: .: (0.000384) Bio::TestGFF3RecordEscape: test_escape: .: (0.000381) test_escape_attribute: .: (0.000162) test_escape_seqid: .: (0.000162) test_unescape: .: (0.000162) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000294) test_eqeq: .: (0.000210) test_new_from_sequences_na: .: (0.000214) test_new_from_sequences_na_aa: .: (0.000496) test_new_from_sequences_na_aa_boundary_gap: .: (0.000372) test_new_from_sequences_na_aa_example: .: (0.000335) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000260) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000277) test_process_sequences_na: .: (0.000230) test_process_sequences_na_aa: .: (0.000226) test_process_sequences_na_aa_reverse_frameshift: .: (0.000472) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000218) test_process_sequences_na_aa_tooshort: .: (0.000318) test_process_sequences_na_tooshort: .: (0.000248) test_to_s: .: (0.000192) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000241) test_attributes_one: .: (0.000363) test_attributes_with_escaping: .: (0.000169) test_id_multiple: .: (0.000227) test_id_multiple2: .: (0.000222) test_id_replace: .: (0.000189) test_id_set: .: (0.000196) test_initialize_9: .: (0.000128) test_phase: .: (0.000185) test_score: .: (0.000175) test_to_s_void: .: (0.000151) Bio::TestGFF3RecordTarget: test_end: .: (0.000246) test_parse: .: (0.000371) test_start: .: (0.000123) test_strand: .: (0.000139) test_target_id: .: (0.000130) test_to_s: .: (0.000202) Bio::TestGFF3SequenceRegion: test_end: .: (0.000224) test_parse: .: (0.000225) test_seqid: .: (0.000146) test_start: .: (0.000131) test_to_s: .: (0.000207) Bio::TestGFFRecord: test_attributes: .: (0.000417) test_comment: .: (0.000161) test_end: .: (0.000146) test_feature: .: (0.000168) test_frame: .: (0.000156) test_score: .: (0.000158) test_seqname: .: (0.000170) test_source: .: (0.000158) test_start: .: (0.000160) test_strand: .: (0.000154) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000234) Bio::TestGeneAssociation: test_aspect: .: (0.000430) test_assigned_by: .: (0.000137) test_date: .: (0.000136) test_db: .: (0.000159) test_db_object_id: .: (0.000141) test_db_object_name: .: (0.000150) test_db_object_symbol: .: (0.000148) test_db_object_synonym: .: (0.000148) test_db_object_type: .: (0.000149) test_db_reference: .: (0.000146) test_evidence: .: (0.000151) test_goid: .: (0.000165) test_parser: .: (0.000596) test_qualifier: .: (0.000156) test_taxon: .: (0.000133) test_to_str: .: (0.000142) test_with: .: (0.000141) Bio::TestGenscanReport: test_date_run: .: (0.000772) test_gccontent: .: (0.000638) test_genscan_version: .: (0.004149) test_isochore: .: (0.000537) test_length: .: (0.000563) test_matrix: .: (0.000781) test_predictions_size: .: (0.000537) test_query_name: .: (0.000789) test_time: .: (0.000566) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000922) test_donor_score: .: (0.000554) test_exon_type: .: (0.000527) test_exon_type_long: .: (0.000572) test_first: .: (0.000548) test_initiation_score: .: (0.000733) test_last: .: (0.000520) test_number: .: (0.000668) test_p_value: .: (0.000545) test_phase: .: (0.000542) test_range: .: (0.000712) test_score: .: (0.000524) test_strand: .: (0.000720) test_t_score: .: (0.000553) test_termination_score: .: (0.000534) Bio::TestGenscanReportGene: test_aaseq: .: (0.000713) test_naseq: .: (0.000550) test_number: .: (0.000797) test_polyA: .: (0.000537) test_promoter: .: (0.000766) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000726) test_reports_ary_contents: .: (0.000554) Bio::TestHMMERReportConstants: test_rs: .: (0.000146) Bio::TestHMMERReportHit: test_accession: .: (0.000683) test_append_hsp: .: (0.000472) test_bit_score: .: (0.000465) test_definition: .: (0.000569) test_description: .: (0.000483) test_each: .: (0.000608) test_each_hsp: .: (0.000573) test_entry_id: .: (0.000632) test_evalue: .: (0.000538) test_hit: .: (0.000532) test_hit_id: .: (0.000552) test_hsps: .: (0.000561) test_num: .: (0.000521) test_score: .: (0.000524) test_target_def: .: (0.000645) test_target_id: .: (0.000544) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000652) test_each: .: (0.000551) test_each_hit: .: (0.000616) test_histogram: .: (0.000533) test_hits: .: (0.000538) test_hsps: .: (0.000528) test_parameter: .: (0.000606) test_program: .: (0.000565) test_query_info: .: (0.000550) test_statistical_detail: .: (0.000638) test_total_seq_searched: .: (0.000641) test_whole_seq_top_hits: .: (0.000578) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000928) test_histogram: .: (0.000632) test_statistical_detail: .: (0.000633) test_total_seq_searched: .: (0.000599) test_whole_seq_top_hit: .: (0.000654) Bio::TestHMMERReportHsp: test_accession: .: (0.000714) test_bit_score: .: (0.000572) test_csline: .: (0.000690) test_domain: .: (0.000533) test_evalue: .: (0.000533) test_flatseq: .: (0.000551) test_hmm_f: .: (0.000692) test_hmm_t: .: (0.000559) test_hmmseq: .: (0.000532) test_hsp: .: (0.000697) test_midline: .: (0.000575) test_query_frame: .: (0.000595) test_query_from: .: (0.000544) test_query_seq: .: (0.000763) test_query_to: .: (0.000613) test_rfline: .: (0.000557) test_score: .: (0.000531) test_seq_f: .: (0.000755) test_seq_ft: .: (0.000617) test_seq_t: .: (0.000543) test_set_alignment: .: (0.000518) test_targat_to: .: (0.000757) test_target_frame: .: (0.000541) test_target_from: .: (0.000579) test_target_seq: .: (0.000535) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000532) test_find_hetatm: .: (0.000258) test_hetatms: .: (0.000274) Bio::TestHeterogen: test_addAtom: .: (0.000307) test_each: .: (0.000198) test_each_hetatm: .: (0.000192) test_get_residue_id_from_atom: .: (0.000403) test_het_atom: .: (0.000177) test_iCode: .: (0.000165) test_inspect: .: (0.000245) test_resSeq: .: (0.000191) test_sort: .: (0.000215) test_square_bracket: .: (0.000220) test_to_s: .: (0.000293) test_update_resudue_id: .: (0.000434) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000235) test_find_heterogen: .: (0.000147) test_heterogens: .: (0.000168) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000318) test_match_description: .: (0.000197) test_match_evalue: .: (0.000192) test_match_ipr_description: .: (0.000192) test_match_ipr_id: .: (0.000192) test_match_match_end: .: (0.000187) test_match_match_start: .: (0.000406) test_match_method: .: (0.000161) test_matches_size: .: (0.000156) test_query_id: .: (0.000182) test_query_length: .: (0.000174) Bio::TestIprscanRawReport: test_entry_id: .: (0.202804) test_match_accession: .: (0.021444) test_match_crc64: .: (0.001764) test_match_date: .: (0.001776) test_match_description: .: (0.001818) test_match_evalue: .: (0.001576) test_match_go_terms: .: (0.001639) test_match_ipr_description: .: (0.001766) test_match_ipr_id: .: (0.001553) test_match_match_end: .: (0.001501) test_match_match_start: .: (0.001663) test_match_method: .: (0.001542) test_match_query_id: .: (0.001605) test_match_query_length: .: (0.001770) test_match_status: .: (0.001631) test_obj: .: (0.001643) test_query_id: .: (0.001588) test_query_length: .: (0.001523) test_self_reports_in_raw: .: (0.003845) Bio::TestIprscanReport: test_output_raw: .: (0.203988) test_to_raw: .: (0.000545) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000772) test_match_accession: .: (0.000401) test_match_date: .: (0.000427) test_match_description: .: (0.000421) test_match_evalue: .: (0.000563) test_match_go_terms: .: (0.000427) test_match_ipr_description: .: (0.000392) test_match_ipr_id: .: (0.000404) test_match_match_end: .: (0.000528) test_match_match_start: .: (0.000393) test_match_method: .: (0.000381) test_match_status: .: (0.000371) test_matches_size: .: (0.000582) test_query_id: .: (0.000413) test_query_length: .: (0.000367) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000532) test_to_hash_match?: .: (0.000675) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.001131) Bio::TestKeggCompound: test_comment: .: (0.000484) test_dblinks_as_hash: .: (0.000332) test_dblinks_as_strings: .: (0.000301) test_entry_id: .: (0.000280) test_enzymes: .: (0.000715) test_formula: .: (0.000318) test_kcf: .: (0.000253) test_mass: .: (0.000297) test_name: .: (0.000291) test_names: .: (0.000293) test_pathways_as_hash: .: (0.000415) test_pathways_as_strings: .: (0.000446) test_reactions: .: (0.000518) test_remark: .: (0.000279) test_rpairs: .: (0.000287) Bio::TestKeggEnzyme: test_all_reac: .: (0.000546) test_classes: .: (0.000480) test_cofactors: .: (0.000418) test_comment: .: (0.000431) test_dblinks_as_hash: .: (0.000463) test_dblinks_as_strings: .: (0.000404) test_diseases: .: (0.000397) test_entry: .: (0.000548) test_entry_id: .: (0.000459) test_genes: .: (0.008514) test_genes_as_hash: .: (0.010220) test_genes_as_strings: .: (0.002746) test_inhibitors: .: (0.000815) test_iubmb_reactions: .: (0.000549) test_kegg_reactions: .: (0.000561) test_motifs: .: (0.000507) test_name: .: (0.000562) test_names: .: (0.000572) test_obsolete?: .: (0.000845) test_orthologs_as_hash: .: (0.000550) test_orthologs_as_strings: .: (0.000500) test_pathways_as_hash: .: (0.000610) test_pathways_as_strings: .: (0.000574) test_products: .: (0.000529) test_reaction: .: (0.000598) test_structures: .: (0.000664) test_substrates: .: (0.000544) test_sysname: .: (0.000530) Bio::TestKeggGenesDblinks: test_data: .: (0.000273) test_dblinks_0: .: (0.000156) test_dblinks_1: .: (0.000397) test_dblinks_2: .: (0.000146) Bio::TestKeggGenesStructure: test_data: .: (0.000247) test_ids: .: (0.000187) test_ids_in_array: .: (0.000198) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.006632) test_graphics__size: .: (0.005945) test_id: .: (0.005766) test_link: .: (0.005808) test_name: .: (0.005722) test_reaction: .: (0.007816) test_type: .: (0.005903) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.005467) test_graphics__size: .: (0.005376) test_id: .: (0.005487) test_link: .: (0.005377) test_name: .: (0.005967) test_reaction: .: (0.006600) test_type: .: (0.005965) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.005699) test_category: .: (0.005878) test_entry_id: .: (0.005702) test_fgcolor=: .: (0.005718) test_height=: .: (0.006351) test_label=: .: (0.005666) test_shape=: .: (0.005529) test_width=: .: (0.005645) test_x=: .: (0.005504) test_y=: .: (0.005495) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.006343) test_graphics__size: .: (0.005650) test_id: .: (0.005493) test_link: .: (0.005405) test_name: .: (0.005501) test_reaction: .: (0.005443) test_type: .: (0.005967) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000244) test_graphics=: .: (0.000141) test_id=: .: (0.000196) test_link=: .: (0.000161) test_name=: .: (0.000160) test_reaction=: .: (0.000148) test_type=: .: (0.000147) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000298) test_category=: .: (0.000154) test_entry_id=: .: (0.000253) test_fgcolor=: .: (0.000182) test_height=: .: (0.000153) test_label=: .: (0.000176) test_pathway=: .: (0.000155) test_shape=: .: (0.000181) test_width=: .: (0.000180) test_x=: .: (0.000177) test_y=: .: (0.000169) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.006343) test_coords: .: (0.005448) test_fgcolor: .: (0.005266) test_height: .: (0.005493) test_name: .: (0.005483) test_type: .: (0.005339) test_width: .: (0.006244) test_x: .: (0.005491) test_y: .: (0.005386) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.005643) test_coords: .: (0.005775) test_fgcolor: .: (0.006306) test_height: .: (0.006337) test_name: .: (0.005593) test_type: .: (0.005650) test_width: .: (0.005471) test_x: .: (0.005423) test_y: .: (0.005467) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000307) test_coords=: .: (0.000124) test_fgcolor=: .: (0.000126) test_height=: .: (0.000146) test_name=: .: (0.000182) test_type=: .: (0.000165) test_width=: .: (0.000143) test_x=: .: (0.000142) test_y=: .: (0.000136) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.006770) test_entries__size: .: (0.005493) test_image: .: (0.005623) test_link: .: (0.005422) test_name: .: (0.005387) test_number: .: (0.005462) test_org: .: (0.005383) test_reactions=: .: (0.006210) test_reactions__size: .: (0.005480) test_relations=: .: (0.005579) test_relations__size: .: (0.005408) test_title: .: (0.005369) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.011568) test_name: .: (0.010939) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000231) test_initialize_0: .: (0.000123) test_initialize_1: .: (0.000118) test_initialize_2: .: (0.000126) test_name=: .: (0.000154) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.005717) test_name: .: (0.005701) test_products: .: (0.005538) test_substrates: .: (0.006592) test_type: .: (0.005624) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000229) test_name=: .: (0.000144) test_products=: .: (0.000158) test_substraces=: .: (0.000138) test_type=: .: (0.000166) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000328) test_entry_id=: .: (0.000142) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.005741) test_entry2: .: (0.005617) test_name: .: (0.005730) test_type: .: (0.005444) test_value: .: (0.006085) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000351) test_node1=: .: (0.000163) test_node2=: .: (0.000205) test_rel=: .: (0.000179) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000230) test_entry2=: .: (0.000154) test_name=: .: (0.000155) test_type=: .: (0.000156) test_value=: .: (0.000152) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.011383) test_name: .: (0.010671) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000263) test_initialize_0: .: (0.000112) test_initialize_1: .: (0.000120) test_initialize_2: .: (0.000123) test_name=: .: (0.000158) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000227) test_initialize_0: .: (0.000121) test_initialize_1: .: (0.000107) test_initialize_2: .: (0.000123) test_name=: .: (0.000154) Bio::TestKeggModule: test_compounds: .: (0.000564) test_compounds_as_hash: .: (0.000319) test_compounds_as_strings: .: (0.000228) test_definition: .: (0.000259) test_entry_id: .: (0.000223) test_keggclass: .: (0.000228) test_name: .: (0.000242) test_new: .: (0.000267) test_orthologs: .: (0.000315) test_orthologs_as_array: .: (0.000364) test_orthologs_as_hash: .: (0.000309) test_orthologs_as_strings: .: (0.000265) test_pathways: .: (0.000287) test_pathways_as_hash: .: (0.000279) test_pathways_as_strings: .: (0.000263) test_reactions: .: (0.000339) test_reactions_as_hash: .: (0.000397) test_reactions_as_strings: .: (0.000291) Bio::TestKeggOrthology: test_dblinks: .: (0.000528) test_dblinks_as_hash: .: (0.000408) test_dblinks_as_strings: .: (0.000399) test_definition: .: (0.000412) test_entry_id: .: (0.000389) test_genes_as_hash: .: (0.008399) test_genes_as_strings: .: (0.002532) test_keggclass: .: (0.000418) test_keggclasses: .: (0.000468) test_modules: .: (0.000472) test_modules_as_hash: .: (0.000355) test_modules_as_strings: .: (0.000373) test_name: .: (0.000361) test_names: .: (0.000360) test_pathways_as_strings: .: (0.000356) test_pathways_in_keggclass: .: (0.000475) test_references: .: (0.000602) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000336) test_compounds_as_strings: .: (0.000223) test_dblinks_as_hash: .: (0.000238) test_dblinks_as_strings: .: (0.000220) test_description: .: (0.000244) test_diseases_as_hash: .: (0.000264) test_diseases_as_strings: .: (0.000263) test_entry_id: .: (0.000259) test_enzymes_as_strings: .: (0.000330) test_genes_as_hash: .: (0.000269) test_genes_as_strings: .: (0.000222) test_keggclass: .: (0.000251) test_ko_pathway: .: (0.000251) test_modules_as_hash: .: (0.000329) test_modules_as_strings: .: (0.000270) test_name: .: (0.000238) test_organism: .: (0.000249) test_orthologs_as_hash: .: (0.000361) test_orthologs_as_strings: .: (0.000254) test_pathways_as_hash: .: (0.000327) test_pathways_as_strings: .: (0.000280) test_reactions_as_hash: .: (0.000252) test_reactions_as_strings: .: (0.000235) test_references: .: (0.000247) test_rel_pathways_as_hash: .: (0.000282) test_rel_pathways_as_strings: .: (0.000263) Bio::TestKeggReaction: test_definition: .: (0.000441) test_entry_id: .: (0.000347) test_enzymes: .: (0.000325) test_equation: .: (0.000333) test_name: .: (0.000365) test_orthologs_as_hash: .: (0.000319) test_orthologs_as_strings: .: (0.000259) test_pathways_as_hash: .: (0.000291) test_pathways_as_strings: .: (0.000253) test_rpairs_as_hash: .: (0.000472) test_rpairs_as_strings: .: (0.000265) test_rpairs_as_tokens: .: (0.000311) Bio::TestLasergene: test_methods: .: (0.004534) Bio::TestLocations: test_complement: .: (0.000327) test_hat: .: (0.000162) test_normal: .: (0.000177) test_replace_single_base: .: (0.000328) test_should_not_modify_argument: .: (0.000144) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002937) test_locations_to_s: .: (0.001323) Bio::TestMEDLINE: test_authors: .: (0.000625) test_authors_with_last_name_all_caps: .: (0.000213) test_authors_with_suffix: .: (0.000288) Bio::TestMEDLINE_20146148: test_ab: .: (0.001023) test_ad: .: (0.000308) test_au: .: (0.000300) test_authors: .: (0.000321) test_doi: .: (0.000516) test_dp: .: (0.000424) test_ip: .: (0.000335) test_mh: .: (0.000310) test_pages: .: (0.000297) test_pg: .: (0.002476) test_pii: .: (0.000383) test_pmid: .: (0.000298) test_pt: .: (0.000373) test_reference: .: (0.000777) test_self_new: .: (0.000329) test_so: .: (0.000345) test_ta: .: (0.000616) test_ti: .: (0.000433) test_ui: .: (0.000361) test_vi: .: (0.000288) test_year: .: (0.000544) Bio::TestMapSimple: test_attributes: .: (0.000276) Bio::TestMapping: test_add_mapping_as_map: .: (0.000304) test_add_mapping_as_marker: .: (0.000229) test_contains_marker?: .: (0.000217) test_mapped_to?: .: (0.000212) test_mapping_location_comparison: .: (0.000388) test_mappings_as_map_each: .: (0.000154) test_mappings_as_marker_each: .: (0.000398) test_mappings_on: .: (0.000234) test_multiple_mappings_between_same_marker_and_map: .: (0.000386) test_positions_on: .: (0.000213) test_raise_error_kind_of: .: (0.000400) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000350) test_check_options_with_invalid_opts: .: (0.000218) test_check_options_with_valid_opts: .: (0.000201) test_command_to_be_run: .: (0.000613) test_config_defaults: .: (0.000308) test_minimal_config: .: (0.000214) test_more_config: .: (0.000193) test_run: .: (0.000137) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000492) test_report_has_motifs: .: (0.000268) Bio::TestModel: test_addChain: .: (0.000200) test_comp: .: (0.000132) test_each: .: (0.000090) test_each_chain: .: (0.000393) test_inspect: .: (0.000139) test_rehash: .: (0.000062) test_square_brace: .: (0.000094) test_to_s: .: (0.000183) Bio::TestModelFinder: test_find_model: .: (0.000312) Bio::TestMotif: test_creation_and_attributes: .: (0.000300) test_length: .: (0.000104) Bio::TestMyGraph: test_cliquishness: .: (0.000509) Bio::TestNA: test_accessor: .: (0.000307) test_na: .: (0.000130) test_name: .: (0.000161) test_names: .: (0.000172) test_to_re: .: (0.000317) test_weight: .: (0.000183) test_weight_rna: .: (0.000134) Bio::TestNAConstants: test_NAMES: .: (0.000219) test_NAMES_1_to_name: .: (0.000123) test_WEIGHT: .: (0.000114) Bio::TestNATranslate: test_translate: .: (0.000372) test_translate_1: .: (0.000200) test_translate_2: .: (0.000478) test_translate_3: .: (0.000122) test_translate_4: .: (0.000373) test_translate_5: .: (0.000142) test_translate_6: .: (0.000191) Bio::TestNCBIDB: test_fetch: .: (0.000323) test_p_entry2hash: .: (0.000107) test_p_subtag2array: .: (0.000118) test_p_toptag2array: .: (0.000119) Bio::TestNewick: test_reparse: .: (0.001333) test_reparse_before_lazy_parsing: .: (0.000395) test_string_tree: .: (0.000709) Bio::TestNewick2: test_string_tree: .: (0.000580) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000452) test_parse_newick_leaf: .: (0.000220) test_parse_newick_tokenize: .: (0.000336) Bio::TestNexus: test_nexus: .: (0.008465) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000456) test_uncapitalized_letter_Q32725_9POAL: .: (0.000156) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000222) test_load_parameters: .: (0.000145) test_parameters: .: (0.000124) test_set_default_parameters: .: (0.000157) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.325395) test_expected_parameters_set_in_control_file: .: (0.037632) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000697) test_new_with_parameters: .: (0.000240) test_new_with_two_argument: .: (0.000149) test_new_without_argument: .: (0.000163) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001832) test_rates_hundred_and_fiftieth_position: .: (0.001868) test_rates_last_position: .: (0.001796) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.006606) test_tree: .: (0.006488) test_tree_length: .: (0.014861) test_tree_log_likelihood: .: (0.006498) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000427) test_parameters_should_be_loaded_from_control: .: (0.000270) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001445) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000283) test_dN_dS: .: (0.000183) test_kappa: .: (0.000198) test_lnL: .: (0.000190) test_m3_classes: .: (0.000260) test_m3_lnL: .: (0.000194) test_m3_to_s: .: (0.000197) test_m3_tree: .: (0.007320) test_omega: .: (0.000188) test_to_s: .: (0.000181) test_tree: .: (0.000491) test_tree_length: .: (0.008485) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.007047) test_p: .: (0.008920) test_position: .: (0.007514) test_probability: .: (0.010912) test_w: .: (0.001992) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000494) test_graph_omega: .: (0.000408) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000524) test_footer: .: (0.000176) test_header: .: (0.000172) test_initialize: .: (0.000187) test_models: .: (0.000195) test_nb_sites: .: (0.000475) test_num_codons: .: (0.000211) test_num_sequences: .: (0.000429) test_significant: .: (0.000264) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000335) test_nb_sites: .: (0.000257) test_significant: .: (0.000187) test_sites: .: (0.001131) Bio::TestPDB: test_accession: .: (0.001267) test_addModel: .: (0.000642) test_authors: .: (0.000894) test_bracket: .: (0.000663) test_classification: .: (0.000643) test_dbref: .: (0.001032) test_definition: .: (0.000600) test_each: .: (0.000925) test_each_model: .: (0.000627) test_entry_id: .: (0.001044) test_helix: .: (0.000663) test_inspect: .: (0.000875) test_jrnl: .: (0.000621) test_keywords: .: (0.000859) test_record: .: (0.000642) test_remark: .: (0.001181) test_seqres: .: (0.001467) test_sheet: .: (0.001063) test_ssbond: .: (0.000637) test_to_s: .: (0.001064) test_turn: .: (0.000623) test_version: .: (0.000778) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000244) test_U12: .: (0.000175) test_U13: .: (0.000188) test_U22: .: (0.000172) test_U23: .: (0.000180) test_U33: .: (0.000175) test_altLoc: .: (0.000186) test_chainID: .: (0.000180) test_charge: .: (0.000188) test_element: .: (0.000178) test_iCode: .: (0.000175) test_name: .: (0.000388) test_resName: .: (0.000182) test_resSeq: .: (0.000174) test_segID: .: (0.000155) test_serial: .: (0.000199) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000232) test_anisou: .: (0.000140) test_chainID: .: (0.000134) test_charge: .: (0.000135) test_comparable: .: (0.000162) test_do_parse: .: (0.000136) test_element: .: (0.000112) test_iCode: .: (0.000140) test_name: .: (0.000151) test_occupancy: .: (0.000509) test_original_data: .: (0.000208) test_record_name: .: (0.000197) test_resName: .: (0.000147) test_resSeq: .: (0.000178) test_residue: .: (0.000165) test_segID: .: (0.000132) test_serial: .: (0.000138) test_sigatm: .: (0.000137) test_tempFactor: .: (0.000180) test_ter: .: (0.000147) test_to_a: .: (0.000149) test_to_s: .: (0.000169) test_x: .: (0.000180) test_xyz: .: (0.000185) test_y: .: (0.000500) test_z: .: (0.000171) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000257) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000250) test_idcode: .: (0.000142) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000281) test_chainID2: .: (0.000178) test_icode1: .: (0.000166) test_icode2: .: (0.000185) test_measure: .: (0.000223) test_modNum: .: (0.000173) test_pep1: .: (0.000220) test_pep2: .: (0.000214) test_seqNum1: .: (0.000169) test_seqNum2: .: (0.000203) test_serNum: .: (0.000171) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000360) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000257) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000242) test_alpha: .: (0.000189) test_b: .: (0.000173) test_beta: .: (0.000195) test_c: .: (0.000161) test_gamma: .: (0.000159) test_sGroup: .: (0.000195) test_z: .: (0.000423) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000294) test_database: .: (0.000206) test_dbAccession: .: (0.000202) test_dbIdCode: .: (0.000225) test_dbseqBegin: .: (0.000213) test_dbseqEnd: .: (0.000181) test_idCode: .: (0.000247) test_idbnsBeg: .: (0.000243) test_insertBegin: .: (0.000190) test_insertEnd: .: (0.000183) test_seqBegin: .: (0.000180) test_seqEnd: .: (0.000480) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000220) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000255) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000221) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000249) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000237) test_depDate: .: (0.000147) test_idCode: .: (0.000127) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000256) test_hetID: .: (0.000361) test_iCode: .: (0.000187) test_numHetAtoms: .: (0.000159) test_seqNum: .: (0.000151) test_text: .: (0.000203) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000252) test_anisou: .: (0.000143) test_chainID: .: (0.000138) test_charge: .: (0.000144) test_comparable: .: (0.000174) test_do_parse: .: (0.000141) test_element: .: (0.000134) test_iCode: .: (0.000133) test_name: .: (0.000132) test_occupancy: .: (0.000181) test_original_data: .: (0.000139) test_record_name: .: (0.000177) test_resName: .: (0.000128) test_resSeq: .: (0.000137) test_residue: .: (0.000119) test_segID: .: (0.000134) test_serial: .: (0.000132) test_sigatm: .: (0.000135) test_tempFactor: .: (0.000162) test_ter: .: (0.000134) test_to_a: .: (0.000145) test_to_s: .: (0.000169) test_x: .: (0.000166) test_xyz: .: (0.000157) test_y: .: (0.000170) test_z: .: (0.000173) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000655) test_ChainH: .: (0.000195) test_ICode1: .: (0.000204) test_altLoc1: .: (0.000198) test_altLoc2: .: (0.000193) test_altLocH: .: (0.000190) test_chainID2: .: (0.000189) test_iCode2: .: (0.000188) test_iCodeH: .: (0.000186) test_name1: .: (0.000184) test_name2: .: (0.000202) test_nameH: .: (0.000361) test_resName1: .: (0.000216) test_resName2: .: (0.000194) test_resSeq1: .: (0.000197) test_resSeq2: .: (0.000240) test_resSeqH: .: (0.000215) test_sym1: .: (0.000203) test_sym2: .: (0.000209) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000269) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000335) test_altLoc2: .: (0.000373) test_chainID1: .: (0.000151) test_chainID2: .: (0.000155) test_iCode1: .: (0.000186) test_iCode2: .: (0.000168) test_name1: .: (0.000176) test_name2: .: (0.000184) test_resName1: .: (0.000192) test_resName2: .: (0.000180) test_resSeq1: .: (0.000182) test_resSeq2: .: (0.000180) test_sym1: .: (0.000178) test_sym2: .: (0.000191) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000558) test_numCoord: .: (0.000182) test_numHelix: .: (0.000139) test_numHet: .: (0.000153) test_numRemark: .: (0.000129) test_numSeq: .: (0.000152) test_numSheet: .: (0.000160) test_numSite: .: (0.000221) test_numTer: .: (0.000197) test_numTurn: .: (0.000195) test_numXform: .: (0.000155) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000274) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000294) test_comment: .: (0.000194) test_iCode: .: (0.000224) test_idCode: .: (0.000225) test_resName: .: (0.000172) test_seqNum: .: (0.000215) test_stdRes: .: (0.000185) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000285) test_Mn2: .: (0.000154) test_Mn3: .: (0.000150) test_Vn: .: (0.000130) test_iGiven: .: (0.000135) test_serial: .: (0.000144) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000263) test_Mn2: .: (0.000149) test_Mn3: .: (0.000363) test_Vn: .: (0.000149) test_iGiven: .: (0.000135) test_serial: .: (0.000155) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000242) test_Mn2: .: (0.000167) test_Mn3: .: (0.000137) test_Vn: .: (0.000185) test_iGiven: .: (0.000152) test_serial: .: (0.000196) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000231) test_rIdCode: .: (0.000172) test_repDate: .: (0.000162) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000260) test_On2: .: (0.000143) test_On3: .: (0.000391) test_Tn: .: (0.000140) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000377) test_modId: .: (0.000185) test_modNum: .: (0.000197) test_modType: .: (0.000142) test_record: .: (0.000137) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000268) test_text: .: (0.000103) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000163) test_Sn2: .: (0.000071) test_Sn3: .: (0.000116) test_Un: .: (0.000070) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000148) test_Sn2: .: (0.000338) test_Sn3: .: (0.000068) test_Un: .: (0.000061) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000252) test_Sn2: .: (0.000169) test_Sn3: .: (0.000144) test_Un: .: (0.000151) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000309) test_conflict: .: (0.000182) test_database: .: (0.000182) test_dbIdCode: .: (0.000175) test_dbRes: .: (0.000181) test_dbSeq: .: (0.000176) test_iCode: .: (0.000171) test_idCode: .: (0.000390) test_resName: .: (0.000189) test_seqNum: .: (0.000187) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000274) test_numRes: .: (0.000146) test_resName: .: (0.000152) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000278) test_curChainId: .: (0.000216) test_curICode: .: (0.000211) test_curResName: .: (0.000203) test_curResSeq: .: (0.000268) test_endChainID: .: (0.000241) test_endICode: .: (0.000171) test_endResName: .: (0.000241) test_endSeqNum: .: (0.000188) test_initChainID: .: (0.000266) test_initICode: .: (0.000219) test_initResName: .: (0.000218) test_initSeqNum: .: (0.000215) test_numStrands: .: (0.000212) test_prevAtom: .: (0.000220) test_prevChainId: .: (0.000207) test_prevICode: .: (0.000223) test_prevResName: .: (0.000225) test_prevResSeq: .: (0.000225) test_sense: .: (0.000210) test_sheetID: .: (0.000206) test_strand: .: (0.000238) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000389) test_chainID: .: (0.000132) test_charge: .: (0.000145) test_element: .: (0.000099) test_iCode: .: (0.000090) test_name: .: (0.000104) test_resName: .: (0.000138) test_resSeq: .: (0.000095) test_segID: .: (0.000089) test_serial: .: (0.000087) test_sigOcc: .: (0.000126) test_sigTemp: .: (0.000099) test_sigX: .: (0.000089) test_sigY: .: (0.000124) test_sigZ: .: (0.000091) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000229) test_SigmaU12: .: (0.000100) test_SigmaU13: .: (0.000089) test_SigmaU22: .: (0.000129) test_SigmaU23: .: (0.000346) test_SigmaU33: .: (0.000254) test_altLoc: .: (0.000191) test_chainID: .: (0.000188) test_charge: .: (0.000173) test_element: .: (0.000185) test_iCode: .: (0.000185) test_name: .: (0.000189) test_resName: .: (0.000174) test_resSeq: .: (0.000189) test_segID: .: (0.000182) test_serial: .: (0.000179) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000339) test_chainID2: .: (0.000233) test_chainID3: .: (0.000196) test_chainID4: .: (0.000189) test_iCode1: .: (0.000187) test_iCode2: .: (0.000187) test_iCode3: .: (0.000190) test_iCode4: .: (0.000187) test_numRes: .: (0.000188) test_resName1: .: (0.000185) test_resName2: .: (0.000205) test_resName3: .: (0.000195) test_resName4: .: (0.000181) test_seq1: .: (0.000199) test_seq2: .: (0.000185) test_seq3: .: (0.000205) test_seq4: .: (0.000206) test_seqNum: .: (0.000199) test_siteID: .: (0.000214) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000317) test_altLoc2: .: (0.000184) test_atom1: .: (0.000177) test_atom2: .: (0.000150) test_chainID1: .: (0.000155) test_chainID2: .: (0.000164) test_iCode1: .: (0.000169) test_iCode2: .: (0.000169) test_resName1: .: (0.000166) test_resName2: .: (0.000167) test_resSeq1: .: (0.000166) test_resSeq2: .: (0.000165) test_sym1: .: (0.000167) test_sym2: .: (0.000167) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000323) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000454) test_sIdCode: .: (0.000162) test_sprsdeDate: .: (0.000204) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000266) test_iCode: .: (0.000158) test_resName: .: (0.000154) test_resSeq: .: (0.000216) test_serial: .: (0.000156) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000266) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000289) test_t1: .: (0.000207) test_t2: .: (0.000213) test_t3: .: (0.000171) test_text: .: (0.000154) Bio::TestPROSITE: test_ac: .: (0.001422) test_cc: .: (0.001290) test_de: .: (0.001052) test_division: .: (0.001207) test_dr: .: (0.011688) test_dt: .: (0.001043) test_false_neg: .: (0.001053) test_false_pos: .: (0.001063) test_false_positive_sequences: .: (0.001004) test_list_falsenegative: .: (0.011303) test_list_falsepositive: .: (0.055766) test_list_potentialhit: .: (0.012656) test_list_truepositive: .: (0.012330) test_list_unknown: .: (0.013193) test_list_xref: .: (0.011620) test_ma: .: (0.001065) test_max_repeat: .: (0.001040) test_name: .: (0.001124) test_nr: .: (0.001013) test_pa: .: (0.001327) test_pa2re: .: (0.001420) test_partial: .: (0.001416) test_pdb_xref: .: (0.001332) test_pdoc_xref: .: (0.001186) test_positive: .: (0.001254) test_positive_hits: .: (0.001104) test_positive_sequences: .: (0.001566) test_release: .: (0.001485) test_ru: .: (0.001262) test_self_pa2re: .: (0.001389) test_site: .: (0.001578) test_skip_flag: .: (0.001958) test_swissprot_release_number: .: (0.001436) test_swissprot_release_sequences: .: (0.001308) test_taxon_range: .: (0.001530) test_total: .: (0.001211) test_total_hits: .: (0.001357) test_total_sequences: .: (0.001302) test_unknown: .: (0.001305) test_unknown_hits: .: (0.001047) test_unknown_sequences: .: (0.000920) Bio::TestPROSITEConst: test_delimiter: .: (0.000356) test_tagsize: .: (0.000122) Bio::TestPTS1: test_function_set: .: (0.000221) test_function_set_number_1: .: (0.000153) test_function_set_number_2: .: (0.000130) test_function_set_number_3: .: (0.000135) test_function_show: .: (0.000130) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000217) Bio::TestPTS1New: test_fungi: .: (0.000242) test_general: .: (0.000133) test_metazoa: .: (0.000129) Bio::TestQualifier: test_qualifier: .: (0.000231) test_value: .: (0.000113) Bio::TestREBASE: test_methods: .: (0.000758) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.027220) test_bit_score: .: (0.000622) test_evalue: .: (0.000508) test_gaps: .: (0.000500) test_hit_from: .: (0.000522) test_hit_to: .: (0.000493) test_hseq: .: (0.000635) test_identity: .: (0.000510) test_midline: .: (0.000516) test_percent_identity: .: (0.000474) test_positive: .: (0.000494) test_qseq: .: (0.000660) test_query_from: .: (0.000560) test_query_to: .: (0.000559) test_score: .: (0.000513) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000563) test_hits_size: .: (0.001256) test_iterations_size: .: (0.000987) test_program: .: (0.000454) test_query_def: .: (0.001155) test_query_len: .: (0.001018) test_version: .: (0.000491) test_version_date: .: (0.000615) test_version_number: .: (0.000495) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000616) test_definition: .: (0.000611) test_evalue: .: (0.000516) test_hsps_size: .: (0.000626) test_identity: .: (0.000543) test_lap_at: .: (0.000549) test_len: .: (0.000517) test_midline: .: (0.000631) test_overlap: .: (0.000699) test_query_end: .: (0.000577) test_query_seq: .: (0.000587) test_query_start: .: (0.000571) test_target_def: .: (0.000672) test_target_end: .: (0.000572) test_target_len: .: (0.000544) test_target_seq: .: (0.000573) test_target_start: .: (0.000558) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000575) test_get_entry: .: (0.000387) test_rewind: .: (0.000161) test_skip_leader: .: (0.000460) Bio::TestReference: test_abstract: .: (0.000258) test_affiliations: .: (0.000147) test_authors: .: (0.000125) test_format_bibitem: .: (0.000184) test_format_bibtex: .: (0.000253) test_format_bibtex_with_arguments: .: (0.000446) test_format_cell: .: (0.000163) test_format_current: .: (0.000143) test_format_endnote: .: (0.000167) test_format_general: .: (0.000158) test_format_genome_biol: .: (0.000158) test_format_genome_res: .: (0.000178) test_format_nar: .: (0.000203) test_format_nature: .: (0.000191) test_format_rd: .: (0.000163) test_format_science: .: (0.000217) test_format_trends: .: (0.000374) test_issue: .: (0.000115) test_journal: .: (0.000116) test_mesh: .: (0.000117) test_pages: .: (0.000139) test_pubmed: .: (0.000116) test_pubmed_url: .: (0.000127) test_url: .: (0.000118) test_volume: .: (0.000118) test_year: .: (0.000117) Bio::TestReference_noURL: test_format_endnote: .: (0.000248) test_url: .: (0.000128) Bio::TestReferences: test_append: .: (0.000319) test_each: .: (0.002390) Bio::TestRelation: test_comparison_operator: .: (0.000233) test_uniq: .: (0.000150) Bio::TestResidue: test_addAtom: .: (0.000336) test_each: .: (0.000207) test_each_atom: .: (0.000230) test_get_residue_id_from_atom: .: (0.000196) test_het_atom: .: (0.000449) test_iCode: .: (0.000155) test_inspect: .: (0.000242) test_resSeq: .: (0.000168) test_sort: .: (0.000207) test_square_bracket: .: (0.000210) test_to_s: .: (0.000304) test_update_resudue_id: .: (0.000204) Bio::TestResidueFinder: test_each_residue: .: (0.000542) test_find_residue: .: (0.000171) test_residues: .: (0.000162) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.120847) test_cut_from_bio_sequence_na: .: (0.021635) test_cut_without_permutations: .: (0.016282) test_view_ranges: .: (0.016477) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000934) test_cuts_after_remove_incomplete_cuts: .: (0.000566) test_strands_for_display: .: (0.001991) test_strands_for_display_current: .: (0.000536) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000467) test_fragments_for_display_1: .: (0.003264) test_fragments_for_display_10: .: (0.000722) test_fragments_for_display_2: .: (0.000795) test_fragments_for_display_3: .: (0.000857) test_fragments_for_display_4: .: (0.000916) test_fragments_for_display_5: .: (0.000495) test_fragments_for_display_6: .: (0.000509) test_fragments_for_display_7: .: (0.000635) test_fragments_for_display_8: .: (0.000457) test_fragments_for_display_9: .: (0.000559) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000335) test_obj_3: .: (0.000255) test_obj_7: .: (0.000210) test_obj_z: .: (0.000220) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000244) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000181) test_bracket_eq: .: (0.000117) test_concat: .: (0.000087) test_delete: .: (0.000246) test_dup: .: (0.000117) test_each: .: (0.000102) test_eqeq: .: (0.000075) test_eqeq_false: .: (0.000066) test_eqeq_other: .: (0.000061) test_eqeq_self: .: (0.000059) test_include?: .: (0.000183) test_internal_data: .: (0.000126) test_internal_data_eq: .: (0.000141) test_length: .: (0.000144) test_ltlt: .: (0.000145) test_ltlt_larger: .: (0.000155) test_ltlt_middle: .: (0.000151) test_plus: .: (0.000316) test_plus_error: .: (0.000199) test_push: .: (0.000140) test_reverse_each: .: (0.000163) test_self_bracket: .: (0.000134) test_self_new: .: (0.000156) test_size: .: (0.000139) test_sort!: .: (0.000128) test_to_a: .: (0.000136) test_uniq!: .: (0.000129) test_unshift: .: (0.000194) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003242) test_complement: .: (0.003069) test_complement_with_cut_symbols: .: (0.003136) test_cut_locations: .: (0.003055) test_cut_locations_in_enzyme_notation: .: (0.003030) test_primary: .: (0.003024) test_primary_with_cut_symbols: .: (0.003209) test_to_re: .: (0.003000) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000725) test_align_with_cuts: .: (0.000657) test_argument_error: .: (0.000903) test_ds: .: (0.000610) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000518) test_complement: .: (0.000215) test_contents: .: (0.000200) test_primary: .: (0.000192) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000350) test_complement: .: (0.000209) test_contents: .: (0.000179) test_primary: .: (0.000270) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000285) test_contents: .: (0.000184) test_primary: .: (0.000158) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000281) test_complement_to_array_index: .: (0.000255) test_complement_to_array_index_class: .: (0.000211) test_contents: .: (0.000184) test_primary: .: (0.000178) test_primary_to_array_index: .: (0.000244) test_primary_to_array_index_class: .: (0.000276) test_to_array_index: .: (0.000485) test_to_array_index_class: .: (0.000335) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000374) test_rebase: .: (0.000185) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000790) test_creation_with_no_cuts: .: (0.000425) test_cut_locations: .: (0.000377) test_cut_locations_in_enzyme_notation: .: (0.000473) test_orientation: .: (0.000387) test_pattern: .: (0.000394) test_pattern_palindromic?: .: (0.000547) test_stripped: .: (0.000371) test_to_re: .: (0.000334) test_with_cut_symbols: .: (0.000386) test_with_spaces: .: (0.000513) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000703) test_creation_with_no_cuts: .: (0.000429) test_cut_locations: .: (0.000430) test_cut_locations_in_enzyme_notation: .: (0.000377) test_orientation: .: (0.000364) test_pattern: .: (0.000455) test_pattern_palindromic?: .: (0.000438) test_stripped: .: (0.000397) test_to_re: .: (0.000342) test_with_cut_symbols: .: (0.000454) test_with_spaces: .: (0.000422) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000399) test_initialize_with_pattern: .: (0.000330) test_max: .: (0.000213) test_min: .: (0.000154) test_to_array_index: .: (0.000176) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000229) test_bracket_eq: .: (0.000154) test_concat: .: (0.000149) test_delete: .: (0.000134) test_dup: .: (0.000182) test_each: .: (0.000185) test_eqeq: .: (0.000139) test_eqeq_false: .: (0.000127) test_eqeq_other: .: (0.000122) test_eqeq_self: .: (0.000119) test_include?: .: (0.000128) test_internal_data_hash: .: (0.000122) test_internal_data_hash_eq: .: (0.000243) test_length: .: (0.000121) test_ltlt: .: (0.000138) test_ltlt_noeffect: .: (0.000136) test_plus: .: (0.000138) test_plus_error: .: (0.000163) test_private_push_element: .: (0.000134) test_private_push_element_intermediate: .: (0.000138) test_private_push_element_last: .: (0.000148) test_private_push_element_noeffect: .: (0.000130) test_private_sorted_keys: .: (0.000125) test_private_unshift_element: .: (0.000132) test_private_unshift_element_first: .: (0.000152) test_private_unshift_element_intermediate: .: (0.000151) test_private_unshift_element_noeffect: .: (0.000135) test_push: .: (0.000146) test_reverse_each: .: (0.000213) test_self_bracket: .: (0.000134) test_self_new: .: (0.000138) test_size: .: (0.000123) test_sort!: .: (0.000119) test_to_a: .: (0.000124) test_uniq!: .: (0.000117) test_unshift: .: (0.000140) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000291) test_left_padding: .: (0.000165) test_right_padding: .: (0.000134) test_strip_padding: .: (0.000149) Bio::TestSOFT: test_dataset: .: (0.045930) test_series: .: (0.004189) Bio::TestSOSUIReport: test_entry_id: .: (0.000265) test_prediction: .: (0.000161) test_tmh: .: (0.000215) test_tmhs: .: (0.000176) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000193) test_rs: .: (0.000213) Bio::TestSOSUITMH: test_grade: .: (0.000254) test_range: .: (0.000179) test_sequence: .: (0.000184) Bio::TestSampleGraph: test_bellman_ford: .: (0.000413) test_bfs_shortest_path: .: (0.000189) test_breadth_first_search: .: (0.000185) test_depth_first_search: .: (0.000294) test_dijkstra: .: (0.000258) test_dump_list: .: (0.000298) test_dump_matrix: .: (0.000299) test_extract_subgraph_by_label: .: (0.000231) test_extract_subgraph_by_list: .: (0.000211) test_extract_subgraph_retains_disconnected_nodes: .: (0.000178) test_small_world_aka_node_degree_histogram: .: (0.000184) test_to_matrix: .: (0.000340) test_to_matrix_fixed_index: .: (0.000264) test_undirected_cliquishness: .: (0.000351) Bio::TestScf_version_2: test_complement: .: (0.007665) test_seq: .: (0.007319) test_to_biosequence: .: (0.007337) Bio::TestScf_version_3: test_complement: .: (0.023146) test_seq: .: (0.022881) test_to_biosequence: .: (0.022819) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000218) test_AA_new_sequence_all_legal_symbols: .: (0.000139) test_AA_new_sequence_removes_whitespace: .: (0.000128) test_AA_new_sequence_upcases_symbols: .: (0.000131) test_DNA_new_blank_sequence: .: (0.000127) test_DNA_new_sequence_downcases_symbols: .: (0.000124) test_DNA_new_sequence_removes_whitespace: .: (0.000121) test_NA_randomize_with_counts: .: (0.000601) test_NA_randomize_with_counts_and_block: .: (0.000662) test_RNA_new_sequence: .: (0.000120) test_ambiguous_dna_sequence_complement: .: (0.000123) test_ambiguous_rna_sequence_complement: .: (0.000122) test_amino_acid_codes: .: (0.000153) test_amino_acid_molecular_weight: .: (0.000232) test_amino_acid_names: .: (0.000169) test_amino_acid_randomize_can_be_chained: .: (0.000830) test_amino_acid_randomize_has_same_composition: .: (0.000460) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000420) test_dna_composition: .: (0.000199) test_dna_gc_percent: .: (0.000148) test_dna_molecular_weight: .: (0.000179) test_dna_pikachu: .: (0.000129) test_dna_sequence_complement: .: (0.000132) test_dna_sequence_translate: .: (0.000330) test_dna_to_re: .: (0.000174) test_element_reference_operator_with_one_argument: .: (0.000125) test_element_reference_operator_with_two_arguments: .: (0.000130) test_invalid_nucleic_acid_illegal_bases: .: (0.000144) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000174) test_nucleic_acid_names: .: (0.000149) test_randomize_dna_can_be_chained: .: (0.000414) test_randomize_dna_retains_composition: .: (0.000211) test_randomize_dna_with_block: .: (0.000250) test_rna_composition: .: (0.000143) test_rna_gc_percent: .: (0.000177) test_rna_molecular_weight: .: (0.000257) test_rna_pikachu: .: (0.000125) test_rna_sequence_complement: .: (0.000117) test_rna_sequence_translate: .: (0.000286) test_rna_to_re: .: (0.000180) test_total: .: (0.000144) test_two_consecutive_dna_randomizations_not_equal: .: (0.000255) test_valid_dna_sequence_illegal_bases: .: (0.000133) Bio::TestSequenceAA: test_codes: .: (0.000252) test_molecular_weight: .: (0.000200) test_names: .: (0.000148) test_to_re: .: (0.000258) test_to_s: .: (0.000112) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000247) Bio::TestSequenceAANew: test_new: .: (0.000174) test_new_n: .: (0.000126) test_new_r: .: (0.000111) test_new_t: .: (0.000118) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000226) test_concat: .: (0.000144) test_push: .: (0.000122) test_seq: .: (0.000114) test_splicing: .: (0.000224) test_sum: .: (0.000120) test_to_s: .: (0.000163) test_to_str: .: (0.000114) test_total: .: (0.000127) test_window_search: .: (0.000293) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.003924) test_normalize_A: .: (0.000128) test_normalize_a: .: (0.000131) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000836) test_randomize_with_block: .: (0.002564) test_randomize_with_hash: .: (0.000852) test_randomize_with_hash_block: .: (0.003230) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.000808) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.000660) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000232) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000139) test_subseq_returns_subsequence: .: (0.000133) test_to_s_returns_self_as_string: .: (0.000131) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000221) test_window_search_with_width_3_step_two_with_residual: .: (0.000150) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000253) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000271) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000240) test_na_self_randomize: .: (0.000185) Bio::TestSequenceDBLink: test_database: .: (0.000240) test_id: .: (0.000115) test_secondary_ids: .: (0.000114) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000239) test_parse_uniprot_DR_line: .: (0.000175) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000904) test_output_width_35: .: (0.000320) test_output_width_nil: .: (0.000405) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000466) test_output_after_adding_sequence: .: (0.000297) test_output_after_truncating_sequence: .: (0.000235) test_output_from_error_probabilities: .: (0.002142) test_output_width45: .: (0.000320) test_output_with_converting_score_phred2solexa: .: (0.000560) test_output_with_converting_score_solexa2phred: .: (0.000342) test_output_with_default_score: .: (0.000242) Bio::TestSequenceMasker: test_mask: .: (0.000250) test_mask_with_enumerator: .: (0.000290) test_mask_with_enumerator_empty_mask_char: .: (0.000196) test_mask_with_enumerator_excess: .: (0.000468) test_mask_with_enumerator_longer_mask_char: .: (0.000170) test_mask_with_enumerator_shorter: .: (0.000201) test_mask_with_error_probability: .: (0.000191) test_mask_with_quality_score: .: (0.000170) Bio::TestSequenceNA: test_at_content: .: (0.000361) test_at_skew: .: (0.000269) test_codon_usage: .: (0.000264) test_complement: .: (0.000124) test_dna: .: (0.000125) test_dna!: .: (0.000139) test_forward_complement: .: (0.000152) test_gc_content: .: (0.000260) test_gc_percent: .: (0.000180) test_gc_skew: .: (0.000332) test_iliegal_bases: .: (0.000123) test_molecular_weight: .: (0.000188) test_names: .: (0.000160) test_reverse_complement: .: (0.000216) test_rna: .: (0.000135) test_rna!: .: (0.000129) test_splicing: .: (0.000200) test_to_re: .: (0.000209) test_to_s: .: (0.000117) Bio::TestSequenceNACommon: test_composition: .: (0.000242) test_concat: .: (0.000120) test_push: .: (0.000124) test_seq: .: (0.000116) test_splicing: .: (0.000185) test_sum: .: (0.000292) test_to_s: .: (0.000156) test_to_str: .: (0.000140) test_total: .: (0.000129) test_window_search: .: (0.000299) Bio::TestSequenceNANew: test_new: .: (0.000245) test_new_n: .: (0.000130) test_new_r: .: (0.000125) test_new_t: .: (0.000117) Bio::TestSequenceNATranslation: test_translate: .: (0.000390) test_translate_0: .: (0.000726) test_translate_1: .: (0.000239) test_translate_2: .: (0.000252) test_translate_3: .: (0.000221) test_translate_4: .: (0.000242) test_translate_5: .: (0.000250) test_translate_6: .: (0.000280) test_translate_7: .: (0.000446) test_translate_given_codon_table: .: (0.031769) test_translate_n1: .: (0.000426) test_translate_n2: .: (0.000371) test_translate_n3: .: (0.000371) test_translate_unknown_o: .: (0.000259) test_translate_unknown_x: .: (0.000229) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000341) test_convert_scores_from_phred_to_solexa: .: (0.000372) test_convert_scores_from_solexa_to_phred: .: (0.000185) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000194) test_convert_scores_from_phred: .: (0.000126) test_convert_scores_from_phred_to_solexa: .: (0.000322) test_convert_scores_from_solexa: .: (0.000176) test_convert_scores_from_solexa_to_phred: .: (0.000178) test_convert_scores_to_phred: .: (0.000112) test_convert_scores_to_solexa: .: (0.000437) test_p2q: .: (0.000163) test_phred_p2q: .: (0.000189) test_phred_q2p: .: (0.002953) test_q2p: .: (0.002924) test_quality_score_type: .: (0.000150) test_self_convert_scores_to_solexa: .: (0.000310) test_self_p2q: .: (0.000162) test_self_q2p: .: (0.002974) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000271) test_convert_scores_from_phred: .: (0.000338) test_convert_scores_from_phred_to_solexa: .: (0.001735) test_convert_scores_from_solexa: .: (0.000385) test_convert_scores_from_solexa_to_phred: .: (0.000233) test_convert_scores_to_phred: .: (0.000223) test_convert_scores_to_solexa: .: (0.000119) test_p2q: .: (0.000234) test_q2p: .: (0.004173) test_quality_score_type: .: (0.000122) test_self_convert_scores_to_phred: .: (0.000210) test_self_p2q: .: (0.000292) test_self_q2p: .: (0.004199) test_solexa_p2q: .: (0.000571) test_solexa_q2p: .: (0.003584) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000276) test_center: .: (0.000152) test_chomp: .: (0.000183) test_chop: .: (0.000178) test_delete: .: (0.000144) test_delete_prefix: .: (0.000150) test_delete_suffix: .: (0.000196) test_downcase: .: (0.000156) test_each_char: .: (0.000238) test_each_char_enum: .: (0.000215) test_each_grapheme_cluster: .: (0.000568) test_each_grapheme_cluster_enum: .: (0.000170) test_each_line: .: (0.000195) test_each_line_enum: .: (0.000155) test_gsub: .: (0.000155) test_gsub_with_block: .: (0.000406) test_ljust: .: (0.000156) test_lstrip: .: (0.000128) test_multiply: .: (0.000131) test_next: .: (0.000158) test_reverse: .: (0.000142) test_rjust: .: (0.000154) test_rstrip: .: (0.000139) test_slice: .: (0.000289) test_slice2: .: (0.000150) test_split: .: (0.000226) test_squeeze: .: (0.000135) test_strip: .: (0.000176) test_sub: .: (0.000231) test_sub_with_block: .: (0.000364) test_succ: .: (0.000129) test_swapcase: .: (0.000187) test_tr: .: (0.000217) test_tr_s: .: (0.000136) test_upcase: .: (0.000154) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000365) test_partition_nomatch: .: (0.000196) test_partition_sep_TSeq: .: (0.000188) test_partition_sep_regexp: .: (0.000199) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000350) test_rpartition_nomatch: .: (0.000143) test_rpartition_sep_TSeq: .: (0.000172) test_rpartition_sep_regexp: .: (0.000250) Bio::TestShRNA: test_blocK_it: .: (0.016656) test_blocK_it_: .: (0.112999) test_blocK_it_BLOCK_IT: .: (0.025712) test_blocK_it_BLOCK_iT: .: (0.020163) test_blocK_it_piGene: .: (0.025763) test_bottom_strand: .: (0.020599) test_bottom_strand_class: .: (0.018259) test_bottom_strand_nil: .: (0.031163) test_design: .: (0.027618) test_design_BLOCK_IT: .: (0.023283) test_report: .: (0.020456) test_report_before_design: .: (0.020202) test_top_strand: .: (0.015768) test_top_strand_class: .: (0.017357) test_top_strand_nil: .: (0.014898) Bio::TestShRNANew: test_new: .: (0.000419) Bio::TestSiRNA: test_antisense_size: .: (0.000198) test_design: .: (0.016872) test_design_reynolds: .: (0.021022) test_design_uitei: .: (0.014547) test_max_gc_percent: .: (0.000128) test_min_gc_percent: .: (0.000117) test_reynolds: .: (0.024809) test_reynolds?: .: (0.000210) test_uitei: .: (0.015835) test_uitei?: .: (0.000149) Bio::TestSiRNANew: test_new: .: (0.000571) Bio::TestSiRNAPair: test_antisense: .: (0.015023) test_gc_percent: .: (0.016698) test_report: .: (0.015595) test_rule: .: (0.015020) test_sense: .: (0.021641) test_start: .: (0.019810) test_stop: .: (0.026959) test_target: .: (0.016520) Bio::TestSiRNAPairNew: test_new: .: (0.000424) Bio::TestSim4Report: test_all_hits: .: (0.000434) test_each: .: (0.000258) test_each_hit: .: (0.000219) test_hits: .: (0.000231) test_num_hits: .: (0.000330) test_query_def: .: (0.000214) test_query_id: .: (0.000200) test_query_len: .: (0.000204) test_seq1: .: (0.000248) Bio::TestSim4Report2: test_all_hits: .: (0.000355) test_each: .: (0.000225) test_each_hit: .: (0.000220) test_hits: .: (0.000238) test_num_hits: .: (0.000198) test_query_def: .: (0.000366) test_query_id: .: (0.000208) test_query_len: .: (0.000194) test_seq1: .: (0.000302) Bio::TestSim4Report4: test_all_hits: .: (0.000398) test_each: .: (0.000272) test_each_hit: .: (0.000281) test_hits: .: (0.000211) test_num_hits: .: (0.000162) test_query_def: .: (0.000376) test_query_id: .: (0.000213) test_query_len: .: (0.000200) test_seq1: .: (0.000241) Bio::TestSim4ReportHit: test_align: .: (0.000368) test_complement?: .: (0.000200) test_definition: .: (0.000199) test_each: .: (0.000342) test_exons: .: (0.000426) test_hit_id: .: (0.000219) test_hsps: .: (0.000435) test_introns: .: (0.000381) test_len: .: (0.000218) test_query_def: .: (0.000208) test_query_id: .: (0.000207) test_query_len: .: (0.000200) test_segmentpairs: .: (0.000588) test_seq1: .: (0.000297) test_seq2: .: (0.000269) test_target_def: .: (0.000235) test_target_id: .: (0.000204) test_target_len: .: (0.000202) Bio::TestSim4ReportHit2: test_align: .: (0.000427) test_complement?: .: (0.000210) test_definition: .: (0.000204) test_each: .: (0.000565) test_exons: .: (0.000412) test_hit_id: .: (0.000211) test_hsps: .: (0.000365) test_introns: .: (0.000353) test_len: .: (0.000236) test_query_def: .: (0.000208) test_query_id: .: (0.000199) test_query_len: .: (0.000236) test_segmentpairs: .: (0.000389) test_seq1: .: (0.000266) test_seq2: .: (0.000257) test_target_def: .: (0.000194) test_target_id: .: (0.000204) test_target_len: .: (0.000200) Bio::TestSim4ReportHit4: test_align: .: (0.000511) test_complement?: .: (0.000466) test_definition: .: (0.000238) test_each: .: (0.000561) test_exons: .: (0.000540) test_hit_id: .: (0.000265) test_hsps: .: (0.000514) test_introns: .: (0.000683) test_len: .: (0.000287) test_query_def: .: (0.000273) test_query_id: .: (0.000271) test_query_len: .: (0.000256) test_segmentpairs: .: (0.000539) test_seq1: .: (0.000323) test_seq2: .: (0.000491) test_target_def: .: (0.000279) test_target_id: .: (0.000259) test_target_len: .: (0.000252) Bio::TestSim4ReportSegment: test_from: .: (0.000262) test_self_new: .: (0.000181) test_seq: .: (0.000130) test_to: .: (0.000131) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000363) test_direction: .: (0.000256) test_hit_from: .: (0.000388) test_hit_to: .: (0.000245) test_hseq: .: (0.000244) test_midline: .: (0.000277) test_percent_identity: .: (0.000251) test_qseq: .: (0.000256) test_query_from: .: (0.000270) test_query_to: .: (0.000362) test_seq1: .: (0.000276) test_seq2: .: (0.000266) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000362) test_direction: .: (0.000277) test_hit_from: .: (0.000248) test_hit_to: .: (0.000356) test_hseq: .: (0.000266) test_midline: .: (0.000229) test_percent_identity: .: (0.000230) test_qseq: .: (0.000252) test_query_from: .: (0.000229) test_query_to: .: (0.000226) test_seq1: .: (0.000448) test_seq2: .: (0.000259) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000591) test_direction: .: (0.000453) test_hit_from: .: (0.000461) test_hit_to: .: (0.000732) test_hseq: .: (0.000482) test_midline: .: (0.000449) test_percent_identity: .: (0.000452) test_qseq: .: (0.000823) test_query_from: .: (0.000530) test_query_to: .: (0.000450) test_seq1: .: (0.000541) test_seq2: .: (0.000501) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.001006) test_direction: .: (0.000450) test_hit_from: .: (0.000445) test_hit_to: .: (0.000445) test_hseq: .: (0.000468) test_midline: .: (0.000775) test_percent_identity: .: (0.000567) test_qseq: .: (0.000443) test_query_from: .: (0.000443) test_query_to: .: (0.000451) test_seq1: .: (0.000782) test_seq2: .: (0.000545) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000414) test_direction: .: (0.000301) test_hit_from: .: (0.000455) test_hit_to: .: (0.000343) test_hseq: .: (0.000294) test_midline: .: (0.000290) test_percent_identity: .: (0.000465) test_qseq: .: (0.000340) test_query_from: .: (0.000294) test_query_to: .: (0.000289) test_seq1: .: (0.000320) test_seq2: .: (0.000464) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000345) test_direction: .: (0.000249) test_hit_from: .: (0.000246) test_hit_to: .: (0.000259) test_hseq: .: (0.000259) test_midline: .: (0.000272) test_percent_identity: .: (0.000259) test_qseq: .: (0.000264) test_query_from: .: (0.000247) test_query_to: .: (0.000228) test_seq1: .: (0.000254) test_seq2: .: (0.000280) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000462) test_direction: .: (0.000582) test_hit_from: .: (0.000365) test_hit_to: .: (0.000309) test_hseq: .: (0.000304) test_midline: .: (0.000304) test_percent_identity: .: (0.000300) test_qseq: .: (0.000298) test_query_from: .: (0.000528) test_query_to: .: (0.000306) test_seq1: .: (0.000346) test_seq2: .: (0.000366) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000284) test_entry_id: .: (0.000118) test_filename: .: (0.000115) test_len: .: (0.000109) test_self_new: .: (0.000126) test_self_parse: .: (0.000160) Bio::TestTMHMMReport: test_entry_id: .: (0.000801) test_exp_aas_in_tmhs: .: (0.000391) test_exp_first_60aa: .: (0.000390) test_helix: .: (0.000433) test_predicted_tmhs: .: (0.000379) test_query_len: .: (0.000591) test_tmhs: .: (0.000398) test_to_s: .: (0.000522) test_total_prob_of_N_in: .: (0.000388) Bio::TestTMHMMReport_reports: test_reports: .: (0.000242) Bio::TestTMHMMTMH: test_entry_id: .: (0.000750) test_pos: .: (0.000389) test_range: .: (0.000391) test_status: .: (0.000376) test_version: .: (0.000401) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000494) test_cutoff: .: (0.000242) test_entry_id: .: (0.000208) test_length: .: (0.000211) test_loc: .: (0.000218) test_name: .: (0.000240) test_networks: .: (0.000253) test_prediction: .: (0.000279) test_query_len: .: (0.000197) test_query_sequences: .: (0.000200) test_rc: .: (0.000207) test_version: .: (0.000344) Bio::TestTargetPReportConst: test_delimiter: .: (0.000201) test_rs: .: (0.000120) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000265) test_togows_access_wait: .: (2.005524) Bio::TestTogoWSREST: test_debug: .: (0.000748) test_debug_default: .: (0.000201) test_internal_http: .: (0.000236) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000217) test_entry: .: (0.000127) test_entry_database_list: .: (0.000129) test_new: .: (0.000578) test_new_with_uri_object: .: (0.000230) test_new_with_uri_string: .: (0.000214) test_retrieve: .: (0.000106) test_search: .: (0.000125) test_search_database_list: .: (0.000116) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000354) test_prepare_return_value: .: (0.000301) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000382) Bio::TestTree: test_get_edge_distance: .: (0.000452) test_get_edge_distance_string: .: (0.000198) test_get_node_name: .: (0.000159) test_initialize: .: (0.000152) test_options: .: (0.000134) test_root: .: (0.000109) test_root=: .: (0.000139) Bio::TestTree2: test_add_edge: .: (0.000334) test_add_node: .: (0.000227) test_adjacency_matrix: .: (0.000257) test_adjacency_matrix_with_block: .: (0.000222) test_adjacent_nodes: .: (0.000220) test_adjacent_nodes_nonexistent: .: (0.000154) test_ancestors: .: (0.000339) test_children: .: (0.000185) test_clear: .: (0.000170) test_clear_node: .: (0.000221) test_clear_node_nonexistent: .: (0.000242) test_collect_edge!: .: (0.000250) test_collect_node!: .: (0.000259) test_concat: .: (0.000240) test_descendents: .: (0.000181) test_distance_matrix: .: (0.000554) test_each_edge: .: (0.000285) test_each_node: .: (0.000312) test_each_out_edge: .: (0.000191) test_each_out_edge_chimpanzee: .: (0.000260) test_each_out_edge_human: .: (0.000240) test_each_out_edge_mammals: .: (0.000285) test_each_out_edge_nonexistent: .: (0.000192) test_each_out_edge_primates: .: (0.000303) test_each_out_edge_rat: .: (0.000334) test_each_out_edge_rodents: .: (0.000210) test_edges: .: (0.000185) test_get_edge: .: (0.000289) test_get_edge_indirect: .: (0.000154) test_get_edge_merged: .: (0.000173) test_get_edge_nonexistent: .: (0.000162) test_get_node_bootstrap: .: (0.000171) test_get_node_bootstrap_string=: .: (0.000183) test_get_node_by_name: .: (0.000263) test_get_node_by_name_noexistent: .: (0.000282) test_include?: .: (0.000195) test_include_nonexistent: .: (0.000158) test_insert_node: .: (0.000268) test_leaves: .: (0.000211) test_leaves_noargs: .: (0.000219) test_lowest_common_ancestor: .: (0.000272) test_nodes: .: (0.000223) test_number_of_edges: .: (0.000220) test_number_of_nodes: .: (0.000215) test_out_degree: .: (0.000234) test_out_degree_nonexistent: .: (0.000184) test_out_edges: .: (0.000391) test_out_edges_mammals: .: (0.000252) test_out_edges_nonexistent: .: (0.000191) test_out_edges_primates: .: (0.000248) test_out_edges_rodents: .: (0.000287) test_parent: .: (0.000242) test_path: .: (0.000244) test_remove_edge: .: (0.000237) test_remove_edge_if: .: (0.000250) test_remove_edge_if_nothing_removed: .: (0.000296) test_remove_edge_nonexistent: .: (0.000594) test_remove_node: .: (0.000254) test_remove_node_if: .: (0.000187) test_remove_node_if_false: .: (0.000207) test_remove_node_nonexistent: .: (0.000233) test_remove_nonsense_nodes: .: (0.000243) test_subtree: .: (0.000295) test_subtree_with_all_paths: .: (0.000408) test_total_distance: .: (0.000174) Bio::TestTreeEdge: test_distance: .: (0.000217) test_distance=: .: (0.000270) test_distance_string: .: (0.000115) test_distance_string=: .: (0.000133) test_initialize: .: (0.000138) test_inspect: .: (0.000131) test_to_s: .: (0.000127) Bio::TestTreeNode: test_bootstrap: .: (0.000196) test_bootstrap=: .: (0.000160) test_bootstrap_string: .: (0.000119) test_bootstrap_string=: .: (0.000167) test_initialize: .: (0.000150) test_inspect: .: (0.000187) test_name: .: (0.000127) test_to_s: .: (0.000149) Bio::TestUniProt: test_gene_name: .: (0.003410) Bio::TestUniProtKB: test_ac: .: (0.003080) test_accession: .: (0.002725) test_cc: .: (0.003734) test_cc_alternative_products: .: (0.008321) test_cc_database: .: (0.004572) test_cc_mass_spectrometry: .: (0.004437) test_de: .: (0.003049) test_dr: .: (0.004362) test_dr_with_key: .: (0.004703) test_dr_with_key_empty: .: (0.004035) test_dt: .: (0.002702) test_dt_annotation: .: (0.002548) test_dt_created: .: (0.002738) test_dt_sequence: .: (0.002646) test_entry: .: (0.002755) test_ft: .: (0.024522) test_gene_name: .: (0.036938) test_gene_names: .: (0.003324) test_gn: .: (0.003027) test_gn_old_parser: .: (0.003360) test_gn_uniprot_parser: .: (0.003252) test_id_line: .: (0.002983) test_id_line_data_class: .: (0.003093) test_id_line_entry_name: .: (0.003490) test_id_line_molecule_type: .: (0.002936) test_id_line_sequence_length: .: (0.003085) test_kw: .: (0.002832) test_molecule: .: (0.002924) test_oc: .: (0.002837) test_og_1: .: (0.002910) test_og_2: .: (0.002827) test_og_3: .: (0.002890) test_og_4: .: (0.002652) test_og_5: .: (0.002834) test_og_6: .: (0.003719) test_os: .: (0.002949) test_os_access: .: (0.003122) test_os_access2: .: (0.002843) test_ox: .: (0.002870) test_protein_name: .: (0.002978) test_ref: .: (0.006924) test_seq: .: (0.002702) test_sequence_length: .: (0.002876) test_sq: .: (0.002629) test_sq_crc64: .: (0.002749) test_sq_len: .: (0.002652) test_sq_mw: .: (0.002797) test_synonyms: .: (0.002649) Bio::TestUniProtKB_CC: test_allergen: .: (0.000417) test_alternative_products_access_as_hash: .: (0.000230) test_alternative_products_ai: .: (0.000295) test_alternative_products_apu: .: (0.000405) test_alternative_products_as: .: (0.000260) test_alternative_products_rf: .: (0.000118) test_biophysicochemical_properties: .: (0.000484) test_biotechnology: .: (0.000291) test_catalytic_activity: .: (0.000239) test_caution: .: (0.000790) test_cofactor: .: (0.000205) test_developmental_stage: .: (0.000215) test_disease: .: (0.000291) test_domain: .: (0.000308) test_enzyme_regulation: .: (0.000207) test_function: .: (0.000225) test_induction: .: (0.000312) test_interaction: .: (0.000300) test_mass_spectrometry: .: (0.000280) test_miscellaneous: .: (0.000212) test_pathway: .: (0.000224) test_pharmaceutical: .: (0.000253) test_polymorphism: .: (0.000341) test_ptm: .: (0.000264) test_rna_editing: .: (0.000308) test_similarity: .: (0.000352) test_subcellular_location: .: (0.000264) test_subunit: .: (0.000230) test_tissue_specificity: .: (0.000243) test_toxic_dose: .: (0.000195) test_web_resource: .: (0.000296) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000398) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000651) test_protein_name: .: (0.000316) test_synonyms: .: (0.000328) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000225) test_entry: .: (0.000150) test_entry_id: .: (0.000318) test_entry_name: .: (0.000162) test_id_line: .: (0.000173) test_molecule: .: (0.000131) test_sequence_length: .: (0.000158) Bio::TestUniProtKB_P03589: test_ac: .: (0.000532) test_accession: .: (0.001754) test_cc: .: (0.000660) test_cc_alternative_products: .: (0.000578) test_cc_database: .: (0.000864) test_cc_mass_spectrometry: .: (0.000603) test_de: .: (0.000669) test_dr: .: (0.000699) test_dr_with_key: .: (0.000788) test_dr_with_key_empty: .: (0.000544) test_dt: .: (0.000566) test_dt_annotation: .: (0.000438) test_dt_created: .: (0.000360) test_dt_sequence: .: (0.000570) test_entry: .: (0.000444) test_ft: .: (0.000547) test_gene_name: .: (0.000551) test_gene_names: .: (0.000415) test_gn: .: (0.000444) test_gn_old_parser: .: (0.000660) test_gn_uniprot_parser: .: (0.000444) test_id_line: .: (0.000362) test_id_line_data_class: .: (0.000581) test_id_line_entry_name: .: (0.000441) test_id_line_sequence_length: .: (0.000362) test_kw: .: (0.000681) test_oc: .: (0.000432) test_oh: .: (0.000867) test_os: .: (0.000483) test_os_access: .: (0.000428) test_os_access2: .: (0.000654) test_ox: .: (0.000447) test_protein_name: .: (0.000419) test_protein_name_after_calling_de: .: (0.000644) test_ref: .: (0.000518) test_seq: .: (0.000684) test_sequence_length: .: (0.000566) test_sq: .: (0.000400) test_sq_crc64: .: (0.000413) test_sq_len: .: (0.000561) test_sq_mw: .: (0.000466) test_synonyms: .: (0.000434) Bio::TestUniProtKB_P28907: test_ac: .: (0.001490) test_accession: .: (0.001204) test_cc: .: (0.001638) test_cc_alternative_products: .: (0.001855) test_cc_database: .: (0.001625) test_cc_mass_spectrometry: .: (0.001976) test_de: .: (0.001244) test_dr: .: (0.003042) test_dr_with_key: .: (0.003023) test_dr_with_key_empty: .: (0.002704) test_dt: .: (0.001074) test_dt_annotation: .: (0.001087) test_dt_created: .: (0.001126) test_dt_sequence: .: (0.001232) test_entry: .: (0.001110) test_ft: .: (0.002093) test_gene_name: .: (0.001178) test_gene_names: .: (0.001164) test_gn: .: (0.001099) test_gn_old_parser: .: (0.001322) test_gn_uniprot_parser: .: (0.001096) test_id_line: .: (0.001164) test_id_line_data_class: .: (0.001133) test_id_line_entry_name: .: (0.001103) test_id_line_sequence_length: .: (0.001085) test_kw: .: (0.001198) test_oc: .: (0.001135) test_os: .: (0.001200) test_os_access: .: (0.001194) test_os_access2: .: (0.001144) test_ox: .: (0.001275) test_protein_name: .: (0.002400) test_protein_name_after_calling_de: .: (0.001350) test_ref: .: (0.002124) test_seq: .: (0.001247) test_sequence_length: .: (0.001112) test_sq: .: (0.001158) test_sq_crc64: .: (0.001309) test_sq_len: .: (0.001199) test_sq_mw: .: (0.001254) test_synonyms: .: (0.001419) test_synonyms_after_calling_de: .: (0.001182) Bio::TestUniProtKB_P49144: test_ac: .: (0.000815) test_accession: .: (0.000572) test_cc: .: (0.001029) test_cc_alternative_products: .: (0.000987) test_cc_database: .: (0.000830) test_cc_mass_spectrometry: .: (0.000930) test_de: .: (0.000712) test_dr: .: (0.001100) test_dr_with_key: .: (0.001081) test_dr_with_key_empty: .: (0.000845) test_dt: .: (0.000801) test_dt_annotation: .: (0.000665) test_dt_created: .: (0.000611) test_dt_sequence: .: (0.000683) test_entry: .: (0.000593) test_ft: .: (0.001547) test_gene_name: .: (0.000782) test_gene_names: .: (0.000653) test_gn: .: (0.000583) test_gn_old_parser: .: (0.000934) test_gn_uniprot_parser: .: (0.000586) test_id_line: .: (0.000642) test_id_line_data_class: .: (0.000582) test_id_line_entry_name: .: (0.000753) test_id_line_sequence_length: .: (0.000485) test_kw: .: (0.000836) test_oc: .: (0.000588) test_os: .: (0.000688) test_os_access: .: (0.000542) test_os_access2: .: (0.000862) test_ox: .: (0.000573) test_protein_name: .: (0.000693) test_protein_name_after_calling_de: .: (0.000588) test_ref: .: (0.000786) test_seq: .: (0.000747) test_sequence_length: .: (0.000535) test_sq: .: (0.000799) test_sq_crc64: .: (0.000555) test_sq_len: .: (0.000726) test_sq_mw: .: (0.000571) test_synonyms: .: (0.000714) test_synonyms_after_calling_de: .: (0.000712) Bio::TestUniProtKB_Ref: test_RA: .: (0.000389) test_RC: .: (0.000291) test_RG: .: (0.000244) test_RL: .: (0.000238) test_RN: .: (0.000400) test_RP: .: (0.000283) test_RT: .: (0.000252) test_RX: .: (0.000290) test_ref: .: (0.000375) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000262) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000427) test_alternative_products_with_ft: .: (0.000689) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000319) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000309) test_RL_lines: .: (0.000187) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000575) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000433) test_RG_line: .: (0.000171) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000593) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000304) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000291) test_RL_line: .: (0.000251) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000733) test_RP_line: .: (0.000182) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000144) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000303) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000269) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000252) test_CC_interaction_isoform: .: (0.000347) test_CC_interaction_no_gene_name: .: (0.000214) test_CC_interaction_self_association: .: (0.000254) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000328) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000333) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000440) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000531) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000328) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000269) test_DT_line: .: (0.000252) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.002986) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000639) test_CC_web_resource: .: (0.000127) test_FT_VER_SEQ: .: (0.000194) test_OH_line_exception: .: (0.000292) test_OH_lines: .: (0.000336) Bio::TestUtils: test_centreOfGravity: .: (0.000710) test_dihedral_angle: .: (0.000447) test_distance: .: (0.000366) test_geometricCentre: .: (0.000273) test_rad2deg: .: (0.000334) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000292) test_dijkstra_on_weighted_graph: .: (0.000162) Finished in 13.117235513 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 300.44 tests/s, 1646.76 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.5-1_amd64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_amd64.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/3150131 and its subdirectories I: Current time: Thu Jul 3 16:54:52 -12 2025 I: pbuilder-time-stamp: 1751604892 Fri May 31 22:31:53 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri May 31 22:31:53 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri May 31 22:34:44 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri May 31 22:34:45 UTC 2024 I: ruby-bio_2.0.5-1_amd64.changes: Format: 1.8 Date: Sun, 03 Mar 2024 14:21:49 +0100 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.5-1 Distribution: unstable Urgency: medium Maintainer: Debian Ruby Team Changed-By: Lucas Nussbaum Description: ruby-bio - Ruby tools for computational molecular biology Changes: ruby-bio (2.0.5-1) unstable; urgency=medium . [ Debian Janitor ] * Update standards version to 4.6.2, no changes needed. . [ Lucas Nussbaum ] * New upstream version 2.0.5 Checksums-Sha1: 1f09a2591e5cf4b31591e407f53b2f6c5881d609 656832 ruby-bio_2.0.5-1_all.deb d1fedaa03ee7e5dbf50d85a915d1dc90d8687e54 8305 ruby-bio_2.0.5-1_amd64.buildinfo Checksums-Sha256: 9f50f668237d86011e1cb40b1f1bb964dfb322d827a0a1a7423df712652ac5f3 656832 ruby-bio_2.0.5-1_all.deb b84d7f86e35d7f93b710f3ffeee0199c6d3eb710a104cafa4e4e7c7116d6dcf7 8305 ruby-bio_2.0.5-1_amd64.buildinfo Files: 6b30eeea4b84581b7c9732444564d65b 656832 ruby optional ruby-bio_2.0.5-1_all.deb 4430d7fc9ad8bfdf4338ad51ae114c7f 8305 ruby optional ruby-bio_2.0.5-1_amd64.buildinfo Fri May 31 22:34:46 UTC 2024 I: diffoscope 268 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_16-22454.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/ruby-bio_2.0.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/ruby-bio_2.0.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/ruby-bio_2.0.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/b1/ruby-bio_2.0.5-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.gRDLdcBv/b2/ruby-bio_2.0.5-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.358s) 0.358s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 683ms CPU time consumed: 684ms Fri May 31 22:34:47 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Fri May 31 22:34:47 UTC 2024 I: ruby-bio from trixie built successfully and reproducibly on amd64. Fri May 31 22:34:48 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 31 22:34:48 UTC 2024 I: Submitting 12K b1/ruby-bio_2.0.5-1_amd64.buildinfo.asc Fri May 31 22:34:50 UTC 2024 I: Submitting 12K b2/ruby-bio_2.0.5-1_amd64.buildinfo.asc Fri May 31 22:34:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 31 22:34:50 UTC 2024 I: Done submitting .buildinfo files. Fri May 31 22:34:50 UTC 2024 I: Removing signed ruby-bio_2.0.5-1_amd64.buildinfo.asc files: removed './b1/ruby-bio_2.0.5-1_amd64.buildinfo.asc' removed './b2/ruby-bio_2.0.5-1_amd64.buildinfo.asc'