Sun Jun 2 15:52:03 UTC 2024 I: starting to build ruby-bio/unstable/amd64 on jenkins on '2024-06-02 15:51' Sun Jun 2 15:52:03 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_25/8005/console.log Sun Jun 2 15:52:03 UTC 2024 I: Downloading source for unstable/ruby-bio=2.0.5-1 --2024-06-02 15:52:03-- 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% 241M=0s 2024-06-02 15:52:03 (241 MB/s) - ‘ruby-bio_2.0.5-1.dsc’ saved [2108/2108] Sun Jun 2 15:52:03 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----- Sun Jun 2 15:52:03 UTC 2024 I: Checking whether the package is not for us Sun Jun 2 15:52:03 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Jun 2 15:52:03 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Jun 2 15:53:47 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 2 03:52:05 -12 2024 I: pbuilder-time-stamp: 1717343525 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/3392535/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=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1f8c0d2693f64ce1a0dfaf497d1db1b0' 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='3392535' 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.YvZYz0iV/pbuilderrc_0Y7G --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/b1 --logfile b1/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 1 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3392535/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 ... 19719 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} 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 gnupg-utils gpg-wks-client 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, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 43.6 MB of archives. After unpacking 165 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-4 [95.7 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.43-7 [119 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.43-7 [363 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.43-7 [701 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.43-7 [523 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.43-7 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.43-7 [250 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.43-7 [375 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 92 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.23.7 [1068 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-46 [73.3 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 120 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 122 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 gem2deb-test-runner amd64 2.2.3 [17.8 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 ruby3.1-dev amd64 3.1.2-8.3 [1001 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 ruby-all-dev amd64 1:3.1+nmu1 [5672 B] Get: 128 http://deb.debian.org/debian unstable/main amd64 gem2deb amd64 2.2.3 [47.8 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 ruby-libxml amd64 3.2.4-2+b2 [83.5 kB] Fetched 43.6 MB in 1s (66.1 MB/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 ... 19719 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 ... 20035 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 ... 21027 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_2.40.1-4_amd64.deb ... Unpacking bsdextrautils (2.40.1-4) ... 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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Unpacking debhelper (13.15.3) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../033-libassuan0_2.5.6-1+b1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1+b1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../034-gpgconf_2.2.43-7_amd64.deb ... Unpacking gpgconf (2.2.43-7) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../035-libksba8_1.6.6-1_amd64.deb ... Unpacking libksba8:amd64 (1.6.6-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../036-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../037-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. 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_2.2.43-7_amd64.deb ... Unpacking dirmngr (2.2.43-7) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../041-gnupg-l10n_2.2.43-7_all.deb ... Unpacking gnupg-l10n (2.2.43-7) ... Selecting previously unselected package gpg. Preparing to unpack .../042-gpg_2.2.43-7_amd64.deb ... Unpacking gpg (2.2.43-7) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../043-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 .../044-gpg-agent_2.2.43-7_amd64.deb ... Unpacking gpg-agent (2.2.43-7) ... Selecting previously unselected package gpgsm. Preparing to unpack .../045-gpgsm_2.2.43-7_amd64.deb ... Unpacking gpgsm (2.2.43-7) ... Selecting previously unselected package gnupg. Preparing to unpack .../046-gnupg_2.2.43-7_all.deb ... Unpacking gnupg (2.2.43-7) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../047-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 .../048-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 .../049-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 .../050-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 .../051-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 .../052-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 .../053-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 .../054-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 .../055-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 .../056-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 .../057-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 .../058-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 .../059-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 .../060-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 .../061-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 .../062-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../063-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../064-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../065-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../066-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../067-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../068-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../069-liburi-perl_5.28-1_all.deb ... Unpacking liburi-perl (5.28-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../070-libhtml-parser-perl_3.82-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.82-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../071-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:amd64. Preparing to unpack .../072-libclone-perl_0.46-1+b2_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1+b2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../073-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../074-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../075-libhttp-message-perl_6.46-1_all.deb ... Unpacking libhttp-message-perl (6.46-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../076-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 .../077-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 .../078-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 .../079-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 .../080-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 .../081-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 .../082-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 .../083-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 .../084-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../085-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../086-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../087-wdiff_1.2.2-6_amd64.deb ... Unpacking wdiff (1.2.2-6) ... Selecting previously unselected package devscripts. Preparing to unpack .../088-devscripts_2.23.7_all.deb ... Unpacking devscripts (2.23.7) ... Selecting previously unselected package xml-core. Preparing to unpack .../089-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../090-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../091-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../092-libosp5_1.5.2-15_amd64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../093-opensp_1.5.2-15_amd64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../094-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 .../095-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../096-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 .../097-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../098-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 .../099-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 .../100-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../101-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../102-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../103-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 .../104-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 .../105-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 .../106-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../107-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../108-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../109-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../110-gem2deb-test-runner_2.2.3_amd64.deb ... Unpacking gem2deb-test-runner (2.2.3) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../111-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 .../112-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 .../113-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 .../114-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 .../115-gem2deb_2.2.3_amd64.deb ... Unpacking gem2deb (2.2.3) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../116-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 .../117-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 .../118-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 (2.40.1-4) ... 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: Sun Jun 2 15:52:45 UTC 2024. Universal Time is now: Sun Jun 2 15:52:45 UTC 2024. 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 (2.2.43-7) ... 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 (2.12.7+dfsg-2) ... 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 (2.2.43-7) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.43-7) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.43-7) ... 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 (2.2.43-7) ... 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 (2.2.43-7) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gnupg (2.2.43-7) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... 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 ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up devscripts (2.23.7) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (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 libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-all-dev:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.2.1-1) ... Setting up rdtool (0.6.38-4.1) ... Setting up gem2deb-test-runner (2.2.3) ... Setting up gem2deb (2.2.3) ... Processing triggers for libc-bin (2.38-12) ... 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/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000700) test_dbs: .: (0.000323) test_go_ids: .: (0.000300) test_go_terms: .: (0.000491) test_parser: .: (0.000541) test_set_date: .: (0.000273) test_set_desc: .: (0.000271) test_to_str: .: (0.000289) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.001055) test_mktmpdir_without_block: .: (0.000760) test_remove_entry_secure: .: (0.000477) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.004358) test_call_command_fork: .: (0.000253) test_call_command_open3: .: (0.004674) test_call_command_popen: .: (0.003545) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.003222) test_call_command_fork: .: (0.000203) test_call_command_open3: .: (0.003332) test_call_command_popen: .: (0.002676) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.002687) test_call_command_fork: .: (0.000186) test_call_command_open3: .: (0.002492) test_call_command_popen: .: (0.002985) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.002726) test_call_command_fork_chdir: .: (0.000303) test_call_command_popen_chdir: .: (0.001927) test_query_command_chdir: .: (0.003181) test_query_command_fork_chdir: .: (0.012656) test_query_command_popen_chdir: .: (0.002963) Bio::FuncTestCommandQuery: test_query_command: .: (0.010512) test_query_command_fork: .: (0.001727) test_query_command_open3: .: (0.010169) test_query_command_popen: .: (0.009251) Bio::FuncTestCommandTmpdir: test_close!: .: (0.001244) test_initialize: .: (0.000473) test_path: .: (0.000357) test_path_after_close: .: (0.000712) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.017235) test_output_fasta: .: (0.010388) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000551) test_accession: .: (0.000229) test_accessions: .: (0.000230) test_comment: .: (0.000199) test_common_name: .: (0.000263) test_definition: .: (0.000236) test_features: .: (0.000416) test_gi: .: (0.000220) test_keywords: .: (0.000213) test_locus: .: (0.000165) test_nid: .: (0.000261) test_organism: .: (0.000209) test_origin: .: (0.000153) test_references: .: (0.000734) test_segment: .: (0.000167) test_source: .: (0.000305) test_taxonomy: .: (0.000188) test_version: .: (0.000174) test_versions: .: (0.000165) Bio::TestAA: test_13: .: (0.000225) test_1n: .: (0.000098) test_name2one: .: (0.000163) test_name2three: .: (0.000121) test_one2name: .: (0.000109) test_one2three: .: (0.000098) test_three2name: .: (0.000274) test_three2one: .: (0.000186) test_to_1_1: .: (0.000146) test_to_1_3: .: (0.000168) test_to_1_name: .: (0.000169) test_to_3_1: .: (0.000153) test_to_3_3: .: (0.000108) test_to_3_name: .: (0.000123) test_to_re: .: (0.000143) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000209) Bio::TestAAindex: test_api: .: (0.000175) test_auto_aax1: .: (0.000295) test_auto_aax2: .: (0.000565) Bio::TestAAindex1: test_author: .: (0.000383) test_comment: .: (0.000220) test_correlation_coefficient: .: (0.000465) test_dblinks: .: (0.000225) test_definition: .: (0.000224) test_entry_id: .: (0.000215) test_index: .: (0.000313) test_journal: .: (0.000256) test_title: .: (0.000485) Bio::TestAAindex2: test_access_A_R: .: (0.001065) test_access_R_A: .: (0.000797) test_author: .: (0.000281) test_cols: .: (0.000441) test_comment: .: (0.000237) test_dblinks: .: (0.000221) test_definition: .: (0.000232) test_entry_id: .: (0.000218) test_journal: .: (0.000248) test_matrix: .: (0.000812) test_matrix_1_2: .: (0.000852) test_matrix_2_2: .: (0.009112) test_matrix_A_R: .: (0.000947) test_matrix_R_A: .: (0.001473) test_matrix_determinant: .: (0.004636) test_matrix_rank: .: (0.005034) test_matrix_transpose: .: (0.001112) test_rows: .: (0.000273) test_title: .: (0.000311) Bio::TestAAindexConstant: test_delimiter: .: (0.000310) test_tagsize: .: (0.000143) Bio::TestAbif: test_complement: .: (0.015244) test_seq: .: (0.013461) test_to_biosequence: .: (0.014400) Bio::TestActsLikeMap: test_mixin: .: (0.000438) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000840) Bio::TestActsLikeMarker: test_mixin: .: (0.000315) Bio::TestAlignment: test_add_seq_no_key: .: (0.000371) test_add_seq_using_seq_with_aaseq_method: .: (0.000178) test_add_seq_using_seq_with_definition_method: .: (0.000144) test_add_seq_using_seq_with_entry_id_method: .: (0.000148) test_add_seq_using_seq_with_naseq_method: .: (0.000163) test_add_seq_using_seq_with_seq_method: .: (0.000155) test_consensus_iupac_gap_modes: .: (0.000532) test_consensus_iupac_missing_char: .: (0.000222) test_consensus_iupac_missing_char_option: .: (0.000622) test_consensus_iupac_no_gaps: .: (0.000328) test_consensus_iupac_of_ambiguous_bases: .: (0.000521) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.006953) test_consensus_opt_gap_mode: .: (0.001369) test_consensus_opt_missing_char: .: (0.000308) test_consensus_string_no_gaps: .: (0.000301) test_consensus_threshold_four_sequences: .: (0.000435) test_consensus_threshold_two_sequences: .: (0.000477) test_convert_match: .: (0.000584) test_convert_unmatch: .: (0.000197) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000231) test_convert_unmatch_different_match_char: .: (0.000215) test_convert_unmatch_multiple_sequences: .: (0.000298) test_default_gap_char: .: (0.000110) test_default_gap_regexp_matches_default_gap_char: .: (0.000118) test_default_missing_char: .: (0.000110) test_each_site_equal_length: .: (0.000223) test_each_site_unequal_length: .: (0.000593) test_equals: .: (0.000342) test_match_line_protein: .: (0.000735) test_normalizebang_extends_sequences_with_gaps: .: (0.000220) test_seq_length_is_max_seq_length: .: (0.000233) test_seq_length_when_one_sequence: .: (0.000134) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000127) test_seqclass_when_seqclass_set: .: (0.000129) test_seqclass_when_sequence_used: .: (0.000184) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000123) test_set_and_get_gap_char: .: (0.000114) test_store_cannot_override_key: .: (0.000126) test_store_with_default_keys_and_user_defined_keys: .: (0.000135) test_store_with_nil_key_uses_next_number_for_key: .: (0.000425) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000311) test_alignment_concat: .: (0.000178) test_alignment_length: .: (0.000111) test_alignment_lstrip!: .: (0.000203) test_alignment_lstrip_nil: .: (0.000149) test_alignment_normalize!: .: (0.000125) test_alignment_rstrip!: .: (0.000208) test_alignment_rstrip_nil: .: (0.000140) test_alignment_site: .: (0.000180) test_alignment_slice: .: (0.000129) test_alignment_strip!: .: (0.000299) test_alignment_strip_nil: .: (0.000158) test_alignment_subseq: .: (0.000279) test_alignment_window: .: (0.000123) test_collect_each_site: .: (0.000179) test_consensus_each_site_default: .: (0.000195) test_consensus_each_site_gap_mode_1: .: (0.000381) test_consensus_each_site_gap_mode_minus1: .: (0.000211) test_consensus_iupac: .: (0.000477) test_consensus_string_default: .: (0.000203) test_consensus_string_half: .: (0.000180) test_convert_match: .: (0.000167) test_convert_unmatch: .: (0.000139) test_each_seq: .: (0.000153) test_each_site: .: (0.000254) test_each_site_step: .: (0.000682) test_each_window: .: (0.000225) test_match_line: .: (0.001198) test_match_line_amino: .: (0.002106) test_match_line_nuc: .: (0.000232) test_private_alignment_site: .: (0.000139) test_remove_all_gaps!: .: (0.000175) test_seqclass: .: (0.000127) test_seqclass=: .: (0.000179) test_seqclass_default: .: (0.000109) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.005242) test_determine_seq_method: .: (0.002489) test_entries: .: (0.000429) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000366) test_avoid_same_name_numbering: .: (0.000238) test_clustal_have_same_name_true: .: (0.000147) test_have_same_name_false: .: (0.000141) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000248) test_gap_char_default: .: (0.000191) test_gap_char_never_nil: .: (0.000170) test_gap_regexp: .: (0.000428) test_gap_regexp=: .: (0.000202) test_gap_regexp_never_nil: .: (0.000167) test_get_all_property_default: .: (0.000167) test_get_all_property_nodefault: .: (0.000157) test_is_gap_default_false: .: (0.000137) test_is_gap_default_true: .: (0.000138) test_is_gap_nodefault_false: .: (0.000131) test_is_gap_nodefault_true: .: (0.000132) test_missing_char=: .: (0.000131) test_missing_char_default: .: (0.000161) test_missing_char_never_nil: .: (0.000127) test_seqclass=: .: (0.000132) test_seqclass_default: .: (0.000126) test_seqclass_never_nil: .: (0.000126) test_set_all_property: .: (0.000282) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000734) test_consensus_string_50percent: .: (0.000163) test_consensus_string_50percent_nil: .: (0.000133) test_consensus_string_default: .: (0.000109) test_consensus_string_default_nil: .: (0.000118) test_has_gap_false: .: (0.000117) test_has_gap_true: .: (0.000111) test_match_line_amino_100percent: .: (0.000158) test_match_line_amino_missing: .: (0.000213) test_match_line_amino_strong: .: (0.000384) test_match_line_amino_weak: .: (0.000188) test_match_line_nuc_100percent: .: (0.000152) test_match_line_nuc_missing: .: (0.000148) test_remove_gaps!: .: (0.000123) test_remove_gaps_bang_not_removed: .: (0.000109) Bio::TestAtomFinder: test_atoms: .: (0.076491) test_each_atom: .: (0.011655) test_find_atom: .: (0.000277) Bio::TestBioFastaDefline: test_acc_version: .: (0.000621) test_accession: .: (0.000549) test_accessions: .: (0.000453) test_description: .: (0.000894) test_descriptions: .: (0.000443) test_entry_id: .: (0.000381) test_get: .: (0.000472) test_get_all_by_type: .: (0.000710) test_get_by_type: .: (0.000386) test_gi: .: (0.000432) test_id_strings: .: (0.000795) test_locus: .: (0.000985) test_method_missing: .: (0.000477) test_to_s: .: (0.000444) test_words: .: (0.001618) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.001070) test_goid2term: .: (0.000442) test_parse_goids: .: (0.000443) Bio::TestBioGenBank: test_basecount: .: (0.001032) test_circular: .: (0.000341) test_classification: .: (0.000371) test_date: .: (0.000305) test_date_modified: .: (0.000950) test_division: .: (0.000298) test_each_cds_feature: .: (0.001507) test_each_cds_qualifiers: .: (0.001003) test_each_gene: .: (0.001391) test_entry_id: .: (0.000284) test_length: .: (0.000267) test_locus_circular: .: (0.000332) test_locus_class: .: (0.000370) test_locus_date: .: (0.000311) test_locus_division: .: (0.000315) test_locus_entry_id: .: (0.000350) test_locus_length: .: (0.000645) test_locus_natype: .: (0.000355) test_locus_strand: .: (0.000308) test_natype: .: (0.000274) test_seq: .: (0.000356) test_seq_len: .: (0.000327) test_strand: .: (0.000280) test_strandedness: .: (0.000284) test_to_biosequence: .: (0.002901) Bio::TestBioGenPept: test_circular: .: (0.000825) test_date: .: (0.000275) test_dbsource: .: (0.000221) test_division: .: (0.000230) test_entry_id: .: (0.000234) test_length: .: (0.000235) test_locus: .: (0.000240) test_seq: .: (0.000262) test_seq_len: .: (0.000239) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000489) test_aaseq: .: (0.000705) test_chromosome: .: (0.000267) test_codon_usage: .: (0.000450) test_cu_list: .: (0.000239) test_dblinks_as_hash: .: (0.000319) test_dblinks_as_strings: .: (0.000267) test_definition: .: (0.000277) test_division: .: (0.000249) test_eclinks: .: (0.000827) test_entry: .: (0.000288) test_entry_id: .: (0.000239) test_gbposition: .: (0.000256) test_gene: .: (0.000263) test_genes: .: (0.000266) test_keggclass: .: (0.000291) test_keggclasses: .: (0.000302) test_locations: .: (0.000835) test_motifs_as_hash: .: (0.000399) test_motifs_as_strings: .: (0.000259) test_name: .: (0.000273) test_names_as_array: .: (0.000302) test_new: .: (0.000275) test_ntlen: .: (0.000352) test_ntseq: .: (0.000428) test_organism: .: (0.000313) test_orthologs_as_hash: .: (0.000285) test_orthologs_as_strings: .: (0.000300) test_pathway: .: (0.000278) test_pathway_after_pathways_as_strings: .: (0.000357) test_pathway_before_pathways_as_strings: .: (0.000386) test_pathways_as_hash: .: (0.000375) test_pathways_as_strings: .: (0.000254) test_position: .: (0.000299) test_structure: .: (0.000260) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001733) test_comment: .: (0.000504) test_data_source: .: (0.000545) test_definition: .: (0.000520) test_disease: .: (0.000491) test_entry_id: .: (0.000493) test_lineage: .: (0.000567) test_nalen: .: (0.000525) test_name: .: (0.000507) test_new: .: (0.000520) test_num_gene: .: (0.000477) test_num_rna: .: (0.000486) test_original_databases: .: (0.000476) test_original_db: .: (0.000479) test_plasmids: .: (0.000528) test_references: .: (0.003464) test_statistics: .: (0.000534) test_taxid: .: (0.000512) test_taxonomy: .: (0.000556) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000655) test_comment: .: (0.000376) test_data_source: .: (0.000292) test_definition: .: (0.000400) test_disease: .: (0.000384) test_entry_id: .: (0.000359) test_lineage: .: (0.000439) test_nalen: .: (0.000437) test_name: .: (0.000300) test_new: .: (0.000278) test_num_gene: .: (0.000313) test_num_rna: .: (0.000268) test_original_databases: .: (0.000305) test_original_db: .: (0.000330) test_plasmids: .: (0.000479) test_references: .: (0.000482) test_statistics: .: (0.000395) test_taxid: .: (0.000393) test_taxonomy: .: (0.000404) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000522) test_compounds_as_strings: .: (0.000264) test_dblinks_as_hash: .: (0.000352) test_dblinks_as_strings: .: (0.000236) test_description: .: (0.000314) test_diseases_as_hash: .: (0.000228) test_diseases_as_strings: .: (0.000253) test_entry_id: .: (0.000288) test_enzymes_as_strings: .: (0.000280) test_genes_as_hash: .: (0.000210) test_genes_as_strings: .: (0.000245) test_keggclass: .: (0.000232) test_ko_pathway: .: (0.000277) test_modules_as_hash: .: (0.000230) test_modules_as_strings: .: (0.000252) test_name: .: (0.000237) test_new: .: (0.000295) test_organism: .: (0.000225) test_orthologs_as_hash: .: (0.000253) test_orthologs_as_strings: .: (0.000206) test_pathways_as_hash: .: (0.000331) test_pathways_as_strings: .: (0.000211) test_reactions_as_hash: .: (0.000250) test_reactions_as_strings: .: (0.000201) test_references: .: (0.000250) test_rel_pathways_as_hash: .: (0.000252) test_rel_pathways_as_strings: .: (0.000263) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000702) test_compounds_as_strings: .: (0.000407) test_dblinks_as_hash: .: (0.000257) test_dblinks_as_strings: .: (0.000280) test_description: .: (0.000346) test_diseases_as_hash: .: (0.000305) test_diseases_as_strings: .: (0.000254) test_entry_id: .: (0.000315) test_enzymes_as_strings: .: (0.000273) test_genes_as_hash: .: (0.000336) test_genes_as_strings: .: (0.000297) test_keggclass: .: (0.000331) test_ko_pathway: .: (0.000271) test_modules_as_hash: .: (0.000301) test_modules_as_strings: .: (0.000291) test_name: .: (0.000328) test_new: .: (0.000296) test_organism: .: (0.000258) test_orthologs_as_hash: .: (0.000285) test_orthologs_as_strings: .: (0.000238) test_pathways_as_hash: .: (0.000293) test_pathways_as_strings: .: (0.000254) test_reactions_as_hash: .: (0.000288) test_reactions_as_strings: .: (0.000248) test_references: .: (0.000277) test_rel_pathways_as_hash: .: (0.000308) test_rel_pathways_as_strings: .: (0.000245) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000420) test_compounds_as_strings: .: (0.000263) test_dblinks_as_hash: .: (0.000203) test_dblinks_as_strings: .: (0.000198) test_description: .: (0.000229) test_diseases_as_hash: .: (0.000207) test_diseases_as_strings: .: (0.000253) test_entry_id: .: (0.000222) test_enzymes_as_strings: .: (0.000236) test_genes_as_hash: .: (0.000201) test_genes_as_strings: .: (0.000269) test_keggclass: .: (0.000228) test_ko_pathway: .: (0.000249) test_modules_as_hash: .: (0.000277) test_modules_as_strings: .: (0.000249) test_name: .: (0.000235) test_new: .: (0.000260) test_organism: .: (0.000228) test_orthologs_as_hash: .: (0.000319) test_orthologs_as_strings: .: (0.000236) test_pathways_as_hash: .: (0.000257) test_pathways_as_strings: .: (0.000205) test_reactions_as_hash: .: (0.000235) test_reactions_as_strings: .: (0.000195) test_references: .: (0.000245) test_rel_pathways_as_hash: .: (0.000217) test_rel_pathways_as_strings: .: (0.000318) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000397) test_compounds_as_strings: .: (0.000253) test_dblinks_as_hash: .: (0.000310) test_dblinks_as_strings: .: (0.000265) test_description: .: (0.000479) test_diseases_as_hash: .: (0.000321) test_diseases_as_strings: .: (0.000267) test_entry_id: .: (0.000301) test_enzymes_as_strings: .: (0.000257) test_genes_as_hash: .: (0.000284) test_genes_as_strings: .: (0.000261) test_keggclass: .: (0.000334) test_ko_pathway: .: (0.000281) test_modules_as_hash: .: (0.000423) test_modules_as_strings: .: (0.000336) test_name: .: (0.000356) test_new: .: (0.000281) test_organism: .: (0.000329) test_orthologs_as_hash: .: (0.000275) test_orthologs_as_strings: .: (0.000308) test_pathways_as_hash: .: (0.000350) test_pathways_as_strings: .: (0.000260) test_reactions_as_hash: .: (0.000297) test_reactions_as_strings: .: (0.000250) test_references: .: (0.001080) test_rel_pathways_as_hash: .: (0.000443) test_rel_pathways_as_strings: .: (0.000388) Bio::TestBioKeggDRUG: test_activity: .: (0.000711) test_comment: .: (0.000318) test_dblinks_as_hash: .: (0.000466) test_dblinks_as_strings: .: (0.000368) test_entry_id: .: (0.000349) test_formula: .: (0.000289) test_kcf: .: (0.000333) test_mass: .: (0.000298) test_name: .: (0.000404) test_names: .: (0.000346) test_pathways_as_hash: .: (0.000382) test_pathways_as_strings: .: (0.000344) test_products: .: (0.000345) test_remark: .: (0.000330) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000497) test_composition: .: (0.000383) test_compounds: .: (0.000289) test_dblinks_as_hash: .: (0.000593) test_dblinks_as_strings: .: (0.000394) test_entry_id: .: (0.000293) test_enzymes: .: (0.000367) test_kcf: .: (0.000256) test_keggclass: .: (0.000317) test_mass: .: (0.000308) test_name: .: (0.000312) test_orthologs_as_hash: .: (0.000445) test_orthologs_as_strings: .: (0.000375) test_pathways_as_hash: .: (0.000333) test_pathways_as_strings: .: (0.000313) test_reactions: .: (0.000301) test_references: .: (0.000380) test_remark: .: (0.000332) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000418) test_composition: .: (0.000253) test_compounds: .: (0.000268) test_dblinks_as_hash: .: (0.000274) test_dblinks_as_strings: .: (0.000263) test_entry_id: .: (0.000239) test_enzymes: .: (0.000283) test_kcf: .: (0.000218) test_keggclass: .: (0.000301) test_mass: .: (0.000251) test_name: .: (0.000263) test_orthologs_as_hash: .: (0.000229) test_orthologs_as_strings: .: (0.000247) test_pathways_as_hash: .: (0.000227) test_pathways_as_strings: .: (0.000281) test_reactions: .: (0.000227) test_references: .: (0.000257) test_remark: .: (0.000233) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000815) test_compounds_as_strings: .: (0.000465) test_dblinks_as_hash: .: (0.000327) test_dblinks_as_strings: .: (0.000348) test_description: .: (0.000322) test_diseases_as_hash: .: (0.000363) test_diseases_as_strings: .: (0.000355) test_entry_id: .: (0.000343) test_enzymes_as_strings: .: (0.000403) test_genes_as_hash: .: (0.000292) test_genes_as_strings: .: (0.000408) test_keggclass: .: (0.000303) test_ko_pathway: .: (0.000378) test_modules_as_hash: .: (0.000437) test_modules_as_strings: .: (0.000412) test_name: .: (0.000316) test_new: .: (0.000354) test_organism: .: (0.000306) test_orthologs_as_hash: .: (0.000329) test_orthologs_as_strings: .: (0.000305) test_pathways_as_hash: .: (0.000407) test_pathways_as_strings: .: (0.000293) test_reactions_as_hash: .: (0.007631) test_reactions_as_strings: .: (0.000592) test_references: .: (0.000687) test_rel_pathways_as_hash: .: (0.000531) test_rel_pathways_as_strings: .: (0.000793) Bio::TestBioLITDB: test_author: .: (0.000464) test_entry_id: .: (0.000258) test_field: .: (0.000227) test_journal: .: (0.000239) test_keyword: .: (0.000278) test_reference: .: (0.000575) test_title: .: (0.000289) test_volume: .: (0.000270) Bio::TestBioNBRF: test_aalen: .: (0.000414) test_aaseq: .: (0.000172) test_entry: .: (0.000159) test_length: .: (0.000268) test_nalen: .: (0.000259) test_naseq: .: (0.000204) test_seq: .: (0.000166) test_seq_class: .: (0.000164) test_to_nbrf: .: (0.000179) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000843) test_to_newick_format_leaf: .: (0.000430) test_to_newick_format_leaf_NHX: .: (0.000239) Bio::TestBl2seqReport: test_db_len: .: (0.000959) test_db_num: .: (0.000558) test_new: .: (0.000341) test_undefed_methods: .: (0.001780) test_undefed_methods_for_iteration: .: (0.001297) Bio::TestBl2seqReportConstants: test_rs: .: (0.000255) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000496) test_hits: .: (0.000347) Bio::TestBlast: test_blast_reports_format0: .: (0.008815) test_blast_reports_format0_with_block: .: (0.000939) test_blast_reports_format7: .: (0.024203) test_blast_reports_format7_with_block: .: (0.020457) test_blast_reports_format7_with_parser: .: (0.020659) test_blast_reports_format7_with_parser_with_block: .: (0.029747) test_blast_reports_format8: .: (0.004600) test_blast_reports_format8_with_block: .: (0.000751) test_blast_reports_format8_with_parser: .: (0.003273) test_blast_reports_format8_with_parser_with_block: .: (0.000316) test_blast_reports_xml: .: (0.068290) test_blast_reports_xml_with_block: .: (0.020835) test_blastll: .: (0.000268) test_db: .: (0.000183) test_exec_genomenet: .: (0.000158) test_exec_local: .: (0.000167) test_exec_ncbi: .: (0.000156) test_filter: .: (0.000174) test_format: .: (0.000186) test_make_command_line: .: (0.000627) test_make_command_line_2: .: (0.000474) test_matrix: .: (0.000179) test_new: .: (0.000550) test_new_opt_string: .: (0.000296) test_option: .: (0.000202) test_option_set: .: (0.000299) test_option_set_m0: .: (0.000269) test_options: .: (0.000212) test_output: .: (0.000178) test_parse_result: .: (0.023797) test_parser: .: (0.000290) test_program: .: (0.000254) test_query: .: (0.000185) test_self_local: .: (0.000512) test_self_remote: .: (0.002597) test_server: .: (0.000215) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000639) test_delete: .: (0.000510) test_equal_equal: .: (0.000614) test_get: .: (0.000473) test_make_command_line_options: .: (0.000392) test_normalize!: .: (0.000254) test_parse: .: (0.000288) test_set: .: (0.000928) Bio::TestBlastReport: test_db: .: (0.020471) test_db_len: .: (0.020257) test_db_num: .: (0.023124) test_each_hit: .: (0.020311) test_each_iteration: .: (0.029697) test_eff_space: .: (0.027055) test_entrez_query: .: (0.024543) test_entropy: .: (0.024516) test_expect: .: (0.025890) test_filter: .: (0.022475) test_gap_extend: .: (0.021064) test_gap_open: .: (0.020454) test_hits: .: (0.020402) test_hsp_len: .: (0.019893) test_inclusion: .: (0.022396) test_iterations: .: (0.020704) test_kappa: .: (0.021247) test_lambda: .: (0.020614) test_matrix: .: (0.020499) test_message: .: (0.020217) test_parameters: .: (0.022536) test_pattern: .: (0.021223) test_program: .: (0.020306) test_query_def: .: (0.020280) test_query_id: .: (0.020359) test_query_len: .: (0.020176) test_reference: .: (0.022469) test_sc_match: .: (0.020906) test_sc_mismatch: .: (0.020881) test_statistics: .: (0.020396) test_version: .: (0.020206) Bio::TestBlastReportDefault: test_db: .: (0.001090) test_db_len: .: (0.000566) test_db_num: .: (0.000476) test_each_hit: .: (0.000492) test_each_iteration: .: (0.000469) test_eff_space: .: (0.000725) test_entropy: .: (0.000554) test_expect: .: (0.000540) test_gap_extend: .: (0.000772) test_gap_open: .: (0.000548) test_gapped_entropy: .: (0.000543) test_gapped_kappa: .: (0.000550) test_gapped_lambda: .: (0.000515) test_hits: .: (0.000476) test_iterations: .: (0.000473) test_kappa: .: (0.000477) test_lambda: .: (0.000601) test_matrix: .: (0.000663) test_message: .: (0.000499) test_pattern: .: (0.000493) test_program: .: (0.000460) test_query_def: .: (0.000477) test_query_len: .: (0.000497) test_reference: .: (0.000495) test_sc_match: .: (0.000587) test_sc_mismatch: .: (0.000743) test_version: .: (0.000559) Bio::TestBlastReportHit: test_Hit_accession: .: (0.023071) test_Hit_bit_score: .: (0.021131) test_Hit_definition: .: (0.020736) test_Hit_evalue: .: (0.020227) test_Hit_hit_id: .: (0.019096) test_Hit_hsps: .: (0.019616) test_Hit_identity: .: (0.020745) test_Hit_lap_at: .: (0.019591) test_Hit_len: .: (0.019134) test_Hit_midline: .: (0.019235) test_Hit_num: .: (0.018871) test_Hit_overlap: .: (0.018997) test_Hit_query_def: .: (0.027087) test_Hit_query_end: .: (0.029098) test_Hit_query_id: .: (0.027992) test_Hit_query_len: .: (0.026470) test_Hit_query_seq: .: (0.019778) test_Hit_query_start: .: (0.021297) test_Hit_taeget_def: .: (0.023339) test_Hit_target_end: .: (0.032958) test_Hit_target_id: .: (0.023901) test_Hit_target_len: .: (0.022437) test_Hit_target_seq: .: (0.022981) test_Hit_target_start: .: (0.026590) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001305) test_Hit_definition: .: (0.000644) test_Hit_evalue: .: (0.000636) test_Hit_hsps: .: (0.000599) test_Hit_identity: .: (0.000591) test_Hit_lap_at: .: (0.001111) test_Hit_len: .: (0.000594) test_Hit_midline: .: (0.000855) test_Hit_overlap: .: (0.000545) test_Hit_query_end: .: (0.000857) test_Hit_query_seq: .: (0.001137) test_Hit_query_start: .: (0.000968) test_Hit_taeget_def: .: (0.000551) test_Hit_target_end: .: (0.000833) test_Hit_target_id: .: (0.000640) test_Hit_target_len: .: (0.000631) test_Hit_target_seq: .: (0.000880) test_Hit_target_start: .: (0.001361) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.061973) test_Hit_bit_score: .: (0.065587) test_Hit_definition: .: (0.059697) test_Hit_evalue: .: (0.060789) test_Hit_hit_id: .: (0.057751) test_Hit_hsps: .: (0.061246) test_Hit_identity: .: (0.059704) test_Hit_lap_at: .: (0.058309) test_Hit_len: .: (0.059293) test_Hit_midline: .: (0.057665) test_Hit_num: .: (0.061202) test_Hit_overlap: .: (0.057709) test_Hit_query_def: .: (0.059620) test_Hit_query_end: .: (0.058575) test_Hit_query_id: .: (0.076217) test_Hit_query_len: .: (0.077126) test_Hit_query_seq: .: (0.064886) test_Hit_query_start: .: (0.061737) test_Hit_taeget_def: .: (0.057878) test_Hit_target_end: .: (0.060707) test_Hit_target_id: .: (0.057894) test_Hit_target_len: .: (0.061206) test_Hit_target_seq: .: (0.079877) test_Hit_target_start: .: (0.073461) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.070413) test_Hit_bit_score: .: (0.063192) test_Hit_definition: .: (0.064937) test_Hit_evalue: .: (0.062122) test_Hit_hit_id: .: (0.064340) test_Hit_hsps: .: (0.063507) test_Hit_identity: .: (0.061673) test_Hit_lap_at: .: (0.063589) test_Hit_len: .: (0.077040) test_Hit_midline: .: (0.084689) test_Hit_num: .: (0.066104) test_Hit_overlap: .: (0.061617) test_Hit_query_def: .: (0.073498) test_Hit_query_end: .: (0.067429) test_Hit_query_id: .: (0.059540) test_Hit_query_len: .: (0.056963) test_Hit_query_seq: .: (0.059808) test_Hit_query_start: .: (0.056596) test_Hit_taeget_def: .: (0.059117) test_Hit_target_end: .: (0.058249) test_Hit_target_id: .: (0.057394) test_Hit_target_len: .: (0.059415) test_Hit_target_seq: .: (0.057416) test_Hit_target_start: .: (0.059392) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.018972) test_Hit_bit_score: .: (0.018641) test_Hit_definition: .: (0.019825) test_Hit_evalue: .: (0.021958) test_Hit_hit_id: .: (0.019925) test_Hit_hsps: .: (0.020042) test_Hit_identity: .: (0.019454) test_Hit_lap_at: .: (0.019636) test_Hit_len: .: (0.019835) test_Hit_midline: .: (0.021231) test_Hit_num: .: (0.019872) test_Hit_overlap: .: (0.019410) test_Hit_query_def: .: (0.019733) test_Hit_query_end: .: (0.019461) test_Hit_query_id: .: (0.020896) test_Hit_query_len: .: (0.019844) test_Hit_query_seq: .: (0.019377) test_Hit_query_start: .: (0.019191) test_Hit_taeget_def: .: (0.019094) test_Hit_target_end: .: (0.019074) test_Hit_target_id: .: (0.021343) test_Hit_target_len: .: (0.019628) test_Hit_target_seq: .: (0.019291) test_Hit_target_start: .: (0.019129) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000517) test_Hit_bit_score: .: (0.000235) test_Hit_definition: .: (0.000222) test_Hit_evalue: .: (0.000224) test_Hit_hit_id: .: (0.000226) test_Hit_hsps: .: (0.000360) test_Hit_identity: .: (0.000249) test_Hit_lap_at: .: (0.000239) test_Hit_len: .: (0.000220) test_Hit_midline: .: (0.000241) test_Hit_num: .: (0.000226) test_Hit_overlap: .: (0.000228) test_Hit_query_def: .: (0.000232) test_Hit_query_end: .: (0.000228) test_Hit_query_id: .: (0.000226) test_Hit_query_len: .: (0.000228) test_Hit_query_seq: .: (0.000235) test_Hit_query_start: .: (0.000254) test_Hit_taeget_def: .: (0.000255) test_Hit_target_end: .: (0.000253) test_Hit_target_id: .: (0.000280) test_Hit_target_len: .: (0.000289) test_Hit_target_seq: .: (0.000224) test_Hit_target_start: .: (0.000223) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.019542) test_Hsp_bit_score: .: (0.022022) test_Hsp_density: .: (0.020295) test_Hsp_evalue: .: (0.019511) test_Hsp_gaps: .: (0.019539) test_Hsp_hit_frame: .: (0.019513) test_Hsp_hit_from: .: (0.021126) test_Hsp_hit_to: .: (0.019794) test_Hsp_hseq: .: (0.019910) test_Hsp_identity: .: (0.019591) test_Hsp_midline: .: (0.019236) test_Hsp_mismatch_count: .: (0.019737) test_Hsp_num: .: (0.021088) test_Hsp_pattern_from: .: (0.019588) test_Hsp_pattern_to: .: (0.019144) test_Hsp_percent_identity: .: (0.018618) test_Hsp_positive: .: (0.018924) test_Hsp_qseq: .: (0.020503) test_Hsp_query_frame: .: (0.019684) test_Hsp_query_from: .: (0.019520) test_Hsp_query_to: .: (0.019279) test_Hsp_score: .: (0.019141) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000842) test_Hsp_bit_score: .: (0.000571) test_Hsp_evalue: .: (0.000584) test_Hsp_gaps: .: (0.000547) test_Hsp_hit_frame: .: (0.000537) test_Hsp_hit_from: .: (0.000766) test_Hsp_hit_to: .: (0.000865) test_Hsp_hseq: .: (0.000732) test_Hsp_identity: .: (0.000564) test_Hsp_midline: .: (0.000735) test_Hsp_percent_identity: .: (0.000524) test_Hsp_positive: .: (0.000519) test_Hsp_qseq: .: (0.000870) test_Hsp_query_frame: .: (0.000574) test_Hsp_query_from: .: (0.000715) test_Hsp_query_to: .: (0.000734) test_Hsp_score: .: (0.000530) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.059394) test_Hsp_bit_score: .: (0.059011) test_Hsp_density: .: (0.057487) test_Hsp_evalue: .: (0.170924) test_Hsp_gaps: .: (0.064372) test_Hsp_hit_frame: .: (0.060659) test_Hsp_hit_from: .: (0.057675) test_Hsp_hit_to: .: (0.060178) test_Hsp_hseq: .: (0.057688) test_Hsp_identity: .: (0.060143) test_Hsp_midline: .: (0.057287) test_Hsp_mismatch_count: .: (0.059442) test_Hsp_num: .: (0.057296) test_Hsp_pattern_from: .: (0.059208) test_Hsp_pattern_to: .: (0.057883) test_Hsp_percent_identity: .: (0.060090) test_Hsp_positive: .: (0.057038) test_Hsp_qseq: .: (0.060742) test_Hsp_query_frame: .: (0.056328) test_Hsp_query_from: .: (0.069773) test_Hsp_query_to: .: (0.083401) test_Hsp_score: .: (0.062452) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.058544) test_Hsp_bit_score: .: (0.057044) test_Hsp_density: .: (0.059134) test_Hsp_evalue: .: (0.060629) test_Hsp_gaps: .: (0.061010) test_Hsp_hit_frame: .: (0.059125) test_Hsp_hit_from: .: (0.080302) test_Hsp_hit_to: .: (0.060612) test_Hsp_hseq: .: (0.060175) test_Hsp_identity: .: (0.057891) test_Hsp_midline: .: (0.060767) test_Hsp_mismatch_count: .: (0.062664) test_Hsp_num: .: (0.061462) test_Hsp_pattern_from: .: (0.062802) test_Hsp_pattern_to: .: (0.061330) test_Hsp_percent_identity: .: (0.065177) test_Hsp_positive: .: (0.075709) test_Hsp_qseq: .: (0.065713) test_Hsp_query_frame: .: (0.061747) test_Hsp_query_from: .: (0.066950) test_Hsp_query_to: .: (0.078675) test_Hsp_score: .: (0.067425) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.019902) test_Hsp_bit_score: .: (0.019204) test_Hsp_density: .: (0.019491) test_Hsp_evalue: .: (0.021384) test_Hsp_gaps: .: (0.019668) test_Hsp_hit_frame: .: (0.019244) test_Hsp_hit_from: .: (0.019533) test_Hsp_hit_to: .: (0.020940) test_Hsp_hseq: .: (0.031537) test_Hsp_identity: .: (0.034112) test_Hsp_midline: .: (0.022882) test_Hsp_mismatch_count: .: (0.022626) test_Hsp_num: .: (0.022965) test_Hsp_pattern_from: .: (0.021899) test_Hsp_pattern_to: .: (0.021002) test_Hsp_percent_identity: .: (0.021660) test_Hsp_positive: .: (0.020826) test_Hsp_qseq: .: (0.019801) test_Hsp_query_frame: .: (0.019685) test_Hsp_query_from: .: (0.019519) test_Hsp_query_to: .: (0.020409) test_Hsp_score: .: (0.020144) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000495) test_Hsp_bit_score: .: (0.000236) test_Hsp_density: .: (0.000222) test_Hsp_evalue: .: (0.000211) test_Hsp_gaps: .: (0.000214) test_Hsp_hit_frame: .: (0.000467) test_Hsp_hit_from: .: (0.000210) test_Hsp_hit_to: .: (0.000205) test_Hsp_hseq: .: (0.000251) test_Hsp_identity: .: (0.000213) test_Hsp_midline: .: (0.000212) test_Hsp_mismatch_count: .: (0.000205) test_Hsp_num: .: (0.000210) test_Hsp_pattern_from: .: (0.000210) test_Hsp_pattern_to: .: (0.000205) test_Hsp_percent_identity: .: (0.000206) test_Hsp_positive: .: (0.000207) test_Hsp_qseq: .: (0.000203) test_Hsp_query_frame: .: (0.000389) test_Hsp_query_from: .: (0.000235) test_Hsp_query_to: .: (0.000253) test_Hsp_score: .: (0.000207) Bio::TestBlastReportIteration: test_hits: .: (0.019754) test_message: .: (0.019219) test_num: .: (0.019816) test_statistics: .: (0.022201) Bio::TestBlastReportIterationDefault: test_hits: .: (0.001201) test_message: .: (0.000701) test_num: .: (0.000719) Bio::TestBlastReportIterationMulti: test_each: .: (0.078128) test_hits: .: (0.076603) test_message: .: (0.083519) test_num: .: (0.085457) test_query_def: .: (0.080791) test_query_id: .: (0.064364) test_query_len: .: (0.059778) test_statistics: .: (0.059988) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.073477) test_hits: .: (0.076592) test_message: .: (0.060302) test_num: .: (0.060408) test_query_def: .: (0.057342) test_query_id: .: (0.059917) test_query_len: .: (0.062176) test_statistics: .: (0.058643) Bio::TestBlastReportIterationREXML: test_hits: .: (0.019947) test_message: .: (0.019000) test_num: .: (0.021239) test_statistics: .: (0.019775) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000700) test_message: .: (0.000352) test_num: .: (0.000431) test_statistics: .: (0.000368) Bio::TestBlastReportMulti: test_db: .: (0.062594) test_db_len: .: (0.067098) test_db_num: .: (0.076879) test_each_hit: .: (0.065027) test_each_iteration: .: (0.060837) test_eff_space: .: (0.060195) test_entropy: .: (0.062176) test_expect: .: (0.077857) test_filter: .: (0.072709) test_gap_extend: .: (0.065619) test_gap_open: .: (0.060450) test_hits: .: (0.057221) test_hsp_len: .: (0.062087) test_iterations: .: (0.062133) test_kappa: .: (0.061275) test_lambda: .: (0.065614) test_matrix: .: (0.068939) test_message: .: (0.060238) test_parameters: .: (0.057700) test_pattern: .: (0.060674) test_program: .: (0.060645) test_query_def: .: (0.059131) test_query_id: .: (0.077729) test_query_len: .: (0.096229) test_reference: .: (0.100113) test_reports: .: (0.069798) test_statistics: .: (0.066971) test_version: .: (0.089526) Bio::TestBlastReportMultiREXML: test_db: .: (0.083822) test_db_len: .: (0.061900) test_db_num: .: (0.058370) test_each_hit: .: (0.060962) test_each_iteration: .: (0.059082) test_eff_space: .: (0.100870) test_entropy: .: (0.079913) test_expect: .: (0.062336) test_filter: .: (0.063597) test_gap_extend: .: (0.069887) test_gap_open: .: (0.061298) test_hits: .: (0.058391) test_hsp_len: .: (0.061549) test_iterations: .: (0.068304) test_kappa: .: (0.059682) test_lambda: .: (0.064391) test_matrix: .: (0.062079) test_message: .: (0.062294) test_parameters: .: (0.062830) test_pattern: .: (0.059300) test_program: .: (0.062827) test_query_def: .: (0.063162) test_query_id: .: (0.060442) test_query_len: .: (0.061037) test_reference: .: (0.058723) test_reports: .: (0.063256) test_statistics: .: (0.062863) test_version: .: (0.060224) Bio::TestBlastReportREXML: test_db: .: (0.019285) test_db_len: .: (0.019030) test_db_num: .: (0.022685) test_each_hit: .: (0.020095) test_each_iteration: .: (0.019266) test_eff_space: .: (0.019619) test_entrez_query: .: (0.019357) test_entropy: .: (0.019438) test_expect: .: (0.021002) test_filter: .: (0.019936) test_gap_extend: .: (0.019861) test_gap_open: .: (0.019528) test_hits: .: (0.024400) test_hsp_len: .: (0.025027) test_inclusion: .: (0.020389) test_iterations: .: (0.020062) test_kappa: .: (0.020176) test_lambda: .: (0.019780) test_matrix: .: (0.021465) test_message: .: (0.019735) test_parameters: .: (0.019217) test_pattern: .: (0.019108) test_program: .: (0.019855) test_query_def: .: (0.020888) test_query_id: .: (0.020087) test_query_len: .: (0.019358) test_reference: .: (0.020327) test_sc_match: .: (0.020074) test_sc_mismatch: .: (0.020268) test_statistics: .: (0.022623) test_version: .: (0.021165) Bio::TestBlastReportTabular: test_db: .: (0.000613) test_db_len: .: (0.000193) test_db_num: .: (0.000162) test_each_hit: .: (0.000174) test_each_iteration: .: (0.000161) test_eff_space: .: (0.000160) test_entrez_query: .: (0.000172) test_entropy: .: (0.000160) test_expect: .: (0.000159) test_filter: .: (0.000158) test_gap_extend: .: (0.000158) test_gap_open: .: (0.000174) test_hits: .: (0.000173) test_hsp_len: .: (0.000163) test_inclusion: .: (0.000396) test_iterations: .: (0.000213) test_kappa: .: (0.000159) test_lambda: .: (0.000170) test_matrix: .: (0.000169) test_message: .: (0.000175) test_parameters: .: (0.000173) test_pattern: .: (0.000170) test_program: .: (0.000157) test_query_def: .: (0.000170) test_query_id: .: (0.000173) test_query_len: .: (0.000156) test_reference: .: (0.000159) test_sc_match: .: (0.000230) test_sc_mismatch: .: (0.000516) test_statistics: .: (0.000290) test_version: .: (0.000265) Bio::TestChain: test_aaseq: .: (0.000505) test_addLigand: .: (0.000136) test_addResidue: .: (0.000129) test_atom_seq: .: (0.000144) test_comp: .: (0.000182) test_each: .: (0.000138) test_each_heterogen: .: (0.000138) test_each_residue: .: (0.000134) test_get_heterogen_by_id: .: (0.000130) test_get_residue_by_id: .: (0.000362) test_inspect: .: (0.000177) test_rehash: .: (0.000137) test_rehash_heterogens: .: (0.000117) test_rehash_residues: .: (0.000121) test_square_brace: .: (0.000129) test_to_s: .: (0.000154) Bio::TestChainFinder: test_chains: .: (0.000308) test_each_chain: .: (0.000147) test_find_chain: .: (0.000133) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.012611) test_header: .: (0.000787) test_match_line: .: (0.001028) test_sequence0: .: (0.000881) test_sequence1: .: (0.000746) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.012791) test_header: .: (0.001106) test_match_line: .: (0.001152) test_sequence0: .: (0.001000) test_sequence1: .: (0.001098) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.018488) test_header: .: (0.001070) test_match_line: .: (0.000810) test_sequence0: .: (0.001165) test_sequence1: .: (0.000786) Bio::TestCodonTable: test_Tables: .: (0.000337) test_accessor: .: (0.000166) test_definition: .: (0.000107) test_each: .: (0.000131) test_revtrans: .: (0.000233) test_self_accessor: .: (0.000350) test_self_copy: .: (0.000949) test_set_accessor: .: (0.188958) test_start: .: (0.000192) test_start_codon?: .: (0.000207) test_stop: .: (0.000155) test_stop_codon?: .: (0.000167) test_table: .: (0.000148) Bio::TestCodonTableConstants: test_Definitions: .: (0.000327) test_Starts: .: (0.000168) test_Tables: .: (0.000141) test_stops: .: (0.000159) Bio::TestColorScheme: test_buried: .: (0.001634) Bio::TestCommand: test_command_constants: .: (0.000302) test_escape_shell: .: (0.000250) test_escape_shell_unix: .: (0.000184) test_escape_shell_windows: .: (0.000193) test_make_cgi_params_by_array_of_array: .: (0.000448) test_make_cgi_params_by_array_of_hash: .: (0.000629) test_make_cgi_params_by_array_of_string: .: (0.000235) test_make_cgi_params_by_hash_in_string: .: (0.000605) test_make_cgi_params_by_hash_in_symbol: .: (0.000582) test_make_cgi_params_by_string: .: (0.000244) test_make_command_line: .: (0.000184) test_make_command_line_unix: .: (0.000174) test_make_command_line_windows: .: (0.000179) test_safe_command_line_array: .: (0.000352) test_safe_command_line_array_passthrough: .: (0.000191) Bio::TestContingencyTable: test_lite_example: .: (0.204119) Bio::TestDB: test_entry_id: .: (0.000847) test_exists: .: (0.000163) test_fetch: .: (0.000265) test_get: .: (0.000150) test_open: .: (0.000147) test_tags: .: (0.000159) Bio::TestDataType: test_const_like_method: .: (0.000834) test_pdb_achar: .: (0.000267) test_pdb_atom: .: (0.000223) test_pdb_character: .: (0.000221) test_pdb_date: .: (0.000303) test_pdb_idcode: .: (0.000243) test_pdb_integer: .: (0.000134) test_pdb_list: .: (0.000155) test_pdb_lstring: .: (0.000456) test_pdb_real: .: (0.000176) test_pdb_resudue_name: .: (0.000235) test_pdb_slist: .: (0.000126) test_pdb_string: .: (0.000233) test_pdb_stringrj: .: (0.000118) test_pdb_symop: .: (0.000219) test_specification_list: .: (0.000143) Bio::TestEMBL: test_ac: .: (0.000781) test_accession: .: (0.000698) test_cc: .: (0.000425) test_de: .: (0.000467) test_division: .: (0.000474) test_dr: .: (0.000421) test_dt: .: (0.000680) test_dt_created: .: (0.000419) test_dt_iterator: .: (0.000577) test_dt_updated: .: (0.000433) test_each_cds: .: (0.000939) test_each_gene: .: (0.000665) test_entry: .: (0.000494) test_fh: .: (0.000420) test_ft: .: (0.000929) test_ft_accessor: .: (0.000621) test_ft_iterator: .: (0.000673) test_id_line: .: (0.000910) test_id_line_data_class: .: (0.000772) test_id_line_division: .: (0.000948) test_id_line_entry_name: .: (0.000880) test_id_line_iterator: .: (0.001159) test_id_line_molecule_type: .: (0.000795) test_id_line_sequence_length: .: (0.000796) test_kw: .: (0.000791) test_molecule: .: (0.000854) test_oc: .: (0.001081) test_og: .: (0.000772) test_os: .: (0.000514) test_ref: .: (0.000581) test_references: .: (0.000930) test_seq: .: (0.001149) test_sequence_length: .: (0.000661) test_sq: .: (0.000797) test_sq_get: .: (0.000616) test_sv: .: (0.000452) test_version: .: (0.000440) Bio::TestEMBL89: test_ac: .: (0.000804) test_accession: .: (0.000602) test_cc: .: (0.000380) test_de: .: (0.000426) test_division: .: (0.000437) test_dr: .: (0.000392) test_dt: .: (0.000751) test_dt_created: .: (0.000624) test_dt_iterator: .: (0.000546) test_dt_updated: .: (0.000558) test_each_cds: .: (0.000987) test_each_gene: .: (0.000600) test_entry: .: (0.000495) test_fh: .: (0.000414) test_ft: .: (0.000732) test_ft_accessor: .: (0.000589) test_ft_iterator: .: (0.000615) test_id_line: .: (0.000438) test_id_line_data_class: .: (0.000552) test_id_line_division: .: (0.000515) test_id_line_entry_name: .: (0.000433) test_id_line_iterator: .: (0.000474) test_id_line_molecule_type: .: (0.000559) test_id_line_sequence_length: .: (0.000432) test_id_line_sequence_version: .: (0.000426) test_kw: .: (0.000428) test_molecule: .: (0.000445) test_oc: .: (0.000725) test_og: .: (0.000368) test_os: .: (0.000446) test_ref: .: (0.000544) test_references: .: (0.000936) test_seq: .: (0.000704) test_sequence_length: .: (0.000546) test_sq: .: (0.000621) test_sq_get: .: (0.000419) test_sv: .: (0.000458) test_version: .: (0.000566) Bio::TestEMBLAPI: test_ac: .: (0.000589) test_accessions: .: (0.000268) Bio::TestEMBLCommon: test_ac: .: (0.000465) test_accession: .: (0.000111) test_accessions: .: (0.000099) test_de: .: (0.000106) test_definition: .: (0.000152) test_description: .: (0.000163) test_dr: .: (0.000115) test_keywords: .: (0.000101) test_kw: .: (0.000109) test_oc: .: (0.000114) test_og: .: (0.000107) test_os: .: (0.000101) test_ref: .: (0.000101) test_references: .: (0.000101) Bio::TestEMBLDB: test_fetch: .: (0.000340) test_p_entry2hash: .: (0.000122) Bio::TestEMBLToBioSequence: test_classification: .: (0.004837) test_date_created: .: (0.000897) test_date_modified: .: (0.000553) test_definition: .: (0.000482) test_division: .: (0.000489) test_entry_id: .: (0.000661) test_entry_version: .: (0.000556) test_features: .: (0.000683) test_keywords: .: (0.000455) test_molecule_type: .: (0.000659) test_primary_accession: .: (0.000685) test_references: .: (0.001149) test_release_created: .: (0.000479) test_release_modified: .: (0.000615) test_secondary_accessions: .: (0.000509) test_sequence_version: .: (0.000697) test_species: .: (0.000687) test_topology: .: (0.000833) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.004004) test_date_created: .: (0.004931) test_date_modified: .: (0.004615) test_definition: .: (0.003756) test_division: .: (0.004406) test_entry_id: .: (0.010246) test_entry_version: .: (0.004679) test_features: .: (0.004806) test_keywords: .: (0.004900) test_molecule_type: .: (0.004816) test_primary_accession: .: (0.003861) test_references: .: (0.005875) test_release_created: .: (0.004986) test_release_modified: .: (0.004821) test_secondary_accessions: .: (0.003780) test_sequence_version: .: (0.003967) test_species: .: (0.003900) test_topology: .: (0.003741) Bio::TestFasta: test_db: .: (0.000296) test_format: .: (0.000103) test_format_arg_integer: .: (0.000141) test_format_arg_str: .: (0.000117) test_ktup: .: (0.000114) test_matrix: .: (0.000120) test_option: .: (0.000178) test_options: .: (0.000128) test_output: .: (0.000095) test_program: .: (0.000112) test_server: .: (0.000108) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000372) test_accession: .: (0.000150) test_accessions: .: (0.000171) test_description: .: (0.000144) test_descriptions: .: (0.000339) test_entry_id: .: (0.000132) test_get_all_by_type: .: (0.000132) test_gi: .: (0.000153) test_id_strings: .: (0.000234) test_list_ids: .: (0.000141) test_locus: .: (0.000140) test_words: .: (0.000176) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000548) test_accession: .: (0.000144) test_accessions: .: (0.000151) test_description: .: (0.000134) test_descriptions: .: (0.000144) test_emb: .: (0.000168) test_entry_id: .: (0.000168) test_get_all_by_type: .: (0.000188) test_get_emb: .: (0.000239) test_gi: .: (0.000149) test_id_strings: .: (0.000228) test_list_ids: .: (0.000179) test_locus: .: (0.000146) test_words: .: (0.000201) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000459) test_accession: .: (0.000138) test_accessions: .: (0.000132) test_description: .: (0.000124) test_descriptions: .: (0.000123) test_entry_id: .: (0.000121) test_get_all_by_type: .: (0.000126) test_gi: .: (0.000173) test_id_strings: .: (0.000181) test_list_ids: .: (0.000127) test_locus: .: (0.000127) test_sp: .: (0.000140) test_words: .: (0.000181) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000701) test_accession: .: (0.000281) test_accessions: .: (0.000240) test_description: .: (0.000174) test_descriptions: .: (0.000175) test_entry_id: .: (0.000172) test_get_all_by_type: .: (0.000179) test_gi: .: (0.000177) test_id_strings: .: (0.000340) test_list_ids: .: (0.000260) test_locus: .: (0.000415) test_words: .: (0.000773) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000379) test_accession: .: (0.000167) test_accessions: .: (0.000156) test_description: .: (0.000156) test_descriptions: .: (0.000152) test_entry_id: .: (0.000204) test_get_all_by_type: .: (0.000243) test_gi: .: (0.000200) test_id_strings: .: (0.000402) test_list_ids: .: (0.000515) test_locus: .: (0.000218) test_words: .: (0.000331) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000371) test_accession: .: (0.000127) test_accessions: .: (0.000132) test_description: .: (0.000129) test_descriptions: .: (0.000116) test_entry_id: .: (0.000109) test_get_all_by_type: .: (0.000113) test_gi: .: (0.000122) test_id_strings: .: (0.000159) test_list_ids: .: (0.000121) test_locus: .: (0.000122) test_words: .: (0.000372) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000317) test_accession: .: (0.000145) test_accessions: .: (0.000131) test_description: .: (0.000120) test_descriptions: .: (0.000156) test_entry_id: .: (0.000194) test_get: .: (0.000211) test_get_all_by_type: .: (0.000137) test_id_strings: .: (0.000224) test_list_ids: .: (0.000124) test_locus: .: (0.000120) test_sp: .: (0.000144) test_words: .: (0.000570) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000455) test_accession: .: (0.000199) test_accessions: .: (0.000182) test_description: .: (0.000169) test_descriptions: .: (0.000172) test_entry_id: .: (0.000187) test_get: .: (0.000194) test_get_all_by_type: .: (0.000132) test_id_strings: .: (0.000255) test_list_ids: .: (0.000128) test_locus: .: (0.000140) test_tr: .: (0.000152) test_words: .: (0.000573) Bio::TestFastaFirstName: test_first_name1: .: (0.000372) test_first_name_multi_identifier: .: (0.000135) test_first_name_single_worded_defintion: .: (0.000126) test_no_definition: .: (0.000131) test_space_before_first_name: .: (0.000126) test_tabbed_defintion: .: (0.000121) Bio::TestFastaFormat: test_aalen: .: (0.000325) test_aaseq: .: (0.000155) test_acc_version: .: (0.000202) test_accession: .: (0.000187) test_accessions: .: (0.000182) test_data: .: (0.000125) test_definition: .: (0.000127) test_entry: .: (0.000304) test_entry_id: .: (0.000192) test_entry_overrun: .: (0.000120) test_first_name: .: (0.000125) test_gi: .: (0.000164) test_identifiers: .: (0.000303) test_length: .: (0.000148) test_query: .: (0.000175) test_seq: .: (0.000134) Bio::TestFastaFormatConst: test_delimiter: .: (0.000274) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000462) test_data: .: (0.000208) test_definition: .: (0.000180) test_entry: .: (0.000253) test_entry_id: .: (0.000217) test_first_name: .: (0.000141) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000348) test_naseq: .: (0.000137) test_naseq_class: .: (0.000134) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000370) Bio::TestFastaInitialize: test_new_1: .: (0.000761) test_option: .: (0.000148) test_option_backward_compatibility: .: (0.000529) Bio::TestFastaNumericFormat: test_arg: .: (0.000454) test_data: .: (0.000220) test_definition: .: (0.000231) test_each: .: (0.000242) test_entry: .: (0.000175) test_entry_id: .: (0.000200) test_length: .: (0.000207) test_to_biosequence: .: (0.001402) Bio::TestFastaQuery: test_query: .: (0.000308) test_self_local: .: (0.000120) test_self_parser: .: (0.000330) test_self_remote: .: (0.000199) Bio::TestFastacmd: test_database: .: (0.000237) test_fastacmd: .: (0.000098) test_methods: .: (0.000152) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000949) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000618) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000957) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000844) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000868) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.001063) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000836) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000594) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000547) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000875) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000613) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000635) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000788) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.001782) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.001930) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.001024) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000569) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000519) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.008682) test_error_probabilities_as_sanger: .: (0.009627) test_error_probabilities_as_solexa: .: (0.150299) test_quality_scores_as_illumina: .: (0.001047) test_quality_scores_as_sanger: .: (0.000546) test_quality_scores_as_solexa: .: (0.000657) test_validate_format: .: (0.001096) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.017429) test_entry_id: .: (0.002504) test_error_probabilities: .: (0.280697) test_nalen: .: (0.001635) test_naseq: .: (0.001652) test_quality_scores: .: (0.002858) test_quality_string: .: (0.001463) test_roundtrip: .: (0.256146) test_seq: .: (0.001780) test_sequence_string: .: (0.001211) test_to_biosequence: .: (0.202451) test_to_biosequence_and_output: .: (0.006985) test_to_s: .: (0.001507) test_validate_format: .: (0.001351) test_validate_format_with_array: .: (0.001482) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000784) test_mask_20_with_empty_string: .: (0.000573) test_mask_20_with_longer_string: .: (0.000791) test_mask_20_with_x: .: (0.000587) test_mask_60: .: (0.000656) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.010486) test_error_probabilities_as_sanger: .: (0.010276) test_error_probabilities_as_solexa: .: (0.010660) test_quality_scores_as_illumina: .: (0.000645) test_quality_scores_as_sanger: .: (0.000519) test_quality_scores_as_solexa: .: (0.000633) test_validate_format: .: (0.001341) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.010915) test_error_probabilities_as_sanger: .: (0.008191) test_error_probabilities_as_solexa: .: (0.007955) test_quality_scores_as_illumina: .: (0.000657) test_quality_scores_as_sanger: .: (0.000561) test_quality_scores_as_solexa: .: (0.000449) test_validate_format: .: (0.001033) Bio::TestFeature: test_append: .: (0.000405) test_append_nil: .: (0.000227) test_assoc: .: (0.000231) test_each: .: (0.000210) test_feature: .: (0.000199) test_locations: .: (0.000302) test_new: .: (0.000200) test_position: .: (0.000206) test_qualifiers: .: (0.000248) Bio::TestFeatures: test_append: .: (0.000453) test_arg: .: (0.000224) test_each: .: (0.000227) test_features: .: (0.000232) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.001750) test_aaindex2: .: (0.000374) test_blast: .: (0.000336) test_blastxml: .: (0.000791) test_embl: .: (0.000407) test_embl_oldrelease: .: (0.000381) test_fastaformat: .: (0.000651) test_fastanumericformat: .: (0.000282) test_fastq: .: (0.000341) test_genbank: .: (0.000587) test_genpept: .: (0.000376) test_hmmer: .: (0.000416) test_maxml_cluster: .: (0.004470) test_maxml_sequence: .: (0.000258) test_medline: .: (0.000300) test_prosite: .: (0.003846) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003417) test_transfac: .: (0.002127) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000515) test_auto_1arg_filename: .: (0.001235) test_auto_1arg_io: .: (0.000498) test_auto_1arg_io_with_block: .: (0.000941) test_auto_1arg_with_block: .: (0.000859) test_auto_2arg_filename_mode: .: (0.000503) test_auto_2arg_filename_mode_with_block: .: (0.001194) test_auto_3arg: .: (0.000494) test_auto_3arg_with_block: .: (0.000855) test_foreach: .: (0.000719) test_new_2arg_class: .: (0.000306) test_new_2arg_nil: .: (0.000554) test_open_0arg: .: (0.000264) test_open_1arg_class: .: (0.000242) test_open_1arg_filename: .: (0.000503) test_open_1arg_io: .: (0.000482) test_open_1arg_io_with_block: .: (0.000890) test_open_1arg_nil: .: (0.000251) test_open_1arg_with_block: .: (0.001172) test_open_2arg_autodetect: .: (0.000469) test_open_2arg_autodetect_io: .: (0.000473) test_open_2arg_autodetect_io_with_block: .: (0.000850) test_open_2arg_autodetect_with_block: .: (0.001066) test_open_2arg_class: .: (0.000344) test_open_2arg_class_io: .: (0.000315) test_open_2arg_class_io_with_block: .: (0.000706) test_open_2arg_class_with_block: .: (0.000684) test_open_2arg_filename_mode: .: (0.000541) test_open_2arg_filename_mode_with_block: .: (0.001068) test_open_3arg: .: (0.000907) test_open_3arg_with_block: .: (0.003244) test_open_4arg: .: (0.002115) test_to_a: .: (0.001029) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000715) test_close: .: (0.000272) test_dbclass: .: (0.000331) test_dbclass_eq: .: (0.000331) test_dbclass_nil: .: (0.000390) test_each: .: (0.000450) test_each_entry: .: (0.000590) test_ended_pos: .: (0.000407) test_entry_pos_flag: .: (0.000582) test_entry_raw: .: (0.000501) test_eof?: .: (0.000443) test_next_entry: .: (0.000551) test_path: .: (0.000278) test_pos: .: (0.000363) test_raw: .: (0.000569) test_rewind: .: (0.000380) test_start_pos: .: (0.000390) test_start_pos_ended_pos_not_recorded: .: (0.000458) test_to_io: .: (0.000282) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000568) test_simpleformat2: .: (0.000348) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000351) test_eof_false_after_prefetch: .: (0.000353) test_eof_false_first: .: (0.000222) test_eof_true: .: (0.000366) test_getc: .: (0.000242) test_getc_after_prefetch: .: (0.000249) test_gets: .: (0.000277) test_gets_equal_prefetch_gets: .: (0.000252) test_gets_paragraph_mode: .: (0.000291) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000426) test_gets_paragraph_mode_within_buffer: .: (0.000496) test_gets_rs: .: (0.000272) test_gets_rs_equal_prefetch_gets: .: (0.000294) test_gets_rs_within_buffer: .: (0.000456) test_pos: .: (0.000233) test_pos=: .: (0.000254) test_prefetch_buffer: .: (0.000236) test_prefetch_gets: .: (0.000260) test_prefetch_gets_with_arg: .: (0.000268) test_rewind: .: (0.000436) test_skip_spaces: .: (0.000291) test_to_io: .: (0.000247) test_ungetc: .: (0.000246) test_ungetc_after_prefetch: .: (0.000253) test_ungets: .: (0.000281) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000528) test_self_open_file: .: (0.000375) test_self_open_file_with_block: .: (0.000437) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000465) test_parse_file_open_arg_int_perm: .: (0.000212) test_parse_file_open_arg_int_perm_opt: .: (0.000216) test_parse_file_open_arg_integer: .: (0.000207) test_parse_file_open_arg_nil: .: (0.000292) test_parse_file_open_arg_opt: .: (0.000309) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000283) test_parse_file_open_arg_str: .: (0.000229) test_parse_file_open_arg_str_opt: .: (0.000235) test_parse_file_open_arg_str_perm: .: (0.000255) test_parse_file_open_arg_str_perm_opt: .: (0.000233) test_parse_file_open_arg_str_with_enc: .: (0.000310) test_parse_file_open_arg_str_with_ext_enc: .: (0.000233) test_parse_file_open_mode_integer: .: (0.000207) test_parse_file_open_mode_nil: .: (0.000227) test_parse_file_open_mode_str: .: (0.000219) test_parse_file_open_mode_str_with_enc: .: (0.000230) test_parse_file_open_mode_str_with_ext_enc: .: (0.000221) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000375) test_entry: .: (0.000238) test_entry_ended_pos: .: (0.000227) test_entry_pos_flag: .: (0.000411) test_entry_start_pos: .: (0.000226) test_get_entry: .: (0.000310) test_rewind: .: (0.000240) test_skip_leader: .: (0.000241) test_stream: .: (0.000208) test_stream_pos: .: (0.000306) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000395) test_delimiter_overrun: .: (0.000209) test_entry: .: (0.000257) test_entry_ended_pos: .: (0.000250) test_entry_ended_pos_default_nil: .: (0.000242) test_entry_start_pos: .: (0.000237) test_entry_start_pos_default_nil: .: (0.000272) test_get_entry: .: (0.000540) test_get_parsed_entry: .: (0.000382) test_header: .: (0.000211) test_skip_leader: .: (0.000265) test_skip_leader_without_header: .: (0.000273) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000469) test_entry_ended_pos: .: (0.000378) test_entry_start_pos: .: (0.000359) test_flag_to_fetch_header: .: (0.000336) test_get_entry: .: (0.000666) test_get_parsed_entry: .: (0.000495) test_rewind: .: (0.000367) test_skip_leader: .: (0.000264) Bio::TestGCGMsf: test_alignment: .: (0.001565) test_checksum: .: (0.000370) test_compcheck: .: (0.000369) test_date: .: (0.000425) test_description: .: (0.000370) test_entry_id: .: (0.000371) test_gap_length_weight: .: (0.000540) test_gap_weight: .: (0.000373) test_heading: .: (0.000362) test_length: .: (0.000415) test_seq_type: .: (0.000374) test_symbol_comparison_table: .: (0.000398) test_validate_checksum: .: (0.002337) Bio::TestGFF: test_record_class: .: (0.000753) test_records: .: (0.000502) Bio::TestGFF2: test_const_version: .: (0.000982) test_gff_version: .: (0.000600) test_metadata: .: (0.000607) test_metadata_size: .: (0.000770) test_records_size: .: (0.000650) test_to_s: .: (0.001066) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000411) test_attributes_case2: .: (0.000531) test_attributes_incompatible_backslash_semicolon: .: (0.000350) Bio::TestGFF2MetaData: test_data: .: (0.000318) test_directive: .: (0.000201) test_parse: .: (0.000222) Bio::TestGFF2Record: test_attribute: .: (0.000656) test_attribute_nonexistent: .: (0.000382) test_attributes: .: (0.000413) test_attributes_to_hash: .: (0.000807) test_comment_only?: .: (0.000546) test_delete_attribute: .: (0.000687) test_delete_attribute_multiple: .: (0.000654) test_delete_attribute_multiple2: .: (0.000784) test_delete_attribute_multiple_nil: .: (0.000964) test_delete_attribute_nil: .: (0.000463) test_delete_attribute_nonexistent: .: (0.000439) test_delete_attributes: .: (0.000463) test_delete_attributes_multiple: .: (0.000443) test_delete_attributes_nonexistent: .: (0.000440) test_end: .: (0.000709) test_eqeq: .: (0.000987) test_eqeq_false: .: (0.000878) test_feature: .: (0.000546) test_frame: .: (0.000383) test_get_attribute: .: (0.000519) test_get_attribute_nonexistent: .: (0.011577) test_get_attributes: .: (0.001041) test_get_attributes_nonexistent: .: (0.000497) test_replace_attributes: .: (0.000530) test_replace_attributes_multiple_multiple_over: .: (0.000597) test_replace_attributes_multiple_multiple_same: .: (0.000579) test_replace_attributes_multiple_multiple_two: .: (0.001001) test_replace_attributes_multiple_single: .: (0.000431) test_replace_attributes_nonexistent: .: (0.000458) test_replace_attributes_nonexistent_multiple: .: (0.000525) test_replace_attributes_single_multiple: .: (0.000532) test_score: .: (0.000906) test_self_parse: .: (0.000882) test_seqname: .: (0.000386) test_set_attribute: .: (0.000580) test_set_attribute_multiple: .: (0.000459) test_set_attribute_nonexistent: .: (0.000450) test_sort_attributes_by_tag!: .: (0.000592) test_sort_attributes_by_tag_bang_test2: .: (0.000551) test_sort_attributes_by_tag_bang_with_block: .: (0.000547) test_source: .: (0.000394) test_start: .: (0.000755) test_strand: .: (0.000379) test_to_s: .: (0.000674) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000597) test_comment_eq: .: (0.000212) test_comment_only?: .: (0.000226) test_comment_only_false: .: (0.000225) test_to_s: .: (0.000232) test_to_s_not_empty: .: (0.000731) Bio::TestGFF3: test_const_version: .: (0.001339) test_gff_version: .: (0.001145) test_records: .: (0.001107) test_sequence_regions: .: (0.001015) test_sequences: .: (0.000863) test_to_s: .: (0.001752) Bio::TestGFF3MetaData: test_data: .: (0.000375) test_directive: .: (0.000185) test_parse: .: (0.000208) Bio::TestGFF3Record: test_attributes: .: (0.000540) test_end: .: (0.000615) test_feature: .: (0.000359) test_frame: .: (0.000429) test_id: .: (0.000374) test_score: .: (0.000386) test_seqname: .: (0.000356) test_source: .: (0.000363) test_start: .: (0.000358) test_strand: .: (0.000366) test_to_s: .: (0.000617) test_to_s_attr_order_changed: .: (0.001131) Bio::TestGFF3RecordEscape: test_escape: .: (0.000417) test_escape_attribute: .: (0.000260) test_escape_seqid: .: (0.000271) test_unescape: .: (0.000261) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000536) test_eqeq: .: (0.000353) test_new_from_sequences_na: .: (0.000909) test_new_from_sequences_na_aa: .: (0.000488) test_new_from_sequences_na_aa_boundary_gap: .: (0.000637) test_new_from_sequences_na_aa_example: .: (0.000570) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000453) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000413) test_process_sequences_na: .: (0.000446) test_process_sequences_na_aa: .: (0.000684) test_process_sequences_na_aa_reverse_frameshift: .: (0.000325) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000376) test_process_sequences_na_aa_tooshort: .: (0.000518) test_process_sequences_na_tooshort: .: (0.000417) test_to_s: .: (0.000337) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000778) test_attributes_one: .: (0.000232) test_attributes_with_escaping: .: (0.000310) test_id_multiple: .: (0.000401) test_id_multiple2: .: (0.000392) test_id_replace: .: (0.000266) test_id_set: .: (0.000306) test_initialize_9: .: (0.000190) test_phase: .: (0.000277) test_score: .: (0.000518) test_to_s_void: .: (0.000216) Bio::TestGFF3RecordTarget: test_end: .: (0.000379) test_parse: .: (0.000306) test_start: .: (0.000214) test_strand: .: (0.000201) test_target_id: .: (0.000207) test_to_s: .: (0.000313) Bio::TestGFF3SequenceRegion: test_end: .: (0.000347) test_parse: .: (0.000353) test_seqid: .: (0.000476) test_start: .: (0.000206) test_to_s: .: (0.000299) Bio::TestGFFRecord: test_attributes: .: (0.000393) test_comment: .: (0.000231) test_end: .: (0.000212) test_feature: .: (0.000229) test_frame: .: (0.000226) test_score: .: (0.000234) test_seqname: .: (0.000231) test_source: .: (0.000237) test_start: .: (0.000235) test_strand: .: (0.000550) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000334) Bio::TestGeneAssociation: test_aspect: .: (0.000358) test_assigned_by: .: (0.000255) test_date: .: (0.000217) test_db: .: (0.000216) test_db_object_id: .: (0.000222) test_db_object_name: .: (0.000225) test_db_object_symbol: .: (0.000227) test_db_object_synonym: .: (0.000232) test_db_object_type: .: (0.000225) test_db_reference: .: (0.000228) test_evidence: .: (0.000229) test_goid: .: (0.000589) test_parser: .: (0.000840) test_qualifier: .: (0.000216) test_taxon: .: (0.000215) test_to_str: .: (0.000232) test_with: .: (0.000215) Bio::TestGenscanReport: test_date_run: .: (0.001679) test_gccontent: .: (0.000935) test_genscan_version: .: (0.000911) test_isochore: .: (0.001304) test_length: .: (0.000892) test_matrix: .: (0.001176) test_predictions_size: .: (0.000945) test_query_name: .: (0.000900) test_time: .: (0.001253) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.001059) test_donor_score: .: (0.001159) test_exon_type: .: (0.000904) test_exon_type_long: .: (0.000894) test_first: .: (0.001196) test_initiation_score: .: (0.000918) test_last: .: (0.001210) test_number: .: (0.000920) test_p_value: .: (0.000877) test_phase: .: (0.001237) test_range: .: (0.000903) test_score: .: (0.001186) test_strand: .: (0.000955) test_t_score: .: (0.000872) test_termination_score: .: (0.001271) Bio::TestGenscanReportGene: test_aaseq: .: (0.001115) test_naseq: .: (0.001209) test_number: .: (0.000937) test_polyA: .: (0.000912) test_promoter: .: (0.001107) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.001190) test_reports_ary_contents: .: (0.000910) Bio::TestHMMERReportConstants: test_rs: .: (0.000350) Bio::TestHMMERReportHit: test_accession: .: (0.001048) test_append_hsp: .: (0.000852) test_bit_score: .: (0.000845) test_definition: .: (0.001069) test_description: .: (0.000898) test_each: .: (0.000908) test_each_hsp: .: (0.000881) test_entry_id: .: (0.000880) test_evalue: .: (0.003971) test_hit: .: (0.005108) test_hit_id: .: (0.005467) test_hsps: .: (0.004798) test_num: .: (0.004662) test_score: .: (0.004286) test_target_def: .: (0.003338) test_target_id: .: (0.004670) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.005177) test_each: .: (0.000940) test_each_hit: .: (0.003068) test_histogram: .: (0.005067) test_hits: .: (0.004842) test_hsps: .: (0.008654) test_parameter: .: (0.022525) test_program: .: (0.001348) test_query_info: .: (0.000978) test_statistical_detail: .: (0.001035) test_total_seq_searched: .: (0.001232) test_whole_seq_top_hits: .: (0.000904) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.001634) test_histogram: .: (0.001403) test_statistical_detail: .: (0.001253) test_total_seq_searched: .: (0.001229) test_whole_seq_top_hit: .: (0.001498) Bio::TestHMMERReportHsp: test_accession: .: (0.001143) test_bit_score: .: (0.001100) test_csline: .: (0.001308) test_domain: .: (0.000958) test_evalue: .: (0.001062) test_flatseq: .: (0.001003) test_hmm_f: .: (0.001207) test_hmm_t: .: (0.000932) test_hmmseq: .: (0.000986) test_hsp: .: (0.000918) test_midline: .: (0.001161) test_query_frame: .: (0.000943) test_query_from: .: (0.001006) test_query_seq: .: (0.001159) test_query_to: .: (0.000933) test_rfline: .: (0.001187) test_score: .: (0.001004) test_seq_f: .: (0.001306) test_seq_ft: .: (0.001103) test_seq_t: .: (0.001036) test_set_alignment: .: (0.000955) test_targat_to: .: (0.001363) test_target_frame: .: (0.001015) test_target_from: .: (0.000983) test_target_seq: .: (0.000970) Bio::TestHetatmFinder: test_each_hetatm: .: (0.001183) test_find_hetatm: .: (0.000406) test_hetatms: .: (0.000515) Bio::TestHeterogen: test_addAtom: .: (0.000563) test_each: .: (0.000656) test_each_hetatm: .: (0.000328) test_get_residue_id_from_atom: .: (0.000305) test_het_atom: .: (0.000268) test_iCode: .: (0.000273) test_inspect: .: (0.000349) test_resSeq: .: (0.000275) test_sort: .: (0.000335) test_square_bracket: .: (0.000760) test_to_s: .: (0.000582) test_update_resudue_id: .: (0.000287) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000437) test_find_heterogen: .: (0.000224) test_heterogens: .: (0.000242) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000447) test_match_description: .: (0.000261) test_match_evalue: .: (0.000729) test_match_ipr_description: .: (0.000268) test_match_ipr_id: .: (0.000257) test_match_match_end: .: (0.000258) test_match_match_start: .: (0.000252) test_match_method: .: (0.000257) test_matches_size: .: (0.000251) test_query_id: .: (0.000254) test_query_length: .: (0.000257) Bio::TestIprscanRawReport: test_entry_id: .: (0.004283) test_match_accession: .: (0.003336) test_match_crc64: .: (0.003843) test_match_date: .: (0.004802) test_match_description: .: (0.003812) test_match_evalue: .: (0.003653) test_match_go_terms: .: (0.003516) test_match_ipr_description: .: (0.003953) test_match_ipr_id: .: (0.003704) test_match_match_end: .: (0.003677) test_match_match_start: .: (0.008477) test_match_method: .: (0.004276) test_match_query_id: .: (0.003658) test_match_query_length: .: (0.003980) test_match_status: .: (0.003629) test_obj: .: (0.003823) test_query_id: .: (0.003439) test_query_length: .: (0.003115) test_self_reports_in_raw: .: (0.007380) Bio::TestIprscanReport: test_output_raw: .: (0.001267) test_to_raw: .: (0.000805) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.001177) test_match_accession: .: (0.000813) test_match_date: .: (0.000748) test_match_description: .: (0.000755) test_match_evalue: .: (0.000942) test_match_go_terms: .: (0.000844) test_match_ipr_description: .: (0.000748) test_match_ipr_id: .: (0.000741) test_match_match_end: .: (0.000951) test_match_match_start: .: (0.000733) test_match_method: .: (0.000743) test_match_status: .: (0.000727) test_matches_size: .: (0.000988) test_query_id: .: (0.000756) test_query_length: .: (0.000785) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.001388) test_to_hash_match?: .: (0.001100) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.002322) Bio::TestKeggCompound: test_comment: .: (0.000751) test_dblinks_as_hash: .: (0.000626) test_dblinks_as_strings: .: (0.000456) test_entry_id: .: (0.000429) test_enzymes: .: (0.000913) test_formula: .: (0.000505) test_kcf: .: (0.000394) test_mass: .: (0.000514) test_name: .: (0.000514) test_names: .: (0.000516) test_pathways_as_hash: .: (0.000907) test_pathways_as_strings: .: (0.000754) test_reactions: .: (0.001048) test_remark: .: (0.000439) test_rpairs: .: (0.000420) Bio::TestKeggEnzyme: test_all_reac: .: (0.001060) test_classes: .: (0.001140) test_cofactors: .: (0.000780) test_comment: .: (0.000808) test_dblinks_as_hash: .: (0.000844) test_dblinks_as_strings: .: (0.000790) test_diseases: .: (0.000688) test_entry: .: (0.000828) test_entry_id: .: (0.000948) test_genes: .: (0.027864) test_genes_as_hash: .: (0.023173) test_genes_as_strings: .: (0.007525) test_inhibitors: .: (0.001248) test_iubmb_reactions: .: (0.000989) test_kegg_reactions: .: (0.000978) test_motifs: .: (0.000926) test_name: .: (0.001092) test_names: .: (0.001543) test_obsolete?: .: (0.001132) test_orthologs_as_hash: .: (0.001029) test_orthologs_as_strings: .: (0.000894) test_pathways_as_hash: .: (0.001072) test_pathways_as_strings: .: (0.000997) test_products: .: (0.001571) test_reaction: .: (0.000935) test_structures: .: (0.001288) test_substrates: .: (0.000896) test_sysname: .: (0.000893) Bio::TestKeggGenesDblinks: test_data: .: (0.000503) test_dblinks_0: .: (0.000783) test_dblinks_1: .: (0.000230) test_dblinks_2: .: (0.000223) Bio::TestKeggGenesStructure: test_data: .: (0.000403) test_ids: .: (0.000294) test_ids_in_array: .: (0.000252) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.015429) test_graphics__size: .: (0.018805) test_id: .: (0.014947) test_link: .: (0.014012) test_name: .: (0.013818) test_reaction: .: (0.015689) test_type: .: (0.013280) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.015228) test_graphics__size: .: (0.013775) test_id: .: (0.013505) test_link: .: (0.013199) test_name: .: (0.013249) test_reaction: .: (0.012897) test_type: .: (0.014493) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.014081) test_category: .: (0.013296) test_entry_id: .: (0.013334) test_fgcolor=: .: (0.012127) test_height=: .: (0.011448) test_label=: .: (0.014000) test_shape=: .: (0.014337) test_width=: .: (0.014120) test_x=: .: (0.013428) test_y=: .: (0.013553) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.013803) test_graphics__size: .: (0.013248) test_id: .: (0.015253) test_link: .: (0.013166) test_name: .: (0.013122) test_reaction: .: (0.013338) test_type: .: (0.012795) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000454) test_graphics=: .: (0.000209) test_id=: .: (0.000230) test_link=: .: (0.000213) test_name=: .: (0.000528) test_reaction=: .: (0.000208) test_type=: .: (0.000207) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000446) test_category=: .: (0.000263) test_entry_id=: .: (0.000318) test_fgcolor=: .: (0.000255) test_height=: .: (0.000245) test_label=: .: (0.000272) test_pathway=: .: (0.000221) test_shape=: .: (0.000498) test_width=: .: (0.000247) test_x=: .: (0.000246) test_y=: .: (0.000242) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.015377) test_coords: .: (0.014975) test_fgcolor: .: (0.013511) test_height: .: (0.013539) test_name: .: (0.014055) test_type: .: (0.013211) test_width: .: (0.014710) test_x: .: (0.013855) test_y: .: (0.013282) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.012946) test_coords: .: (0.013356) test_fgcolor: .: (0.012790) test_height: .: (0.015005) test_name: .: (0.014744) test_type: .: (0.013950) test_width: .: (0.013156) test_x: .: (0.013698) test_y: .: (0.013286) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000422) test_coords=: .: (0.000216) test_fgcolor=: .: (0.000216) test_height=: .: (0.000211) test_name=: .: (0.000212) test_type=: .: (0.000209) test_width=: .: (0.000250) test_x=: .: (0.000205) test_y=: .: (0.000555) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.015250) test_entries__size: .: (0.013276) test_image: .: (0.013230) test_link: .: (0.013244) test_name: .: (0.012939) test_number: .: (0.012774) test_org: .: (0.015112) test_reactions=: .: (0.013396) test_reactions__size: .: (0.011136) test_relations=: .: (0.011733) test_relations__size: .: (0.012395) test_title: .: (0.011089) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.025860) test_name: .: (0.026763) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000395) test_initialize_0: .: (0.000135) test_initialize_1: .: (0.000150) test_initialize_2: .: (0.000145) test_name=: .: (0.000190) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.013657) test_name: .: (0.015630) test_products: .: (0.015440) test_substrates: .: (0.013291) test_type: .: (0.013062) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000649) test_name=: .: (0.000192) test_products=: .: (0.000188) test_substraces=: .: (0.000188) test_type=: .: (0.000191) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000366) test_entry_id=: .: (0.000225) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.013381) test_entry2: .: (0.012864) test_name: .: (0.012854) test_type: .: (0.015053) test_value: .: (0.013303) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000317) test_node1=: .: (0.000555) test_node2=: .: (0.000256) test_rel=: .: (0.000235) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000382) test_entry2=: .: (0.000215) test_name=: .: (0.000199) test_type=: .: (0.000186) test_value=: .: (0.000186) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.027088) test_name: .: (0.024800) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000337) test_initialize_0: .: (0.000115) test_initialize_1: .: (0.000116) test_initialize_2: .: (0.000148) test_name=: .: (0.000172) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000292) test_initialize_0: .: (0.000395) test_initialize_1: .: (0.000117) test_initialize_2: .: (0.000117) test_name=: .: (0.000161) Bio::TestKeggModule: test_compounds: .: (0.000559) test_compounds_as_hash: .: (0.000335) test_compounds_as_strings: .: (0.000290) test_definition: .: (0.000284) test_entry_id: .: (0.000242) test_keggclass: .: (0.000639) test_name: .: (0.000284) test_new: .: (0.000243) test_orthologs: .: (0.000348) test_orthologs_as_array: .: (0.000373) test_orthologs_as_hash: .: (0.000342) test_orthologs_as_strings: .: (0.000323) test_pathways: .: (0.000239) test_pathways_as_hash: .: (0.000591) test_pathways_as_strings: .: (0.000215) test_reactions: .: (0.000377) test_reactions_as_hash: .: (0.000462) test_reactions_as_strings: .: (0.000285) Bio::TestKeggOrthology: test_dblinks: .: (0.000696) test_dblinks_as_hash: .: (0.000500) test_dblinks_as_strings: .: (0.000756) test_definition: .: (0.000478) test_entry_id: .: (0.000471) test_genes_as_hash: .: (0.015798) test_genes_as_strings: .: (0.005225) test_keggclass: .: (0.000634) test_keggclasses: .: (0.000616) test_modules: .: (0.000724) test_modules_as_hash: .: (0.000473) test_modules_as_strings: .: (0.000436) test_name: .: (0.000489) test_names: .: (0.000459) test_pathways_as_strings: .: (0.000468) test_pathways_in_keggclass: .: (0.000612) test_references: .: (0.000808) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000463) test_compounds_as_strings: .: (0.000244) test_dblinks_as_hash: .: (0.000240) test_dblinks_as_strings: .: (0.000240) test_description: .: (0.000260) test_diseases_as_hash: .: (0.000241) test_diseases_as_strings: .: (0.000236) test_entry_id: .: (0.000262) test_enzymes_as_strings: .: (0.000409) test_genes_as_hash: .: (0.000268) test_genes_as_strings: .: (0.000234) test_keggclass: .: (0.000286) test_ko_pathway: .: (0.000250) test_modules_as_hash: .: (0.000334) test_modules_as_strings: .: (0.000262) test_name: .: (0.000261) test_organism: .: (0.000255) test_orthologs_as_hash: .: (0.000236) test_orthologs_as_strings: .: (0.000270) test_pathways_as_hash: .: (0.000258) test_pathways_as_strings: .: (0.000240) test_reactions_as_hash: .: (0.000238) test_reactions_as_strings: .: (0.000235) test_references: .: (0.000268) test_rel_pathways_as_hash: .: (0.000300) test_rel_pathways_as_strings: .: (0.000256) Bio::TestKeggReaction: test_definition: .: (0.000732) test_entry_id: .: (0.000281) test_enzymes: .: (0.000276) test_equation: .: (0.000279) test_name: .: (0.000285) test_orthologs_as_hash: .: (0.000322) test_orthologs_as_strings: .: (0.000274) test_pathways_as_hash: .: (0.000316) test_pathways_as_strings: .: (0.000427) test_rpairs_as_hash: .: (0.000343) test_rpairs_as_strings: .: (0.000266) test_rpairs_as_tokens: .: (0.000309) Bio::TestLasergene: test_methods: .: (0.012350) Bio::TestLocations: test_complement: .: (0.000371) test_hat: .: (0.000183) test_normal: .: (0.000172) test_replace_single_base: .: (0.000186) test_should_not_modify_argument: .: (0.000145) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.005473) test_locations_to_s: .: (0.002531) Bio::TestMEDLINE: test_authors: .: (0.000915) test_authors_with_last_name_all_caps: .: (0.000136) test_authors_with_suffix: .: (0.000140) Bio::TestMEDLINE_20146148: test_ab: .: (0.001071) test_ad: .: (0.000537) test_au: .: (0.000473) test_authors: .: (0.000477) test_doi: .: (0.000773) test_dp: .: (0.000505) test_ip: .: (0.000441) test_mh: .: (0.000470) test_pages: .: (0.000455) test_pg: .: (0.000525) test_pii: .: (0.000442) test_pmid: .: (0.000434) test_pt: .: (0.000442) test_reference: .: (0.001041) test_self_new: .: (0.000496) test_so: .: (0.000437) test_ta: .: (0.000696) test_ti: .: (0.000507) test_ui: .: (0.000434) test_vi: .: (0.000434) test_year: .: (0.000435) Bio::TestMapSimple: test_attributes: .: (0.000496) Bio::TestMapping: test_add_mapping_as_map: .: (0.000422) test_add_mapping_as_marker: .: (0.000201) test_contains_marker?: .: (0.000162) test_mapped_to?: .: (0.000151) test_mapping_location_comparison: .: (0.000390) test_mappings_as_map_each: .: (0.000150) test_mappings_as_marker_each: .: (0.000200) test_mappings_on: .: (0.000678) test_multiple_mappings_between_same_marker_and_map: .: (0.000405) test_positions_on: .: (0.000231) test_raise_error_kind_of: .: (0.000544) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000399) test_check_options_with_invalid_opts: .: (0.000235) test_check_options_with_valid_opts: .: (0.000207) test_command_to_be_run: .: (0.000257) test_config_defaults: .: (0.000592) test_minimal_config: .: (0.000198) test_more_config: .: (0.000212) test_run: .: (0.000126) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000499) test_report_has_motifs: .: (0.000282) Bio::TestModel: test_addChain: .: (0.000305) test_comp: .: (0.000156) test_each: .: (0.000149) test_each_chain: .: (0.000138) test_inspect: .: (0.000539) test_rehash: .: (0.000120) test_square_brace: .: (0.000158) test_to_s: .: (0.000131) Bio::TestModelFinder: test_find_model: .: (0.000282) Bio::TestMotif: test_creation_and_attributes: .: (0.000299) test_length: .: (0.000112) Bio::TestMyGraph: test_cliquishness: .: (0.000636) Bio::TestNA: test_accessor: .: (0.000259) test_na: .: (0.000425) test_name: .: (0.000112) test_names: .: (0.000113) test_to_re: .: (0.000270) test_weight: .: (0.000134) test_weight_rna: .: (0.000124) Bio::TestNAConstants: test_NAMES: .: (0.000216) test_NAMES_1_to_name: .: (0.000105) test_WEIGHT: .: (0.000120) Bio::TestNATranslate: test_translate: .: (0.000412) test_translate_1: .: (0.000179) test_translate_2: .: (0.000133) test_translate_3: .: (0.000129) test_translate_4: .: (0.000190) test_translate_5: .: (0.000480) test_translate_6: .: (0.000132) Bio::TestNCBIDB: test_fetch: .: (0.000284) test_p_entry2hash: .: (0.000099) test_p_subtag2array: .: (0.000096) test_p_toptag2array: .: (0.000094) Bio::TestNewick: test_reparse: .: (0.001610) test_reparse_before_lazy_parsing: .: (0.000856) test_string_tree: .: (0.001112) Bio::TestNewick2: test_string_tree: .: (0.000840) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000263) test_parse_newick_leaf: .: (0.000235) test_parse_newick_tokenize: .: (0.000747) Bio::TestNexus: test_nexus: .: (0.085557) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000407) test_uncapitalized_letter_Q32725_9POAL: .: (0.000200) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000307) test_load_parameters: .: (0.000187) test_parameters: .: (0.000147) test_set_default_parameters: .: (0.000209) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.003332) test_expected_parameters_set_in_control_file: .: (0.001715) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000332) test_new_with_parameters: .: (0.000193) test_new_with_two_argument: .: (0.000185) test_new_without_argument: .: (0.000170) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.002211) test_rates_hundred_and_fiftieth_position: .: (0.001929) test_rates_last_position: .: (0.001997) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.009934) test_tree: .: (0.009736) test_tree_length: .: (0.009512) test_tree_log_likelihood: .: (0.009576) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000656) test_parameters_should_be_loaded_from_control: .: (0.000365) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001796) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000694) test_dN_dS: .: (0.000234) test_kappa: .: (0.000225) test_lnL: .: (0.000224) test_m3_classes: .: (0.000334) test_m3_lnL: .: (0.000234) test_m3_to_s: .: (0.000254) test_m3_tree: .: (0.000724) test_omega: .: (0.000226) test_to_s: .: (0.000215) test_tree: .: (0.000647) test_tree_length: .: (0.000220) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000892) test_p: .: (0.000472) test_position: .: (0.000465) test_probability: .: (0.000460) test_w: .: (0.000934) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000683) test_graph_omega: .: (0.000981) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000365) test_footer: .: (0.000216) test_header: .: (0.000216) test_initialize: .: (0.000240) test_models: .: (0.000251) test_nb_sites: .: (0.001168) test_num_codons: .: (0.000251) test_num_sequences: .: (0.000249) test_significant: .: (0.000273) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000398) test_nb_sites: .: (0.000351) test_significant: .: (0.000242) test_sites: .: (0.001858) Bio::TestPDB: test_accession: .: (0.001973) test_addModel: .: (0.001077) test_authors: .: (0.001377) test_bracket: .: (0.001012) test_classification: .: (0.001369) test_dbref: .: (0.001135) test_definition: .: (0.001498) test_each: .: (0.001556) test_each_model: .: (0.001071) test_entry_id: .: (0.001305) test_helix: .: (0.001550) test_inspect: .: (0.001412) test_jrnl: .: (0.001093) test_keywords: .: (0.001311) test_record: .: (0.001016) test_remark: .: (0.001640) test_seqres: .: (0.001372) test_sheet: .: (0.001755) test_ssbond: .: (0.001128) test_to_s: .: (0.001641) test_turn: .: (0.001042) test_version: .: (0.001350) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000387) test_U12: .: (0.000208) test_U13: .: (0.000208) test_U22: .: (0.000209) test_U23: .: (0.000205) test_U33: .: (0.000209) test_altLoc: .: (0.000224) test_chainID: .: (0.000209) test_charge: .: (0.000208) test_element: .: (0.000232) test_iCode: .: (0.000240) test_name: .: (0.000499) test_resName: .: (0.000293) test_resSeq: .: (0.000229) test_segID: .: (0.000204) test_serial: .: (0.000204) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000363) test_anisou: .: (0.000162) test_chainID: .: (0.000162) test_charge: .: (0.000159) test_comparable: .: (0.000198) test_do_parse: .: (0.000170) test_element: .: (0.000159) test_iCode: .: (0.000189) test_name: .: (0.000160) test_occupancy: .: (0.000243) test_original_data: .: (0.000172) test_record_name: .: (0.000165) test_resName: .: (0.000179) test_resSeq: .: (0.000163) test_residue: .: (0.000177) test_segID: .: (0.000159) test_serial: .: (0.000154) test_sigatm: .: (0.000156) test_tempFactor: .: (0.000196) test_ter: .: (0.000161) test_to_a: .: (0.000169) test_to_s: .: (0.000197) test_x: .: (0.000195) test_xyz: .: (0.000645) test_y: .: (0.000265) test_z: .: (0.000223) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000310) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000296) test_idcode: .: (0.000163) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000465) test_chainID2: .: (0.000202) test_icode1: .: (0.000198) test_icode2: .: (0.000197) test_measure: .: (0.000206) test_modNum: .: (0.000570) test_pep1: .: (0.000224) test_pep2: .: (0.000199) test_seqNum1: .: (0.000209) test_seqNum2: .: (0.000204) test_serNum: .: (0.000202) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000312) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000303) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000314) test_alpha: .: (0.000178) test_b: .: (0.000175) test_beta: .: (0.000177) test_c: .: (0.000171) test_gamma: .: (0.000974) test_sGroup: .: (0.000185) test_z: .: (0.000175) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000347) test_database: .: (0.000225) test_dbAccession: .: (0.000292) test_dbIdCode: .: (0.000221) test_dbseqBegin: .: (0.000218) test_dbseqEnd: .: (0.000216) test_idCode: .: (0.000229) test_idbnsBeg: .: (0.000222) test_insertBegin: .: (0.000221) test_insertEnd: .: (0.000512) test_seqBegin: .: (0.000219) test_seqEnd: .: (0.000227) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000354) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000280) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000292) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000282) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000292) test_depDate: .: (0.000176) test_idCode: .: (0.000170) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000583) test_hetID: .: (0.000195) test_iCode: .: (0.000185) test_numHetAtoms: .: (0.000180) test_seqNum: .: (0.000183) test_text: .: (0.000189) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000295) test_anisou: .: (0.000167) test_chainID: .: (0.000159) test_charge: .: (0.000159) test_comparable: .: (0.000200) test_do_parse: .: (0.000163) test_element: .: (0.000160) test_iCode: .: (0.000164) test_name: .: (0.000453) test_occupancy: .: (0.000227) test_original_data: .: (0.000167) test_record_name: .: (0.000162) test_resName: .: (0.000159) test_resSeq: .: (0.000157) test_residue: .: (0.000164) test_segID: .: (0.000158) test_serial: .: (0.000159) test_sigatm: .: (0.000155) test_tempFactor: .: (0.000209) test_ter: .: (0.000158) test_to_a: .: (0.000166) test_to_s: .: (0.000263) test_x: .: (0.000203) test_xyz: .: (0.000182) test_y: .: (0.000606) test_z: .: (0.000222) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000472) test_ChainH: .: (0.000238) test_ICode1: .: (0.000243) test_altLoc1: .: (0.000240) test_altLoc2: .: (0.000306) test_altLocH: .: (0.000247) test_chainID2: .: (0.000241) test_iCode2: .: (0.000239) test_iCodeH: .: (0.000592) test_name1: .: (0.000257) test_name2: .: (0.000238) test_nameH: .: (0.000240) test_resName1: .: (0.000234) test_resName2: .: (0.000246) test_resSeq1: .: (0.000245) test_resSeq2: .: (0.000240) test_resSeqH: .: (0.000236) test_sym1: .: (0.000237) test_sym2: .: (0.000239) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000971) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000380) test_altLoc2: .: (0.000215) test_chainID1: .: (0.000247) test_chainID2: .: (0.000220) test_iCode1: .: (0.000224) test_iCode2: .: (0.000220) test_name1: .: (0.000216) test_name2: .: (0.000215) test_resName1: .: (0.000213) test_resName2: .: (0.000209) test_resSeq1: .: (0.000210) test_resSeq2: .: (0.000454) test_sym1: .: (0.000210) test_sym2: .: (0.000211) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000321) test_numCoord: .: (0.000174) test_numHelix: .: (0.000174) test_numHet: .: (0.000174) test_numRemark: .: (0.000176) test_numSeq: .: (0.000170) test_numSheet: .: (0.000173) test_numSite: .: (0.000220) test_numTer: .: (0.000176) test_numTurn: .: (0.000176) test_numXform: .: (0.000174) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000662) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000330) test_comment: .: (0.000193) test_iCode: .: (0.000189) test_idCode: .: (0.000188) test_resName: .: (0.000190) test_seqNum: .: (0.000188) test_stdRes: .: (0.000190) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000327) test_Mn2: .: (0.000172) test_Mn3: .: (0.000201) test_Vn: .: (0.000170) test_iGiven: .: (0.000171) test_serial: .: (0.000167) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000293) test_Mn2: .: (0.000168) test_Mn3: .: (0.000165) test_Vn: .: (0.000168) test_iGiven: .: (0.000169) test_serial: .: (0.000136) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000300) test_Mn2: .: (0.000125) test_Mn3: .: (0.008764) test_Vn: .: (0.000227) test_iGiven: .: (0.000131) test_serial: .: (0.000123) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000335) test_rIdCode: .: (0.000144) test_repDate: .: (0.000132) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000260) test_On2: .: (0.000120) test_On3: .: (0.000118) test_Tn: .: (0.000121) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000283) test_modId: .: (0.000139) test_modNum: .: (0.000678) test_modType: .: (0.000140) test_record: .: (0.000137) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000240) test_text: .: (0.000118) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000254) test_Sn2: .: (0.000116) test_Sn3: .: (0.000114) test_Un: .: (0.000112) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000241) test_Sn2: .: (0.000117) test_Sn3: .: (0.000114) test_Un: .: (0.000112) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000544) test_Sn2: .: (0.000117) test_Sn3: .: (0.000115) test_Un: .: (0.000205) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000312) test_conflict: .: (0.000156) test_database: .: (0.000155) test_dbIdCode: .: (0.000152) test_dbRes: .: (0.000153) test_dbSeq: .: (0.000151) test_iCode: .: (0.000152) test_idCode: .: (0.000150) test_resName: .: (0.000152) test_seqNum: .: (0.000552) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000279) test_numRes: .: (0.000155) test_resName: .: (0.000161) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000453) test_curChainId: .: (0.000207) test_curICode: .: (0.000204) test_curResName: .: (0.000200) test_curResSeq: .: (0.000198) test_endChainID: .: (0.000497) test_endICode: .: (0.000196) test_endResName: .: (0.000196) test_endSeqNum: .: (0.000194) test_initChainID: .: (0.000197) test_initICode: .: (0.000195) test_initResName: .: (0.000229) test_initSeqNum: .: (0.000196) test_numStrands: .: (0.000195) test_prevAtom: .: (0.000335) test_prevChainId: .: (0.000254) test_prevICode: .: (0.000510) test_prevResName: .: (0.000204) test_prevResSeq: .: (0.000217) test_sense: .: (0.000198) test_sheetID: .: (0.000194) test_strand: .: (0.000196) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000324) test_chainID: .: (0.000160) test_charge: .: (0.000166) test_element: .: (0.000169) test_iCode: .: (0.000158) test_name: .: (0.000482) test_resName: .: (0.000160) test_resSeq: .: (0.000157) test_segID: .: (0.000157) test_serial: .: (0.000156) test_sigOcc: .: (0.000155) test_sigTemp: .: (0.000158) test_sigX: .: (0.000156) test_sigY: .: (0.000157) test_sigZ: .: (0.000154) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000298) test_SigmaU12: .: (0.000156) test_SigmaU13: .: (0.000333) test_SigmaU22: .: (0.000158) test_SigmaU23: .: (0.000155) test_SigmaU33: .: (0.000154) test_altLoc: .: (0.000169) test_chainID: .: (0.000219) test_charge: .: (0.000174) test_element: .: (0.000169) test_iCode: .: (0.000157) test_name: .: (0.000157) test_resName: .: (0.000154) test_resSeq: .: (0.000200) test_segID: .: (0.000156) test_serial: .: (0.000153) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000377) test_chainID2: .: (0.000189) test_chainID3: .: (0.000177) test_chainID4: .: (0.000177) test_iCode1: .: (0.000176) test_iCode2: .: (0.000173) test_iCode3: .: (0.000175) test_iCode4: .: (0.000338) test_numRes: .: (0.000229) test_resName1: .: (0.000225) test_resName2: .: (0.000223) test_resName3: .: (0.000224) test_resName4: .: (0.000225) test_seq1: .: (0.000223) test_seq2: .: (0.000225) test_seq3: .: (0.000243) test_seq4: .: (0.000223) test_seqNum: .: (0.000220) test_siteID: .: (0.000267) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000350) test_altLoc2: .: (0.000198) test_atom1: .: (0.000195) test_atom2: .: (0.000194) test_chainID1: .: (0.000479) test_chainID2: .: (0.000200) test_iCode1: .: (0.000196) test_iCode2: .: (0.000194) test_resName1: .: (0.000197) test_resName2: .: (0.000204) test_resSeq1: .: (0.000251) test_resSeq2: .: (0.000255) test_sym1: .: (0.000293) test_sym2: .: (0.000232) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000448) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000313) test_sIdCode: .: (0.000195) test_sprsdeDate: .: (0.000904) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000453) test_iCode: .: (0.000220) test_resName: .: (0.000226) test_resSeq: .: (0.000237) test_serial: .: (0.000230) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000398) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000510) test_t1: .: (0.000263) test_t2: .: (0.000241) test_t3: .: (0.000250) test_text: .: (0.000246) Bio::TestPROSITE: test_ac: .: (0.003118) test_cc: .: (0.002806) test_de: .: (0.002744) test_division: .: (0.002655) test_dr: .: (0.026903) test_dt: .: (0.003114) test_false_neg: .: (0.003206) test_false_pos: .: (0.003305) test_false_positive_sequences: .: (0.003061) test_list_falsenegative: .: (0.031821) test_list_falsepositive: .: (0.022834) test_list_potentialhit: .: (0.022615) test_list_truepositive: .: (0.094982) test_list_unknown: .: (0.023056) test_list_xref: .: (0.023020) test_ma: .: (0.002770) test_max_repeat: .: (0.002469) test_name: .: (0.002341) test_nr: .: (0.002585) test_pa: .: (0.002194) test_pa2re: .: (0.003273) test_partial: .: (0.005646) test_pdb_xref: .: (0.002927) test_pdoc_xref: .: (0.002941) test_positive: .: (0.002340) test_positive_hits: .: (0.002848) test_positive_sequences: .: (0.002604) test_release: .: (0.002989) test_ru: .: (0.002674) test_self_pa2re: .: (0.002654) test_site: .: (0.002676) test_skip_flag: .: (0.002448) test_swissprot_release_number: .: (0.002619) test_swissprot_release_sequences: .: (0.002849) test_taxon_range: .: (0.002816) test_total: .: (0.002672) test_total_hits: .: (0.002919) test_total_sequences: .: (0.002444) test_unknown: .: (0.002902) test_unknown_hits: .: (0.002476) test_unknown_sequences: .: (0.002388) Bio::TestPROSITEConst: test_delimiter: .: (0.000333) test_tagsize: .: (0.000401) Bio::TestPTS1: test_function_set: .: (0.000299) test_function_set_number_1: .: (0.000201) test_function_set_number_2: .: (0.000160) test_function_set_number_3: .: (0.000159) test_function_show: .: (0.000175) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000265) Bio::TestPTS1New: test_fungi: .: (0.000265) test_general: .: (0.000157) test_metazoa: .: (0.000155) Bio::TestQualifier: test_qualifier: .: (0.000263) test_value: .: (0.000140) Bio::TestREBASE: test_methods: .: (0.001466) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001139) test_bit_score: .: (0.000744) test_evalue: .: (0.000934) test_gaps: .: (0.000801) test_hit_from: .: (0.000814) test_hit_to: .: (0.000768) test_hseq: .: (0.000772) test_identity: .: (0.001042) test_midline: .: (0.000771) test_percent_identity: .: (0.000724) test_positive: .: (0.000710) test_qseq: .: (0.000985) test_query_from: .: (0.000896) test_query_to: .: (0.000818) test_score: .: (0.000768) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000893) test_hits_size: .: (0.001834) test_iterations_size: .: (0.003961) test_program: .: (0.000704) test_query_def: .: (0.001642) test_query_len: .: (0.002102) test_version: .: (0.000672) test_version_date: .: (0.000699) test_version_number: .: (0.000663) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.001443) test_definition: .: (0.000812) test_evalue: .: (0.000841) test_hsps_size: .: (0.000732) test_identity: .: (0.000786) test_lap_at: .: (0.001231) test_len: .: (0.000801) test_midline: .: (0.000841) test_overlap: .: (0.000776) test_query_end: .: (0.001075) test_query_seq: .: (0.000962) test_query_start: .: (0.000834) test_target_def: .: (0.000834) test_target_end: .: (0.001130) test_target_len: .: (0.000868) test_target_seq: .: (0.000844) test_target_start: .: (0.000889) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001313) test_get_entry: .: (0.000670) test_rewind: .: (0.000177) test_skip_leader: .: (0.000278) Bio::TestReference: test_abstract: .: (0.000292) test_affiliations: .: (0.000162) test_authors: .: (0.000154) test_format_bibitem: .: (0.000226) test_format_bibtex: .: (0.000310) test_format_bibtex_with_arguments: .: (0.000332) test_format_cell: .: (0.000500) test_format_current: .: (0.000195) test_format_endnote: .: (0.000211) test_format_general: .: (0.000208) test_format_genome_biol: .: (0.000190) test_format_genome_res: .: (0.000196) test_format_nar: .: (0.000192) test_format_nature: .: (0.000224) test_format_rd: .: (0.000247) test_format_science: .: (0.000275) test_format_trends: .: (0.000163) test_issue: .: (0.000169) test_journal: .: (0.000148) test_mesh: .: (0.000172) test_pages: .: (0.000149) test_pubmed: .: (0.000150) test_pubmed_url: .: (0.000154) test_url: .: (0.000151) test_volume: .: (0.000145) test_year: .: (0.000144) Bio::TestReference_noURL: test_format_endnote: .: (0.000343) test_url: .: (0.000149) Bio::TestReferences: test_append: .: (0.000389) test_each: .: (0.000195) Bio::TestRelation: test_comparison_operator: .: (0.000342) test_uniq: .: (0.000199) Bio::TestResidue: test_addAtom: .: (0.000485) test_each: .: (0.000287) test_each_atom: .: (0.000271) test_get_residue_id_from_atom: .: (0.000255) test_het_atom: .: (0.000503) test_iCode: .: (0.000241) test_inspect: .: (0.000286) test_resSeq: .: (0.000276) test_sort: .: (0.000278) test_square_bracket: .: (0.000258) test_to_s: .: (0.000337) test_update_resudue_id: .: (0.000235) Bio::TestResidueFinder: test_each_residue: .: (0.000329) test_find_residue: .: (0.000196) test_residues: .: (0.000212) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.176532) test_cut_from_bio_sequence_na: .: (0.047939) test_cut_without_permutations: .: (0.030032) test_view_ranges: .: (0.029027) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001811) test_cuts_after_remove_incomplete_cuts: .: (0.000960) test_strands_for_display: .: (0.003781) test_strands_for_display_current: .: (0.001066) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000751) test_fragments_for_display_1: .: (0.001137) test_fragments_for_display_10: .: (0.001552) test_fragments_for_display_2: .: (0.001191) test_fragments_for_display_3: .: (0.001834) test_fragments_for_display_4: .: (0.001360) test_fragments_for_display_5: .: (0.000895) test_fragments_for_display_6: .: (0.001030) test_fragments_for_display_7: .: (0.000927) test_fragments_for_display_8: .: (0.000831) test_fragments_for_display_9: .: (0.000850) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000588) test_obj_3: .: (0.000430) test_obj_7: .: (0.000336) test_obj_z: .: (0.000351) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000491) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000374) test_bracket_eq: .: (0.000373) test_concat: .: (0.000199) test_delete: .: (0.000207) test_dup: .: (0.000288) test_each: .: (0.000264) test_eqeq: .: (0.000188) test_eqeq_false: .: (0.000171) test_eqeq_other: .: (0.000159) test_eqeq_self: .: (0.000159) test_include?: .: (0.000177) test_internal_data: .: (0.000168) test_internal_data_eq: .: (0.000185) test_length: .: (0.000162) test_ltlt: .: (0.000184) test_ltlt_larger: .: (0.000181) test_ltlt_middle: .: (0.000185) test_plus: .: (0.000204) test_plus_error: .: (0.000374) test_push: .: (0.000191) test_reverse_each: .: (0.000260) test_self_bracket: .: (0.000166) test_self_new: .: (0.000192) test_size: .: (0.000165) test_sort!: .: (0.000158) test_to_a: .: (0.000164) test_uniq!: .: (0.000160) test_unshift: .: (0.000196) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.005711) test_complement: .: (0.005179) test_complement_with_cut_symbols: .: (0.005220) test_cut_locations: .: (0.005142) test_cut_locations_in_enzyme_notation: .: (0.005128) test_primary: .: (0.005053) test_primary_with_cut_symbols: .: (0.009042) test_to_re: .: (0.005596) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.001310) test_align_with_cuts: .: (0.001207) test_argument_error: .: (0.001495) test_ds: .: (0.001047) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000642) test_complement: .: (0.000475) test_contents: .: (0.000297) test_primary: .: (0.000299) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000501) test_complement: .: (0.000297) test_contents: .: (0.000285) test_primary: .: (0.000284) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000583) test_contents: .: (0.000241) test_primary: .: (0.000229) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000388) test_complement_to_array_index: .: (0.000353) test_complement_to_array_index_class: .: (0.000327) test_contents: .: (0.000263) test_primary: .: (0.000254) test_primary_to_array_index: .: (0.000374) test_primary_to_array_index_class: .: (0.000573) test_to_array_index: .: (0.000640) test_to_array_index_class: .: (0.000588) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000575) test_rebase: .: (0.000225) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001368) test_creation_with_no_cuts: .: (0.000641) test_cut_locations: .: (0.000636) test_cut_locations_in_enzyme_notation: .: (0.000856) test_orientation: .: (0.000733) test_pattern: .: (0.000650) test_pattern_palindromic?: .: (0.000901) test_stripped: .: (0.000591) test_to_re: .: (0.000522) test_with_cut_symbols: .: (0.000845) test_with_spaces: .: (0.000721) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.001110) test_creation_with_no_cuts: .: (0.000633) test_cut_locations: .: (0.000668) test_cut_locations_in_enzyme_notation: .: (0.000655) test_orientation: .: (0.000769) test_pattern: .: (0.000644) test_pattern_palindromic?: .: (0.000722) test_stripped: .: (0.000626) test_to_re: .: (0.000520) test_with_cut_symbols: .: (0.000631) test_with_spaces: .: (0.000885) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000651) test_initialize_with_pattern: .: (0.000522) test_max: .: (0.000221) test_min: .: (0.000220) test_to_array_index: .: (0.000417) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000356) test_bracket_eq: .: (0.000207) test_concat: .: (0.000180) test_delete: .: (0.000164) test_dup: .: (0.000225) test_each: .: (0.000259) test_eqeq: .: (0.000223) test_eqeq_false: .: (0.000152) test_eqeq_other: .: (0.000144) test_eqeq_self: .: (0.000140) test_include?: .: (0.000164) test_internal_data_hash: .: (0.000147) test_internal_data_hash_eq: .: (0.000389) test_length: .: (0.000157) test_ltlt: .: (0.000179) test_ltlt_noeffect: .: (0.000165) test_plus: .: (0.000178) test_plus_error: .: (0.000223) test_private_push_element: .: (0.000162) test_private_push_element_intermediate: .: (0.000164) test_private_push_element_last: .: (0.000213) test_private_push_element_noeffect: .: (0.000168) test_private_sorted_keys: .: (0.000159) test_private_unshift_element: .: (0.000170) test_private_unshift_element_first: .: (0.000177) test_private_unshift_element_intermediate: .: (0.000186) test_private_unshift_element_noeffect: .: (0.000164) test_push: .: (0.000177) test_reverse_each: .: (0.000461) test_self_bracket: .: (0.000156) test_self_new: .: (0.000180) test_size: .: (0.000152) test_sort!: .: (0.000150) test_to_a: .: (0.000156) test_uniq!: .: (0.000176) test_unshift: .: (0.000181) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000334) test_left_padding: .: (0.000222) test_right_padding: .: (0.000206) test_strip_padding: .: (0.000215) Bio::TestSOFT: test_dataset: .: (0.011508) test_series: .: (0.009896) Bio::TestSOSUIReport: test_entry_id: .: (0.000408) test_prediction: .: (0.000217) test_tmh: .: (0.000210) test_tmhs: .: (0.000236) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000243) test_rs: .: (0.000140) Bio::TestSOSUITMH: test_grade: .: (0.000334) test_range: .: (0.000217) test_sequence: .: (0.000209) Bio::TestSampleGraph: test_bellman_ford: .: (0.000694) test_bfs_shortest_path: .: (0.000276) test_breadth_first_search: .: (0.000270) test_depth_first_search: .: (0.000445) test_dijkstra: .: (0.000483) test_dump_list: .: (0.000379) test_dump_matrix: .: (0.000514) test_extract_subgraph_by_label: .: (0.000338) test_extract_subgraph_by_list: .: (0.000333) test_extract_subgraph_retains_disconnected_nodes: .: (0.000260) test_small_world_aka_node_degree_histogram: .: (0.000242) test_to_matrix: .: (0.000517) test_to_matrix_fixed_index: .: (0.000504) test_undirected_cliquishness: .: (0.000492) Bio::TestScf_version_2: test_complement: .: (0.015833) test_seq: .: (0.014257) test_to_biosequence: .: (0.014169) Bio::TestScf_version_3: test_complement: .: (0.041677) test_seq: .: (0.040929) test_to_biosequence: .: (0.041277) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000339) test_AA_new_sequence_all_legal_symbols: .: (0.000160) test_AA_new_sequence_removes_whitespace: .: (0.000167) test_AA_new_sequence_upcases_symbols: .: (0.000155) test_DNA_new_blank_sequence: .: (0.000153) test_DNA_new_sequence_downcases_symbols: .: (0.000158) test_DNA_new_sequence_removes_whitespace: .: (0.000152) test_NA_randomize_with_counts: .: (0.001272) test_NA_randomize_with_counts_and_block: .: (0.001402) test_RNA_new_sequence: .: (0.000153) test_ambiguous_dna_sequence_complement: .: (0.000162) test_ambiguous_rna_sequence_complement: .: (0.000156) test_amino_acid_codes: .: (0.000197) test_amino_acid_molecular_weight: .: (0.000297) test_amino_acid_names: .: (0.000208) test_amino_acid_randomize_can_be_chained: .: (0.001699) test_amino_acid_randomize_has_same_composition: .: (0.000954) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000975) test_dna_composition: .: (0.000186) test_dna_gc_percent: .: (0.000208) test_dna_molecular_weight: .: (0.000262) test_dna_pikachu: .: (0.000162) test_dna_sequence_complement: .: (0.000152) test_dna_sequence_translate: .: (0.000541) test_dna_to_re: .: (0.000243) test_element_reference_operator_with_one_argument: .: (0.000157) test_element_reference_operator_with_two_arguments: .: (0.000156) test_invalid_nucleic_acid_illegal_bases: .: (0.000203) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000219) test_nucleic_acid_names: .: (0.000339) test_randomize_dna_can_be_chained: .: (0.000488) test_randomize_dna_retains_composition: .: (0.000375) test_randomize_dna_with_block: .: (0.000443) test_rna_composition: .: (0.000209) test_rna_gc_percent: .: (0.000211) test_rna_molecular_weight: .: (0.000369) test_rna_pikachu: .: (0.000159) test_rna_sequence_complement: .: (0.000152) test_rna_sequence_translate: .: (0.000402) test_rna_to_re: .: (0.000231) test_total: .: (0.000168) test_two_consecutive_dna_randomizations_not_equal: .: (0.000410) test_valid_dna_sequence_illegal_bases: .: (0.000158) Bio::TestSequenceAA: test_codes: .: (0.000314) test_molecular_weight: .: (0.000244) test_names: .: (0.000326) test_to_re: .: (0.000213) test_to_s: .: (0.000140) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000348) Bio::TestSequenceAANew: test_new: .: (0.000255) test_new_n: .: (0.000147) test_new_r: .: (0.000172) test_new_t: .: (0.000146) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000322) test_concat: .: (0.000154) test_push: .: (0.000144) test_seq: .: (0.000141) test_splicing: .: (0.000258) test_sum: .: (0.000280) test_to_s: .: (0.000142) test_to_str: .: (0.000145) test_total: .: (0.000158) test_window_search: .: (0.000399) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000275) test_normalize_A: .: (0.000159) test_normalize_a: .: (0.000154) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.008684) test_randomize_with_block: .: (0.006362) test_randomize_with_hash: .: (0.001800) test_randomize_with_hash_block: .: (0.007284) 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' =============================================================================== : (0.001603) 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' =============================================================================== : (0.001087) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000366) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000173) test_subseq_returns_subsequence: .: (0.000154) test_to_s_returns_self_as_string: .: (0.000173) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000291) test_window_search_with_width_3_step_two_with_residual: .: (0.000170) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000303) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000250) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000355) test_na_self_randomize: .: (0.000247) Bio::TestSequenceDBLink: test_database: .: (0.000473) test_id: .: (0.000140) test_secondary_ids: .: (0.000142) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000305) test_parse_uniprot_DR_line: .: (0.000200) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.001477) test_output_width_35: .: (0.000476) test_output_width_nil: .: (0.000429) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000918) test_output_after_adding_sequence: .: (0.000489) test_output_after_truncating_sequence: .: (0.000305) test_output_from_error_probabilities: .: (0.004111) test_output_width45: .: (0.000359) test_output_with_converting_score_phred2solexa: .: (0.001091) test_output_with_converting_score_solexa2phred: .: (0.000517) test_output_with_default_score: .: (0.000353) Bio::TestSequenceMasker: test_mask: .: (0.000420) test_mask_with_enumerator: .: (0.000250) test_mask_with_enumerator_empty_mask_char: .: (0.000238) test_mask_with_enumerator_excess: .: (0.000789) test_mask_with_enumerator_longer_mask_char: .: (0.000239) test_mask_with_enumerator_shorter: .: (0.000476) test_mask_with_error_probability: .: (0.000228) test_mask_with_quality_score: .: (0.000225) Bio::TestSequenceNA: test_at_content: .: (0.000588) test_at_skew: .: (0.000381) test_codon_usage: .: (0.000206) test_complement: .: (0.000175) test_dna: .: (0.000167) test_dna!: .: (0.000158) test_forward_complement: .: (0.000465) test_gc_content: .: (0.000379) test_gc_percent: .: (0.000266) test_gc_skew: .: (0.000513) test_iliegal_bases: .: (0.000164) test_molecular_weight: .: (0.000237) test_names: .: (0.000221) test_reverse_complement: .: (0.000223) test_rna: .: (0.000351) test_rna!: .: (0.000155) test_splicing: .: (0.000223) test_to_re: .: (0.000241) test_to_s: .: (0.000142) Bio::TestSequenceNACommon: test_composition: .: (0.000342) test_concat: .: (0.000149) test_push: .: (0.000182) test_seq: .: (0.000146) test_splicing: .: (0.000214) test_sum: .: (0.000149) test_to_s: .: (0.000142) test_to_str: .: (0.000143) test_total: .: (0.000158) test_window_search: .: (0.000592) Bio::TestSequenceNANew: test_new: .: (0.000253) test_new_n: .: (0.000147) test_new_r: .: (0.000141) test_new_t: .: (0.000143) Bio::TestSequenceNATranslation: test_translate: .: (0.000580) test_translate_0: .: (0.001006) test_translate_1: .: (0.000332) test_translate_2: .: (0.000326) test_translate_3: .: (0.000298) test_translate_4: .: (0.000332) test_translate_5: .: (0.000299) test_translate_6: .: (0.000325) test_translate_7: .: (0.000651) test_translate_given_codon_table: .: (0.064791) test_translate_n1: .: (0.000765) test_translate_n2: .: (0.000982) test_translate_n3: .: (0.000629) test_translate_unknown_o: .: (0.000351) test_translate_unknown_x: .: (0.000338) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000319) test_convert_scores_from_phred_to_solexa: .: (0.000679) test_convert_scores_from_solexa_to_phred: .: (0.000320) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000570) test_convert_scores_from_phred: .: (0.000150) test_convert_scores_from_phred_to_solexa: .: (0.000630) test_convert_scores_from_solexa: .: (0.000287) test_convert_scores_from_solexa_to_phred: .: (0.000276) test_convert_scores_to_phred: .: (0.000144) test_convert_scores_to_solexa: .: (0.000630) test_p2q: .: (0.000251) test_phred_p2q: .: (0.000238) test_phred_q2p: .: (0.008296) test_q2p: .: (0.008121) test_quality_score_type: .: (0.000163) test_self_convert_scores_to_solexa: .: (0.000658) test_self_p2q: .: (0.000252) test_self_q2p: .: (0.007527) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000705) test_convert_scores_from_phred: .: (0.000641) test_convert_scores_from_phred_to_solexa: .: (0.000624) test_convert_scores_from_solexa: .: (0.000152) test_convert_scores_from_solexa_to_phred: .: (0.000287) test_convert_scores_to_phred: .: (0.000293) test_convert_scores_to_solexa: .: (0.000138) test_p2q: .: (0.000331) test_q2p: .: (0.010516) test_quality_score_type: .: (0.000224) test_self_convert_scores_to_phred: .: (0.000404) test_self_p2q: .: (0.000442) test_self_q2p: .: (0.007642) test_solexa_p2q: .: (0.000543) test_solexa_q2p: .: (0.007588) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000375) test_center: .: (0.000179) test_chomp: .: (0.000208) test_chop: .: (0.000213) test_delete: .: (0.000241) test_delete_prefix: .: (0.000171) test_delete_suffix: .: (0.000169) test_downcase: .: (0.000173) test_each_char: .: (0.000379) test_each_char_enum: .: (0.000252) test_each_grapheme_cluster: .: (0.000504) test_each_grapheme_cluster_enum: .: (0.000246) test_each_line: .: (0.000251) test_each_line_enum: .: (0.000222) test_gsub: .: (0.000200) test_gsub_with_block: .: (0.000713) test_ljust: .: (0.000183) test_lstrip: .: (0.000209) test_multiply: .: (0.000264) test_next: .: (0.000168) test_reverse: .: (0.000171) test_rjust: .: (0.000171) test_rstrip: .: (0.000169) test_slice: .: (0.000178) test_slice2: .: (0.000173) test_split: .: (0.000221) test_squeeze: .: (0.000172) test_strip: .: (0.000254) test_sub: .: (0.000186) test_sub_with_block: .: (0.000326) test_succ: .: (0.000169) test_swapcase: .: (0.000172) test_tr: .: (0.000269) test_tr_s: .: (0.000162) test_upcase: .: (0.000173) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000346) test_partition_nomatch: .: (0.000212) test_partition_sep_TSeq: .: (0.000212) test_partition_sep_regexp: .: (0.000281) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000336) test_rpartition_nomatch: .: (0.000213) test_rpartition_sep_TSeq: .: (0.000210) test_rpartition_sep_regexp: .: (0.000219) Bio::TestShRNA: test_blocK_it: .: (0.109053) test_blocK_it_: .: (0.034085) test_blocK_it_BLOCK_IT: .: (0.034006) test_blocK_it_BLOCK_iT: .: (0.035452) test_blocK_it_piGene: .: (0.033175) test_bottom_strand: .: (0.034065) test_bottom_strand_class: .: (0.034703) test_bottom_strand_nil: .: (0.034326) test_design: .: (0.032401) test_design_BLOCK_IT: .: (0.036514) test_report: .: (0.033545) test_report_before_design: .: (0.032402) test_top_strand: .: (0.034086) test_top_strand_class: .: (0.033671) test_top_strand_nil: .: (0.032212) Bio::TestShRNANew: test_new: .: (0.000603) Bio::TestSiRNA: test_antisense_size: .: (0.000281) test_design: .: (0.037289) test_design_reynolds: .: (0.041884) test_design_uitei: .: (0.033824) test_max_gc_percent: .: (0.000249) test_min_gc_percent: .: (0.000187) test_reynolds: .: (0.046114) test_reynolds?: .: (0.000242) test_uitei: .: (0.032622) test_uitei?: .: (0.000254) Bio::TestSiRNANew: test_new: .: (0.000553) Bio::TestSiRNAPair: test_antisense: .: (0.032908) test_gc_percent: .: (0.034661) test_report: .: (0.032599) test_rule: .: (0.032600) test_sense: .: (0.033905) test_start: .: (0.032878) test_stop: .: (0.032393) test_target: .: (0.041282) Bio::TestSiRNAPairNew: test_new: .: (0.000595) Bio::TestSim4Report: test_all_hits: .: (0.000599) test_each: .: (0.000317) test_each_hit: .: (0.000286) test_hits: .: (0.000335) test_num_hits: .: (0.000520) test_query_def: .: (0.000324) test_query_id: .: (0.000238) test_query_len: .: (0.000249) test_seq1: .: (0.000327) Bio::TestSim4Report2: test_all_hits: .: (0.000452) test_each: .: (0.000293) test_each_hit: .: (0.000288) test_hits: .: (0.000292) test_num_hits: .: (0.000561) test_query_def: .: (0.000328) test_query_id: .: (0.000232) test_query_len: .: (0.000235) test_seq1: .: (0.000301) Bio::TestSim4Report4: test_all_hits: .: (0.000448) test_each: .: (0.000310) test_each_hit: .: (0.000303) test_hits: .: (0.000312) test_num_hits: .: (0.000266) test_query_def: .: (0.000486) test_query_id: .: (0.000264) test_query_len: .: (0.000293) test_seq1: .: (0.000346) Bio::TestSim4ReportHit: test_align: .: (0.000519) test_complement?: .: (0.000252) test_definition: .: (0.000247) test_each: .: (0.000490) test_exons: .: (0.000716) test_hit_id: .: (0.000295) test_hsps: .: (0.000392) test_introns: .: (0.000409) test_len: .: (0.000246) test_query_def: .: (0.000238) test_query_id: .: (0.000236) test_query_len: .: (0.000234) test_segmentpairs: .: (0.000719) test_seq1: .: (0.000368) test_seq2: .: (0.000299) test_target_def: .: (0.000243) test_target_id: .: (0.000243) test_target_len: .: (0.000242) Bio::TestSim4ReportHit2: test_align: .: (0.000495) test_complement?: .: (0.000276) test_definition: .: (0.000246) test_each: .: (0.000688) test_exons: .: (0.000469) test_hit_id: .: (0.000245) test_hsps: .: (0.000428) test_introns: .: (0.000409) test_len: .: (0.000245) test_query_def: .: (0.000234) test_query_id: .: (0.000231) test_query_len: .: (0.000469) test_segmentpairs: .: (0.000470) test_seq1: .: (0.000315) test_seq2: .: (0.000306) test_target_def: .: (0.000234) test_target_id: .: (0.000234) test_target_len: .: (0.000228) Bio::TestSim4ReportHit4: test_align: .: (0.000591) test_complement?: .: (0.000569) test_definition: .: (0.000273) test_each: .: (0.000641) test_exons: .: (0.000603) test_hit_id: .: (0.000284) test_hsps: .: (0.000837) test_introns: .: (0.000587) test_len: .: (0.000275) test_query_def: .: (0.000273) test_query_id: .: (0.000262) test_query_len: .: (0.000250) test_segmentpairs: .: (0.000587) test_seq1: .: (0.000619) test_seq2: .: (0.000362) test_target_def: .: (0.000258) test_target_id: .: (0.000294) test_target_len: .: (0.000254) Bio::TestSim4ReportSegment: test_from: .: (0.000282) test_self_new: .: (0.000187) test_seq: .: (0.000144) test_to: .: (0.000145) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000492) test_direction: .: (0.000575) test_hit_from: .: (0.000373) test_hit_to: .: (0.000372) test_hseq: .: (0.000344) test_midline: .: (0.000339) test_percent_identity: .: (0.000338) test_qseq: .: (0.000343) test_query_from: .: (0.000507) test_query_to: .: (0.000338) test_seq1: .: (0.000402) test_seq2: .: (0.000420) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000469) test_direction: .: (0.000579) test_hit_from: .: (0.000399) test_hit_to: .: (0.000337) test_hseq: .: (0.000336) test_midline: .: (0.000338) test_percent_identity: .: (0.000331) test_qseq: .: (0.000336) test_query_from: .: (0.000508) test_query_to: .: (0.000404) test_seq1: .: (0.000390) test_seq2: .: (0.000381) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000562) test_direction: .: (0.000626) test_hit_from: .: (0.000466) test_hit_to: .: (0.000417) test_hseq: .: (0.000423) test_midline: .: (0.000420) test_percent_identity: .: (0.000623) test_qseq: .: (0.000458) test_query_from: .: (0.000434) test_query_to: .: (0.000421) test_seq1: .: (0.000482) test_seq2: .: (0.000689) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000568) test_direction: .: (0.000464) test_hit_from: .: (0.000416) test_hit_to: .: (0.000425) test_hseq: .: (0.000602) test_midline: .: (0.000452) test_percent_identity: .: (0.000413) test_qseq: .: (0.000416) test_query_from: .: (0.000411) test_query_to: .: (0.000680) test_seq1: .: (0.000522) test_seq2: .: (0.000471) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000542) test_direction: .: (0.000617) test_hit_from: .: (0.000461) test_hit_to: .: (0.000443) test_hseq: .: (0.000419) test_midline: .: (0.000415) test_percent_identity: .: (0.000599) test_qseq: .: (0.000459) test_query_from: .: (0.000414) test_query_to: .: (0.000415) test_seq1: .: (0.000513) test_seq2: .: (0.000645) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000469) test_direction: .: (0.000328) test_hit_from: .: (0.000326) test_hit_to: .: (0.000322) test_hseq: .: (0.000512) test_midline: .: (0.000329) test_percent_identity: .: (0.000333) test_qseq: .: (0.000329) test_query_from: .: (0.000326) test_query_to: .: (0.000327) test_seq1: .: (0.000396) test_seq2: .: (0.000639) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000458) test_direction: .: (0.000360) test_hit_from: .: (0.000326) test_hit_to: .: (0.000326) test_hseq: .: (0.000325) test_midline: .: (0.000507) test_percent_identity: .: (0.000326) test_qseq: .: (0.000327) test_query_from: .: (0.000355) test_query_to: .: (0.000328) test_seq1: .: (0.000430) test_seq2: .: (0.000588) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000325) test_entry_id: .: (0.000158) test_filename: .: (0.000156) test_len: .: (0.000153) test_self_new: .: (0.000169) test_self_parse: .: (0.000205) Bio::TestTMHMMReport: test_entry_id: .: (0.000575) test_exp_aas_in_tmhs: .: (0.000409) test_exp_first_60aa: .: (0.000407) test_helix: .: (0.000456) test_predicted_tmhs: .: (0.000403) test_query_len: .: (0.000398) test_tmhs: .: (0.000640) test_to_s: .: (0.000560) test_total_prob_of_N_in: .: (0.000409) Bio::TestTMHMMReport_reports: test_reports: .: (0.000302) Bio::TestTMHMMTMH: test_entry_id: .: (0.000837) test_pos: .: (0.000426) test_range: .: (0.000414) test_status: .: (0.000428) test_version: .: (0.000401) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000659) test_cutoff: .: (0.000295) test_entry_id: .: (0.000281) test_length: .: (0.000281) test_loc: .: (0.000282) test_name: .: (0.000282) test_networks: .: (0.000285) test_prediction: .: (0.000334) test_query_len: .: (0.000282) test_query_sequences: .: (0.000280) test_rc: .: (0.000279) test_version: .: (0.000448) Bio::TestTargetPReportConst: test_delimiter: .: (0.000249) test_rs: .: (0.000138) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000256) test_togows_access_wait: .: (2.005046) Bio::TestTogoWSREST: test_debug: .: (0.000795) test_debug_default: .: (0.000233) test_internal_http: .: (0.000255) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000275) test_entry: .: (0.000145) test_entry_database_list: .: (0.000146) test_new: .: (0.000371) test_new_with_uri_object: .: (0.000310) test_new_with_uri_string: .: (0.000283) test_retrieve: .: (0.000145) test_search: .: (0.000142) test_search_database_list: .: (0.000143) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000450) test_prepare_return_value: .: (0.000304) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000904) Bio::TestTree: test_get_edge_distance: .: (0.000359) test_get_edge_distance_string: .: (0.000216) test_get_node_name: .: (0.000167) test_initialize: .: (0.000181) test_options: .: (0.000169) test_root: .: (0.000144) test_root=: .: (0.000161) Bio::TestTree2: test_add_edge: .: (0.000505) test_add_node: .: (0.000323) test_adjacency_matrix: .: (0.000410) test_adjacency_matrix_with_block: .: (0.000328) test_adjacent_nodes: .: (0.000534) test_adjacent_nodes_nonexistent: .: (0.000230) test_ancestors: .: (0.000281) test_children: .: (0.000252) test_clear: .: (0.000266) test_clear_node: .: (0.000317) test_clear_node_nonexistent: .: (0.000355) test_collect_edge!: .: (0.000487) test_collect_node!: .: (0.000422) test_concat: .: (0.000591) test_descendents: .: (0.000296) test_distance_matrix: .: (0.000746) test_each_edge: .: (0.000329) test_each_node: .: (0.000313) test_each_out_edge: .: (0.000287) test_each_out_edge_chimpanzee: .: (0.000286) test_each_out_edge_human: .: (0.000279) test_each_out_edge_mammals: .: (0.000347) test_each_out_edge_nonexistent: .: (0.000251) test_each_out_edge_primates: .: (0.000355) test_each_out_edge_rat: .: (0.000279) test_each_out_edge_rodents: .: (0.000357) test_edges: .: (0.000255) test_get_edge: .: (0.000616) test_get_edge_indirect: .: (0.000234) test_get_edge_merged: .: (0.000248) test_get_edge_nonexistent: .: (0.000422) test_get_node_bootstrap: .: (0.000231) test_get_node_bootstrap_string=: .: (0.000237) test_get_node_by_name: .: (0.000336) test_get_node_by_name_noexistent: .: (0.000223) test_include?: .: (0.000313) test_include_nonexistent: .: (0.000228) test_insert_node: .: (0.000428) test_leaves: .: (0.000301) test_leaves_noargs: .: (0.000245) test_lowest_common_ancestor: .: (0.000265) test_nodes: .: (0.000235) test_number_of_edges: .: (0.000429) test_number_of_nodes: .: (0.000221) test_out_degree: .: (0.000307) test_out_degree_nonexistent: .: (0.000271) test_out_edges: .: (0.000285) test_out_edges_mammals: .: (0.000415) test_out_edges_nonexistent: .: (0.000232) test_out_edges_primates: .: (0.000716) test_out_edges_rodents: .: (0.000364) test_parent: .: (0.000280) test_path: .: (0.000455) test_remove_edge: .: (0.000270) test_remove_edge_if: .: (0.000285) test_remove_edge_if_nothing_removed: .: (0.000302) test_remove_edge_nonexistent: .: (0.000326) test_remove_node: .: (0.000320) test_remove_node_if: .: (0.000251) test_remove_node_if_false: .: (0.000282) test_remove_node_nonexistent: .: (0.000322) test_remove_nonsense_nodes: .: (0.000384) test_subtree: .: (0.000712) test_subtree_with_all_paths: .: (0.000700) test_total_distance: .: (0.000333) Bio::TestTreeEdge: test_distance: .: (0.000310) test_distance=: .: (0.000206) test_distance_string: .: (0.000148) test_distance_string=: .: (0.000195) test_initialize: .: (0.000191) test_inspect: .: (0.000149) test_to_s: .: (0.000148) Bio::TestTreeNode: test_bootstrap: .: (0.000254) test_bootstrap=: .: (0.000318) test_bootstrap_string: .: (0.000137) test_bootstrap_string=: .: (0.000441) test_initialize: .: (0.000175) test_inspect: .: (0.000178) test_name: .: (0.000151) test_to_s: .: (0.000140) Bio::TestUniProt: test_gene_name: .: (0.006393) Bio::TestUniProtKB: test_ac: .: (0.007280) test_accession: .: (0.006090) test_cc: .: (0.008274) test_cc_alternative_products: .: (0.015690) test_cc_database: .: (0.009620) test_cc_mass_spectrometry: .: (0.009076) test_de: .: (0.006726) test_dr: .: (0.009159) test_dr_with_key: .: (0.008530) test_dr_with_key_empty: .: (0.009088) test_dt: .: (0.005877) test_dt_annotation: .: (0.006989) test_dt_created: .: (0.005935) test_dt_sequence: .: (0.006348) test_entry: .: (0.006057) test_ft: .: (0.052667) test_gene_name: .: (0.049448) test_gene_names: .: (0.007445) test_gn: .: (0.006910) test_gn_old_parser: .: (0.007091) test_gn_uniprot_parser: .: (0.006546) test_id_line: .: (0.006440) test_id_line_data_class: .: (0.005856) test_id_line_entry_name: .: (0.006317) test_id_line_molecule_type: .: (0.006342) test_id_line_sequence_length: .: (0.005974) test_kw: .: (0.006324) test_molecule: .: (0.008123) test_oc: .: (0.007482) test_og_1: .: (0.006194) test_og_2: .: (0.008549) test_og_3: .: (0.006505) test_og_4: .: (0.007273) test_og_5: .: (0.006733) test_og_6: .: (0.006794) test_os: .: (0.006506) test_os_access: .: (0.006574) test_os_access2: .: (0.006249) test_ox: .: (0.005845) test_protein_name: .: (0.006006) test_ref: .: (0.013709) test_seq: .: (0.006184) test_sequence_length: .: (0.005913) test_sq: .: (0.006077) test_sq_crc64: .: (0.006163) test_sq_len: .: (0.006171) test_sq_mw: .: (0.006212) test_synonyms: .: (0.008069) Bio::TestUniProtKB_CC: test_allergen: .: (0.000440) test_alternative_products_access_as_hash: .: (0.000333) test_alternative_products_ai: .: (0.000423) test_alternative_products_apu: .: (0.000629) test_alternative_products_as: .: (0.000761) test_alternative_products_rf: .: (0.000154) test_biophysicochemical_properties: .: (0.000570) test_biotechnology: .: (0.000330) test_catalytic_activity: .: (0.000269) test_caution: .: (0.000300) test_cofactor: .: (0.000314) test_developmental_stage: .: (0.000300) test_disease: .: (0.000807) test_domain: .: (0.000494) test_enzyme_regulation: .: (0.000281) test_function: .: (0.000318) test_induction: .: (0.000258) test_interaction: .: (0.000335) test_mass_spectrometry: .: (0.000400) test_miscellaneous: .: (0.000610) test_pathway: .: (0.000314) test_pharmaceutical: .: (0.000291) test_polymorphism: .: (0.000403) test_ptm: .: (0.000269) test_rna_editing: .: (0.000342) test_similarity: .: (0.000258) test_subcellular_location: .: (0.000328) test_subunit: .: (0.000232) test_tissue_specificity: .: (0.000289) test_toxic_dose: .: (0.000245) test_web_resource: .: (0.000391) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000538) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000713) test_protein_name: .: (0.000793) test_synonyms: .: (0.000586) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000311) test_entry: .: (0.000176) test_entry_id: .: (0.000176) test_entry_name: .: (0.000172) test_id_line: .: (0.000177) test_molecule: .: (0.000175) test_sequence_length: .: (0.000171) Bio::TestUniProtKB_P03589: test_ac: .: (0.001172) test_accession: .: (0.000695) test_cc: .: (0.001382) test_cc_alternative_products: .: (0.001026) test_cc_database: .: (0.000976) test_cc_mass_spectrometry: .: (0.001276) test_de: .: (0.000729) test_dr: .: (0.001289) test_dr_with_key: .: (0.001060) test_dr_with_key_empty: .: (0.001430) test_dt: .: (0.000704) test_dt_annotation: .: (0.000649) test_dt_created: .: (0.001085) test_dt_sequence: .: (0.000802) test_entry: .: (0.000725) test_ft: .: (0.001417) test_gene_name: .: (0.000751) test_gene_names: .: (0.000981) test_gn: .: (0.000737) test_gn_old_parser: .: (0.000768) test_gn_uniprot_parser: .: (0.001032) test_id_line: .: (0.000669) test_id_line_data_class: .: (0.000708) test_id_line_entry_name: .: (0.000732) test_id_line_sequence_length: .: (0.000916) test_kw: .: (0.000691) test_oc: .: (0.000980) test_oh: .: (0.001193) test_os: .: (0.000672) test_os_access: .: (0.000875) test_os_access2: .: (0.000710) test_ox: .: (0.000660) test_protein_name: .: (0.000955) test_protein_name_after_calling_de: .: (0.000713) test_ref: .: (0.000763) test_seq: .: (0.001368) test_sequence_length: .: (0.000658) test_sq: .: (0.000660) test_sq_crc64: .: (0.000918) test_sq_len: .: (0.000724) test_sq_mw: .: (0.000685) test_synonyms: .: (0.000874) Bio::TestUniProtKB_P28907: test_ac: .: (0.002401) test_accession: .: (0.002274) test_cc: .: (0.003157) test_cc_alternative_products: .: (0.003061) test_cc_database: .: (0.003248) test_cc_mass_spectrometry: .: (0.003097) test_de: .: (0.002676) test_dr: .: (0.005819) test_dr_with_key: .: (0.005596) test_dr_with_key_empty: .: (0.005650) test_dt: .: (0.002228) test_dt_annotation: .: (0.002407) test_dt_created: .: (0.002268) test_dt_sequence: .: (0.002275) test_entry: .: (0.002692) test_ft: .: (0.005504) test_gene_name: .: (0.004130) test_gene_names: .: (0.003099) test_gn: .: (0.002667) test_gn_old_parser: .: (0.002428) test_gn_uniprot_parser: .: (0.002260) test_id_line: .: (0.002316) test_id_line_data_class: .: (0.002507) test_id_line_entry_name: .: (0.005489) test_id_line_sequence_length: .: (0.002590) test_kw: .: (0.002936) test_oc: .: (0.002739) test_os: .: (0.002431) test_os_access: .: (0.002406) test_os_access2: .: (0.002923) test_ox: .: (0.002665) test_protein_name: .: (0.002533) test_protein_name_after_calling_de: .: (0.002831) test_ref: .: (0.003807) test_seq: .: (0.002562) test_sequence_length: .: (0.002494) test_sq: .: (0.002357) test_sq_crc64: .: (0.002567) test_sq_len: .: (0.002343) test_sq_mw: .: (0.002456) test_synonyms: .: (0.002617) test_synonyms_after_calling_de: .: (0.002491) Bio::TestUniProtKB_P49144: test_ac: .: (0.001663) test_accession: .: (0.000971) test_cc: .: (0.001817) test_cc_alternative_products: .: (0.001737) test_cc_database: .: (0.001496) test_cc_mass_spectrometry: .: (0.002047) test_de: .: (0.001072) test_dr: .: (0.001958) test_dr_with_key: .: (0.002024) test_dr_with_key_empty: .: (0.002077) test_dt: .: (0.001036) test_dt_annotation: .: (0.001252) test_dt_created: .: (0.001056) test_dt_sequence: .: (0.001170) test_entry: .: (0.001200) test_ft: .: (0.003749) test_gene_name: .: (0.002127) test_gene_names: .: (0.001785) test_gn: .: (0.001566) test_gn_old_parser: .: (0.002068) test_gn_uniprot_parser: .: (0.001531) test_id_line: .: (0.001967) test_id_line_data_class: .: (0.001521) test_id_line_entry_name: .: (0.001726) test_id_line_sequence_length: .: (0.001456) test_kw: .: (0.001907) test_oc: .: (0.001685) test_os: .: (0.001991) test_os_access: .: (0.001607) test_os_access2: .: (0.001903) test_ox: .: (0.001384) test_protein_name: .: (0.001948) test_protein_name_after_calling_de: .: (0.001696) test_ref: .: (0.001758) test_seq: .: (0.001892) test_sequence_length: .: (0.001531) test_sq: .: (0.001718) test_sq_crc64: .: (0.001285) test_sq_len: .: (0.001473) test_sq_mw: .: (0.001262) test_synonyms: .: (0.001218) test_synonyms_after_calling_de: .: (0.001309) Bio::TestUniProtKB_Ref: test_RA: .: (0.000549) test_RC: .: (0.000361) test_RG: .: (0.000355) test_RL: .: (0.000535) test_RN: .: (0.000350) test_RP: .: (0.000352) test_RT: .: (0.000348) test_RX: .: (0.000357) test_ref: .: (0.000541) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000337) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000648) test_alternative_products_with_ft: .: (0.001090) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000424) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000389) test_RL_lines: .: (0.000192) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000743) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000324) test_RG_line: .: (0.000434) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000633) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000386) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000362) test_RL_line: .: (0.000197) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.001155) test_RP_line: .: (0.000319) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000222) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000372) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000287) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000328) test_CC_interaction_isoform: .: (0.000262) test_CC_interaction_no_gene_name: .: (0.003080) test_CC_interaction_self_association: .: (0.000395) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000383) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000406) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000535) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000814) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000458) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000347) test_DT_line: .: (0.000247) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.005553) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000951) test_CC_web_resource: .: (0.000146) test_FT_VER_SEQ: .: (0.000253) test_OH_line_exception: .: (0.000323) test_OH_lines: .: (0.000766) Bio::TestUtils: test_centreOfGravity: .: (0.000707) test_dihedral_angle: .: (0.000628) test_distance: .: (0.000512) test_geometricCentre: .: (0.000709) test_rad2deg: .: (0.000281) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000398) test_dijkstra_on_weighted_graph: .: (0.000211) Finished in 24.239457541 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 162.59 tests/s, 891.15 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/3392535 and its subdirectories I: Current time: Sun Jun 2 03:53:46 -12 2024 I: pbuilder-time-stamp: 1717343626 Sun Jun 2 15:53:47 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun Jun 2 15:53:47 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun Jun 2 15:54:47 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun Jun 2 15:54:48 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 f79211984a75285968b13b244f4db61ce725d1bd 8139 ruby-bio_2.0.5-1_amd64.buildinfo Checksums-Sha256: 9f50f668237d86011e1cb40b1f1bb964dfb322d827a0a1a7423df712652ac5f3 656832 ruby-bio_2.0.5-1_all.deb db89a8a4309ea4ade5e8cd2f20bbc254352b98aff6247fb33c70bfec855f2801 8139 ruby-bio_2.0.5-1_amd64.buildinfo Files: 6b30eeea4b84581b7c9732444564d65b 656832 ruby optional ruby-bio_2.0.5-1_all.deb 99035835ceb7d7cef9808654e88de85d 8139 ruby optional ruby-bio_2.0.5-1_amd64.buildinfo Sun Jun 2 15:54:49 UTC 2024 I: diffoscope 269 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_25-8005.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/ruby-bio_2.0.5-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/ruby-bio_2.0.5-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/ruby-bio_2.0.5-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/b1/ruby-bio_2.0.5-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.YvZYz0iV/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: 0.376s) 0.376s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 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: 715ms CPU time consumed: 713ms Sun Jun 2 15:54:53 UTC 2024 I: diffoscope 269 found no differences in the changes files, and a .buildinfo file also exists. Sun Jun 2 15:54:53 UTC 2024 I: ruby-bio from unstable built successfully and reproducibly on amd64. Sun Jun 2 15:54:54 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Jun 2 15:54:54 UTC 2024 I: Submitting 12K b1/ruby-bio_2.0.5-1_amd64.buildinfo.asc Sun Jun 2 15:54:56 UTC 2024 I: Submitting 12K b2/ruby-bio_2.0.5-1_amd64.buildinfo.asc Sun Jun 2 15:54:59 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jun 2 15:54:59 UTC 2024 I: Done submitting .buildinfo files. Sun Jun 2 15:54:59 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'