Wed Oct 22 14:16:04 UTC 2025 I: starting to build ruby-bio/forky/amd64 on jenkins on '2025-10-22 14:15' Wed Oct 22 14:16:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/60007/console.log Wed Oct 22 14:16:04 UTC 2025 I: Downloading source for forky/ruby-bio=2.0.6-1 --2025-10-22 14:16:05-- http://deb.debian.org/debian/pool/main/r/ruby-bio/ruby-bio_2.0.6-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1494 (1.5K) [text/prs.lines.tag] Saving to: ‘ruby-bio_2.0.6-1.dsc’ 0K . 100% 184M=0s 2025-10-22 14:16:05 (184 MB/s) - ‘ruby-bio_2.0.6-1.dsc’ saved [1494/1494] Wed Oct 22 14:16:05 UTC 2025 I: ruby-bio_2.0.6-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Homepage: https://bioruby.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-bio Vcs-Git: https://salsa.debian.org/ruby-team/ruby-bio.git Testsuite: autopkgtest-pkg-ruby Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Package-List: ruby-bio deb ruby optional arch=all Checksums-Sha1: a0cd4e46dd790e55ce38de08e2991a0a9b2fc4d1 1452516 ruby-bio_2.0.6.orig.tar.gz 6c20e105f27e196f76781c9d9342544db3970492 14552 ruby-bio_2.0.6-1.debian.tar.xz Checksums-Sha256: c96e0c54dcd9b9d413afad6b8702e4b1be290631b459402024c446ef922605b3 1452516 ruby-bio_2.0.6.orig.tar.gz d712ccb6ae91730a86227eb075ac8fc21db0250cdfc554e902697b23f656234f 14552 ruby-bio_2.0.6-1.debian.tar.xz Files: 9c4372512937a004ed39a200510677fd 1452516 ruby-bio_2.0.6.orig.tar.gz 6ac08c031b6ab46f3064d31334fd4e5e 14552 ruby-bio_2.0.6-1.debian.tar.xz Ruby-Versions: all -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaNZ5ixIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtpiGwD/Yv1EvwHHbzBVJFBwa56R8+C8lUrse+jE bNhr8Y9mgEQBANh5HuGu+dWyvwlxgf0tnSTtdOSIdt/MNxVmxrBpQ3oH =AK7i -----END PGP SIGNATURE----- Wed Oct 22 14:16:05 UTC 2025 I: Checking whether the package is not for us Wed Oct 22 14:16:05 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed Oct 22 14:16:05 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed Oct 22 14:17:40 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 22 02:16:05 -12 2025 I: pbuilder-time-stamp: 1761142565 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ruby-bio_2.0.6-1.dsc] I: copying [./ruby-bio_2.0.6.orig.tar.gz] I: copying [./ruby-bio_2.0.6-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.6-1.dsc: no acceptable signature found dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.6 dpkg-source: info: unpacking ruby-bio_2.0.6.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.6-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable_tests_using_chi2.patch dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4191131/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=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='39eda4b9048c4d13af9f9832c21bf75f' 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='4191131' 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.KNRqlf20/pbuilderrc_tnFD --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/b1 --logfile b1/build.log ruby-bio_2.0.6-1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' 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 ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4191131/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 ... 19898 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gpg{a} gpg-agent{a} gpgconf{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libb-hooks-op-check-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgcrypt20{a} libgmp-dev{a} libgmpxx4ldbl{a} libgpg-error0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libksba8{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.3{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2-16{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} rake{a} rdtool{a} readline-common{a} rsopv{a} ruby{a} ruby-all-dev{a} ruby-csv{a} ruby-did-you-mean{a} ruby-libxml{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rd{a} ruby-ruby2-keywords{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} ruby3.3-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring debian-tag2upload-keyring dput dput-ng dupload equivs fonts-lato git-debpush gnupg libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgitlab-api-v4-perl libgpg-error-l10n libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmetacpan-client-perl libnamespace-clean-perl libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx lzip pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby-sdbm ruby3.3-doc strace unzip wget zip 0 packages upgraded, 129 newly installed, 0 to remove and 0 not upgraded. Need to get 38.4 MB of archives. After unpacking 140 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 38 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.56-2 [89.1 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libassuan9 amd64 3.0.2-2 [61.5 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 gpgconf amd64 2.4.8-3 [129 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libnpth0t64 amd64 1.8-3 [23.2 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 gpg amd64 2.4.8-3 [634 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 pinentry-curses amd64 1.3.2-3 [87.8 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 gpg-agent amd64 2.4.8-3 [271 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 56 http://deb.debian.org/debian forky/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 59 http://deb.debian.org/debian forky/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libdevel-callchecker-perl amd64 0.009-2 [15.6 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 86 http://deb.debian.org/debian forky/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libio-socket-ssl-perl all 2.095-1 [226 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libnet-http-perl all 6.24-1 [23.2 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libwww-perl all 6.80-1 [184 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 rsopv amd64 0.6.4-1 [1385 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 wdiff amd64 1.2.2-9 [122 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 devscripts all 2.25.20 [1045 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 xml-core all 0.19 [20.1 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 docbook all 4.5-11 [126 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libosp5 amd64 1.5.2-15.2 [972 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 opensp amd64 1.5.2-15.2 [448 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 docbook-to-man amd64 1:2.0.0-49 [74.2 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 rubygems-integration all 1.19 [5488 B] Get: 105 http://deb.debian.org/debian forky/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get: 109 http://deb.debian.org/debian forky/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 115 http://deb.debian.org/debian forky/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 117 http://deb.debian.org/debian forky/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 ruby-minitest all 5.25.4-3 [66.3 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 121 http://deb.debian.org/debian forky/main amd64 gem2deb-test-runner amd64 2.2.5 [17.9 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 ruby3.3-dev amd64 3.3.8-2 [1045 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 ruby-all-dev amd64 1:3.3+b1 [6496 B] Get: 126 http://deb.debian.org/debian forky/main amd64 gem2deb amd64 2.2.5 [48.0 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 ruby-rd all 0.6.38-5 [62.0 kB] Get: 128 http://deb.debian.org/debian forky/main amd64 rdtool all 0.6.38-5 [42.5 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 ruby-libxml amd64 5.0.5-1 [83.3 kB] Fetched 38.4 MB in 2s (25.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19898 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_amd64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Preparing to unpack .../066-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 .../067-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 .../068-libhttp-message-perl_7.00-2_all.deb ... Unpacking libhttp-message-perl (7.00-2) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../069-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 .../070-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 .../071-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 .../072-libnet-ssleay-perl_1.94-3_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.94-3) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../073-libio-socket-ssl-perl_2.095-1_all.deb ... Unpacking libio-socket-ssl-perl (2.095-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../074-libnet-http-perl_6.24-1_all.deb ... Unpacking libnet-http-perl (6.24-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../075-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../076-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../077-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../078-libwww-perl_6.80-1_all.deb ... Unpacking libwww-perl (6.80-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../079-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package rsopv. Preparing to unpack .../080-rsopv_0.6.4-1_amd64.deb ... Unpacking rsopv (0.6.4-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../081-wdiff_1.2.2-9_amd64.deb ... Unpacking wdiff (1.2.2-9) ... Selecting previously unselected package devscripts. Preparing to unpack .../082-devscripts_2.25.20_all.deb ... Unpacking devscripts (2.25.20) ... Selecting previously unselected package sgml-base. Preparing to unpack .../083-sgml-base_1.31+nmu1_all.deb ... Unpacking sgml-base (1.31+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../084-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../085-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../086-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../087-libosp5_1.5.2-15.2_amd64.deb ... Unpacking libosp5 (1.5.2-15.2) ... Selecting previously unselected package opensp. Preparing to unpack .../088-opensp_1.5.2-15.2_amd64.deb ... Unpacking opensp (1.5.2-15.2) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../089-docbook-to-man_1%3a2.0.0-49_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-49) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../090-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package ruby-csv. Preparing to unpack .../091-ruby-csv_3.3.4-1_all.deb ... Unpacking ruby-csv (3.3.4-1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../092-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../093-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-ruby2-keywords. Preparing to unpack .../094-ruby-ruby2-keywords_0.0.5-1_all.deb ... Unpacking ruby-ruby2-keywords (0.0.5-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../095-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../096-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../097-libyaml-0-2_0.2.5-2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-2) ... Selecting previously unselected package libruby3.3:amd64. Preparing to unpack .../098-libruby3.3_3.3.8-2_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.8-2) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../099-ruby3.3_3.3.8-2_amd64.deb ... Unpacking ruby3.3 (3.3.8-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../100-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../101-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../102-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package rake. Preparing to unpack .../103-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../104-ruby-minitest_5.25.4-3_all.deb ... Unpacking ruby-minitest (5.25.4-3) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../105-ruby-power-assert_2.0.3-1_all.deb ... Unpacking ruby-power-assert (2.0.3-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../106-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../107-gem2deb-test-runner_2.2.5_amd64.deb ... Unpacking gem2deb-test-runner (2.2.5) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../108-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../109-libgmp-dev_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package ruby3.3-dev:amd64. Preparing to unpack .../110-ruby3.3-dev_3.3.8-2_amd64.deb ... Unpacking ruby3.3-dev:amd64 (3.3.8-2) ... Selecting previously unselected package ruby-all-dev:amd64. Preparing to unpack .../111-ruby-all-dev_1%3a3.3+b1_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:3.3+b1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../112-gem2deb_2.2.5_amd64.deb ... Unpacking gem2deb (2.2.5) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../113-ruby-rd_0.6.38-5_all.deb ... Unpacking ruby-rd (0.6.38-5) ... Selecting previously unselected package rdtool. Preparing to unpack .../114-rdtool_0.6.38-5_all.deb ... Unpacking rdtool (0.6.38-5) ... Selecting previously unselected package ruby-libxml:amd64. Preparing to unpack .../115-ruby-libxml_5.0.5-1_amd64.deb ... Unpacking ruby-libxml:amd64 (5.0.5-1) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up wdiff (1.2.2-9) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:amd64 (1.8-3) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up bsdextrautils (2.41.2-1) ... Setting up libgpg-error0:amd64 (1.56-2) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.28) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libosp5 (1.5.2-15.2) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 22 14:17:09 UTC 2025. Universal Time is now: Wed Oct 22 14:17:09 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ruby-minitest (5.25.4-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20240727.1) ... Setting up rsopv (0.6.4-1) ... update-alternatives: using /usr/bin/rsopv to provide /usr/bin/sopv (sopv) in auto mode Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.4-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up autoconf (2.72-3.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libassuan9:amd64 (3.0.2-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.5.4-1) ... Setting up readline-common (8.3-3) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up liburi-perl (5.30-1) ... Setting up ruby-rd (0.6.38-5) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:amd64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.2-3) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.5.4-5) ... Setting up libnet-http-perl (6.24-1) ... Setting up opensp (1.5.2-15.2) ... Setting up libdevel-callchecker-perl:amd64 (0.009-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.4.8-3) ... Setting up libpython3.13-stdlib:amd64 (3.13.9-1) ... Setting up libio-socket-ssl-perl (2.095-1) ... Setting up gpg (2.4.8-3) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.4.8-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.9-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up python3 (3.13.7-1) ... Setting up rubygems-integration (1.19) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmodule-runtime-perl (0.018-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.28) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.80-1) ... Setting up libruby3.3:amd64 (3.3.8-2) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up devscripts (2.25.20) ... Setting up ruby3.3-dev:amd64 (3.3.8-2) ... Setting up ruby3.3 (3.3.8-2) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby-all-dev:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up rdtool (0.6.38-5) ... Setting up ruby-libxml:amd64 (5.0.5-1) ... Setting up gem2deb-test-runner (2.2.5) ... Setting up gem2deb (2.2.5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-to-man (1:2.0.0-49) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ruby-bio-2.0.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.6-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.6-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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-2.0.6' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.6' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.6' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.6.gemspec /usr/bin/ruby3.3 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.3 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.6/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.3.0:/var/lib/gems/3.3.0:/usr/local/lib/ruby/gems/3.3.0:/usr/lib/ruby/gems/3.3.0:/usr/lib/x86_64-linux-gnu/ruby/gems/3.3.0:/usr/share/rubygems-integration/3.3.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-linux-gnu/rubygems-integration/3.3.0 ruby3.3 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.3 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000746) test_dbs: .: (0.000216) test_go_ids: .: (0.000214) test_go_terms: .: (0.000213) test_parser: .: (0.000377) test_set_date: .: (0.000247) test_set_desc: .: (0.000225) test_to_str: .: (0.000228) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.001101) test_mktmpdir_without_block: .: (0.000588) test_remove_entry_secure: .: (0.000791) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.003164) test_call_command_fork: .: (0.000181) test_call_command_open3: .: (0.002425) test_call_command_popen: .: (0.002262) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.002009) test_call_command_fork: .: (0.000163) test_call_command_open3: .: (0.001907) test_call_command_popen: .: (0.001843) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.002337) test_call_command_fork: .: (0.000168) test_call_command_open3: .: (0.002021) test_call_command_popen: .: (0.001979) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.002273) test_call_command_fork_chdir: .: (0.000315) test_call_command_popen_chdir: .: (0.001529) test_query_command_chdir: .: (0.001764) test_query_command_fork_chdir: .: (0.000324) test_query_command_popen_chdir: .: (0.002470) Bio::FuncTestCommandQuery: test_query_command: .: (0.003237) test_query_command_fork: .: (0.001320) test_query_command_open3: .: (0.003355) test_query_command_popen: .: (0.003120) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000704) test_initialize: .: (0.000944) test_path: .: (0.000275) test_path_after_close: .: (0.000466) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.012550) test_output_fasta: .: (0.006430) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.001354) test_accession: .: (0.000188) test_accessions: .: (0.000185) test_comment: .: (0.001285) test_common_name: .: (0.000208) test_definition: .: (0.001343) test_features: .: (0.003466) test_gi: .: (0.000197) test_keywords: .: (0.000183) test_locus: .: (0.000149) test_nid: .: (0.000183) test_organism: .: (0.001418) test_origin: .: (0.000182) test_references: .: (0.001601) test_segment: .: (0.001136) test_source: .: (0.001510) test_taxonomy: .: (0.001200) test_version: .: (0.000996) test_versions: .: (0.000192) Bio::TestAA: test_13: .: (0.001170) test_1n: .: (0.000127) test_name2one: .: (0.000166) test_name2three: .: (0.001024) test_one2name: .: (0.000136) test_one2three: .: (0.000127) test_three2name: .: (0.000113) test_three2one: .: (0.001229) test_to_1_1: .: (0.000131) test_to_1_3: .: (0.000135) test_to_1_name: .: (0.001210) test_to_3_1: .: (0.000134) test_to_3_3: .: (0.000135) test_to_3_name: .: (0.000148) test_to_re: .: (0.000165) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000645) Bio::TestAAindex: test_api: .: (0.001579) test_auto_aax1: .: (0.000632) test_auto_aax2: .: (0.000482) Bio::TestAAindex1: test_author: .: (0.000298) test_comment: .: (0.000226) test_correlation_coefficient: .: (0.000341) test_dblinks: .: (0.000216) test_definition: .: (0.000214) test_entry_id: .: (0.000227) test_index: .: (0.000907) test_journal: .: (0.000243) test_title: .: (0.000226) Bio::TestAAindex2: test_access_A_R: .: (0.000515) test_access_R_A: .: (0.000457) test_author: .: (0.000220) test_cols: .: (0.000207) test_comment: .: (0.000212) test_dblinks: .: (0.000215) test_definition: .: (0.000232) test_entry_id: .: (0.000231) test_journal: .: (0.000257) test_matrix: .: (0.000816) test_matrix_1_2: .: (0.000477) test_matrix_2_2: .: (0.000549) test_matrix_A_R: .: (0.000568) test_matrix_R_A: .: (0.000450) test_matrix_determinant: .: (0.001381) test_matrix_rank: .: (0.001399) test_matrix_transpose: .: (0.000544) test_rows: .: (0.000212) test_title: .: (0.000219) Bio::TestAAindexConstant: test_delimiter: .: (0.000186) test_tagsize: .: (0.000109) Bio::TestAbif: test_complement: .: (0.008007) test_seq: .: (0.006796) test_to_biosequence: .: (0.007810) Bio::TestActsLikeMap: test_mixin: .: (0.000278) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000367) Bio::TestActsLikeMarker: test_mixin: .: (0.000198) Bio::TestAlignment: test_add_seq_no_key: .: (0.000283) test_add_seq_using_seq_with_aaseq_method: .: (0.000171) test_add_seq_using_seq_with_definition_method: .: (0.000143) test_add_seq_using_seq_with_entry_id_method: .: (0.000152) test_add_seq_using_seq_with_naseq_method: .: (0.000185) test_add_seq_using_seq_with_seq_method: .: (0.000158) test_consensus_iupac_gap_modes: .: (0.000447) test_consensus_iupac_missing_char: .: (0.000205) test_consensus_iupac_missing_char_option: .: (0.000221) test_consensus_iupac_no_gaps: .: (0.000245) test_consensus_iupac_of_ambiguous_bases: .: (0.000385) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002978) test_consensus_opt_gap_mode: .: (0.000479) test_consensus_opt_missing_char: .: (0.000229) test_consensus_string_no_gaps: .: (0.000229) test_consensus_threshold_four_sequences: .: (0.000361) test_consensus_threshold_two_sequences: .: (0.000295) test_convert_match: .: (0.000212) test_convert_unmatch: .: (0.000253) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000185) test_convert_unmatch_different_match_char: .: (0.000171) test_convert_unmatch_multiple_sequences: .: (0.000229) test_default_gap_char: .: (0.000112) test_default_gap_regexp_matches_default_gap_char: .: (0.000127) test_default_missing_char: .: (0.000110) test_each_site_equal_length: .: (0.000279) test_each_site_unequal_length: .: (0.000199) test_equals: .: (0.000216) test_match_line_protein: .: (0.000426) test_normalizebang_extends_sequences_with_gaps: .: (0.000174) test_seq_length_is_max_seq_length: .: (0.000138) test_seq_length_when_one_sequence: .: (0.000125) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000120) test_seqclass_when_seqclass_set: .: (0.000145) test_seqclass_when_sequence_used: .: (0.000127) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000125) test_set_and_get_gap_char: .: (0.000202) test_store_cannot_override_key: .: (0.000129) test_store_with_default_keys_and_user_defined_keys: .: (0.000157) test_store_with_nil_key_uses_next_number_for_key: .: (0.000145) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000248) test_alignment_concat: .: (0.000180) test_alignment_length: .: (0.000113) test_alignment_lstrip!: .: (0.000190) test_alignment_lstrip_nil: .: (0.000150) test_alignment_normalize!: .: (0.000124) test_alignment_rstrip!: .: (0.000245) test_alignment_rstrip_nil: .: (0.000239) test_alignment_site: .: (0.000218) test_alignment_slice: .: (0.000128) test_alignment_strip!: .: (0.000231) test_alignment_strip_nil: .: (0.000156) test_alignment_subseq: .: (0.000163) test_alignment_window: .: (0.000131) test_collect_each_site: .: (0.000160) test_consensus_each_site_default: .: (0.000206) test_consensus_each_site_gap_mode_1: .: (0.000200) test_consensus_each_site_gap_mode_minus1: .: (0.000197) test_consensus_iupac: .: (0.000366) test_consensus_string_default: .: (0.000170) test_consensus_string_half: .: (0.000166) test_convert_match: .: (0.000165) test_convert_unmatch: .: (0.000134) test_each_seq: .: (0.000154) test_each_site: .: (0.000213) test_each_site_step: .: (0.000177) test_each_window: .: (0.000299) test_match_line: .: (0.000653) test_match_line_amino: .: (0.001040) test_match_line_nuc: .: (0.000205) test_private_alignment_site: .: (0.000215) test_remove_all_gaps!: .: (0.000169) test_seqclass: .: (0.000123) test_seqclass=: .: (0.000168) test_seqclass_default: .: (0.000105) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.008409) test_determine_seq_method: .: (0.001088) test_entries: .: (0.000332) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000309) test_avoid_same_name_numbering: .: (0.000177) test_clustal_have_same_name_true: .: (0.000149) test_have_same_name_false: .: (0.000146) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000219) test_gap_char_default: .: (0.000126) test_gap_char_never_nil: .: (0.000118) test_gap_regexp: .: (0.000115) test_gap_regexp=: .: (0.000119) test_gap_regexp_never_nil: .: (0.000112) test_get_all_property_default: .: (0.000118) test_get_all_property_nodefault: .: (0.000133) test_is_gap_default_false: .: (0.000123) test_is_gap_default_true: .: (0.000125) test_is_gap_nodefault_false: .: (0.000140) test_is_gap_nodefault_true: .: (0.000123) test_missing_char=: .: (0.000118) test_missing_char_default: .: (0.000113) test_missing_char_never_nil: .: (0.000115) test_seqclass=: .: (0.000120) test_seqclass_default: .: (0.000115) test_seqclass_never_nil: .: (0.000114) test_set_all_property: .: (0.000129) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000462) test_consensus_string_50percent: .: (0.000119) test_consensus_string_50percent_nil: .: (0.000103) test_consensus_string_default: .: (0.000097) test_consensus_string_default_nil: .: (0.000113) test_has_gap_false: .: (0.000123) test_has_gap_true: .: (0.000117) test_match_line_amino_100percent: .: (0.000148) test_match_line_amino_missing: .: (0.000197) test_match_line_amino_strong: .: (0.000155) test_match_line_amino_weak: .: (0.000262) test_match_line_nuc_100percent: .: (0.000151) test_match_line_nuc_missing: .: (0.000148) test_remove_gaps!: .: (0.000122) test_remove_gaps_bang_not_removed: .: (0.000112) Bio::TestAtomFinder: test_atoms: .: (0.013963) test_each_atom: .: (0.000240) test_find_atom: .: (0.000202) Bio::TestBioFastaDefline: test_acc_version: .: (0.000452) test_accession: .: (0.000385) test_accessions: .: (0.000322) test_description: .: (0.000277) test_descriptions: .: (0.000282) test_entry_id: .: (0.000268) test_get: .: (0.000319) test_get_all_by_type: .: (0.000257) test_get_by_type: .: (0.000272) test_gi: .: (0.000265) test_id_strings: .: (0.000503) test_locus: .: (0.000287) test_method_missing: .: (0.005548) test_to_s: .: (0.000307) test_words: .: (0.000546) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.001041) test_goid2term: .: (0.000614) test_parse_goids: .: (0.000363) Bio::TestBioGenBank: test_basecount: .: (0.000749) test_circular: .: (0.000257) test_classification: .: (0.000295) test_date: .: (0.000246) test_date_modified: .: (0.000718) test_division: .: (0.000256) test_each_cds_feature: .: (0.000605) test_each_cds_qualifiers: .: (0.000646) test_each_gene: .: (0.000540) test_entry_id: .: (0.000237) test_length: .: (0.000233) test_locus_circular: .: (0.000265) test_locus_class: .: (0.000273) test_locus_date: .: (0.000281) test_locus_division: .: (0.000297) test_locus_entry_id: .: (0.000579) test_locus_length: .: (0.000273) test_locus_natype: .: (0.000260) test_locus_strand: .: (0.000260) test_natype: .: (0.000243) test_seq: .: (0.000322) test_seq_len: .: (0.000666) test_strand: .: (0.000308) test_strandedness: .: (0.000273) test_to_biosequence: .: (0.001410) Bio::TestBioGenPept: test_circular: .: (0.000622) test_date: .: (0.000215) test_dbsource: .: (0.000206) test_division: .: (0.000225) test_entry_id: .: (0.000217) test_length: .: (0.000225) test_locus: .: (0.000231) test_seq: .: (0.000247) test_seq_len: .: (0.000235) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000724) test_aaseq: .: (0.000290) test_chromosome: .: (0.000254) test_codon_usage: .: (0.000325) test_cu_list: .: (0.000219) test_dblinks_as_hash: .: (0.000276) test_dblinks_as_strings: .: (0.000239) test_definition: .: (0.000257) test_division: .: (0.000250) test_eclinks: .: (0.000306) test_entry: .: (0.000253) test_entry_id: .: (0.000279) test_gbposition: .: (0.000265) test_gene: .: (0.000273) test_genes: .: (0.000272) test_keggclass: .: (0.000296) test_keggclasses: .: (0.000326) test_locations: .: (0.000334) test_motifs_as_hash: .: (0.000275) test_motifs_as_strings: .: (0.000232) test_name: .: (0.000244) test_names_as_array: .: (0.000261) test_new: .: (0.000253) test_ntlen: .: (0.000403) test_ntseq: .: (0.000427) test_organism: .: (0.000232) test_orthologs_as_hash: .: (0.000249) test_orthologs_as_strings: .: (0.000238) test_pathway: .: (0.004107) test_pathway_after_pathways_as_strings: .: (0.000430) test_pathway_before_pathways_as_strings: .: (0.000296) test_pathways_as_hash: .: (0.000258) test_pathways_as_strings: .: (0.000241) test_position: .: (0.000249) test_structure: .: (0.000269) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001589) test_comment: .: (0.000330) test_data_source: .: (0.000316) test_definition: .: (0.000331) test_disease: .: (0.000316) test_entry_id: .: (0.000333) test_lineage: .: (0.000347) test_nalen: .: (0.000370) test_name: .: (0.000333) test_new: .: (0.000401) test_num_gene: .: (0.000304) test_num_rna: .: (0.000295) test_original_databases: .: (0.000303) test_original_db: .: (0.000486) test_plasmids: .: (0.000289) test_references: .: (0.006332) test_statistics: .: (0.001473) test_taxid: .: (0.001156) test_taxonomy: .: (0.002049) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001595) test_comment: .: (0.001845) test_data_source: .: (0.000253) test_definition: .: (0.001082) test_disease: .: (0.000255) test_entry_id: .: (0.001878) test_lineage: .: (0.000279) test_nalen: .: (0.000258) test_name: .: (0.000844) test_new: .: (0.000587) test_num_gene: .: (0.000243) test_num_rna: .: (0.001308) test_original_databases: .: (0.000866) test_original_db: .: (0.000669) test_plasmids: .: (0.000671) test_references: .: (0.000830) test_statistics: .: (0.001730) test_taxid: .: (0.000287) test_taxonomy: .: (0.000900) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.001412) test_compounds_as_strings: .: (0.000241) test_dblinks_as_hash: .: (0.001077) test_dblinks_as_strings: .: (0.000971) test_description: .: (0.001364) test_diseases_as_hash: .: (0.000352) test_diseases_as_strings: .: (0.000208) test_entry_id: .: (0.000227) test_enzymes_as_strings: .: (0.000208) test_genes_as_hash: .: (0.000221) test_genes_as_strings: .: (0.000210) test_keggclass: .: (0.000241) test_ko_pathway: .: (0.000231) test_modules_as_hash: .: (0.000226) test_modules_as_strings: .: (0.000218) test_name: .: (0.000242) test_new: .: (0.000223) test_organism: .: (0.000233) test_orthologs_as_hash: .: (0.000824) test_orthologs_as_strings: .: (0.000336) test_pathways_as_hash: .: (0.000219) test_pathways_as_strings: .: (0.000204) test_reactions_as_hash: .: (0.000202) test_reactions_as_strings: .: (0.000204) test_references: .: (0.000210) test_rel_pathways_as_hash: .: (0.000253) test_rel_pathways_as_strings: .: (0.000227) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001113) test_compounds_as_strings: .: (0.000285) test_dblinks_as_hash: .: (0.000232) test_dblinks_as_strings: .: (0.000221) test_description: .: (0.000238) test_diseases_as_hash: .: (0.000284) test_diseases_as_strings: .: (0.000249) test_entry_id: .: (0.000261) test_enzymes_as_strings: .: (0.000231) test_genes_as_hash: .: (0.000304) test_genes_as_strings: .: (0.000267) test_keggclass: .: (0.000260) test_ko_pathway: .: (0.000251) test_modules_as_hash: .: (0.000274) test_modules_as_strings: .: (0.000243) test_name: .: (0.000260) test_new: .: (0.000238) test_organism: .: (0.000257) test_orthologs_as_hash: .: (0.000229) test_orthologs_as_strings: .: (0.000227) test_pathways_as_hash: .: (0.000280) test_pathways_as_strings: .: (0.000247) test_reactions_as_hash: .: (0.000237) test_reactions_as_strings: .: (0.000232) test_references: .: (0.000231) test_rel_pathways_as_hash: .: (0.000263) test_rel_pathways_as_strings: .: (0.000269) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000666) test_compounds_as_strings: .: (0.000210) test_dblinks_as_hash: .: (0.000194) test_dblinks_as_strings: .: (0.000195) test_description: .: (0.000214) test_diseases_as_hash: .: (0.000216) test_diseases_as_strings: .: (0.000204) test_entry_id: .: (0.000349) test_enzymes_as_strings: .: (0.000195) test_genes_as_hash: .: (0.000194) test_genes_as_strings: .: (0.000196) test_keggclass: .: (0.000219) test_ko_pathway: .: (0.000225) test_modules_as_hash: .: (0.000206) test_modules_as_strings: .: (0.000203) test_name: .: (0.000227) test_new: .: (0.000205) test_organism: .: (0.000222) test_orthologs_as_hash: .: (0.000267) test_orthologs_as_strings: .: (0.000229) test_pathways_as_hash: .: (0.000215) test_pathways_as_strings: .: (0.000209) test_reactions_as_hash: .: (0.000202) test_reactions_as_strings: .: (0.000202) test_references: .: (0.000201) test_rel_pathways_as_hash: .: (0.000298) test_rel_pathways_as_strings: .: (0.000225) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000499) test_compounds_as_strings: .: (0.000219) test_dblinks_as_hash: .: (0.000226) test_dblinks_as_strings: .: (0.000223) test_description: .: (0.000712) test_diseases_as_hash: .: (0.000231) test_diseases_as_strings: .: (0.000222) test_entry_id: .: (0.000237) test_enzymes_as_strings: .: (0.000220) test_genes_as_hash: .: (0.000220) test_genes_as_strings: .: (0.000232) test_keggclass: .: (0.000280) test_ko_pathway: .: (0.000255) test_modules_as_hash: .: (0.000311) test_modules_as_strings: .: (0.000226) test_name: .: (0.000231) test_new: .: (0.000215) test_organism: .: (0.000235) test_orthologs_as_hash: .: (0.000227) test_orthologs_as_strings: .: (0.000229) test_pathways_as_hash: .: (0.000240) test_pathways_as_strings: .: (0.000235) test_reactions_as_hash: .: (0.000226) test_reactions_as_strings: .: (0.000229) test_references: .: (0.000603) test_rel_pathways_as_hash: .: (0.000264) test_rel_pathways_as_strings: .: (0.000228) Bio::TestBioKeggDRUG: test_activity: .: (0.000594) test_comment: .: (0.000245) test_dblinks_as_hash: .: (0.000279) test_dblinks_as_strings: .: (0.000245) test_entry_id: .: (0.000249) test_formula: .: (0.000257) test_kcf: .: (0.000249) test_mass: .: (0.000270) test_name: .: (0.000310) test_names: .: (0.000297) test_pathways_as_hash: .: (0.000280) test_pathways_as_strings: .: (0.000251) test_products: .: (0.000286) test_remark: .: (0.000290) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000659) test_composition: .: (0.000259) test_compounds: .: (0.002771) test_dblinks_as_hash: .: (0.000459) test_dblinks_as_strings: .: (0.000261) test_entry_id: .: (0.000238) test_enzymes: .: (0.000248) test_kcf: .: (0.000220) test_keggclass: .: (0.000251) test_mass: .: (0.000275) test_name: .: (0.000256) test_orthologs_as_hash: .: (0.000316) test_orthologs_as_strings: .: (0.000243) test_pathways_as_hash: .: (0.000242) test_pathways_as_strings: .: (0.000226) test_reactions: .: (0.000245) test_references: .: (0.000589) test_remark: .: (0.000325) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000483) test_composition: .: (0.000431) test_compounds: .: (0.000224) test_dblinks_as_hash: .: (0.000234) test_dblinks_as_strings: .: (0.000208) test_entry_id: .: (0.000219) test_enzymes: .: (0.000224) test_kcf: .: (0.000263) test_keggclass: .: (0.000250) test_mass: .: (0.000445) test_name: .: (0.000216) test_orthologs_as_hash: .: (0.000203) test_orthologs_as_strings: .: (0.000195) test_pathways_as_hash: .: (0.000211) test_pathways_as_strings: .: (0.000210) test_reactions: .: (0.000242) test_references: .: (0.000208) test_remark: .: (0.000219) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000986) test_compounds_as_strings: .: (0.000274) test_dblinks_as_hash: .: (0.000460) test_dblinks_as_strings: .: (0.000235) test_description: .: (0.000244) test_diseases_as_hash: .: (0.000246) test_diseases_as_strings: .: (0.000242) test_entry_id: .: (0.000294) test_enzymes_as_strings: .: (0.000252) test_genes_as_hash: .: (0.000250) test_genes_as_strings: .: (0.000242) test_keggclass: .: (0.000299) test_ko_pathway: .: (0.000279) test_modules_as_hash: .: (0.000749) test_modules_as_strings: .: (0.000267) test_name: .: (0.000245) test_new: .: (0.000233) test_organism: .: (0.000255) test_orthologs_as_hash: .: (0.000242) test_orthologs_as_strings: .: (0.000272) test_pathways_as_hash: .: (0.000263) test_pathways_as_strings: .: (0.000250) test_reactions_as_hash: .: (0.000438) test_reactions_as_strings: .: (0.000317) test_references: .: (0.000431) test_rel_pathways_as_hash: .: (0.000322) test_rel_pathways_as_strings: .: (0.000272) Bio::TestBioLITDB: test_author: .: (0.000680) test_entry_id: .: (0.000215) test_field: .: (0.000212) test_journal: .: (0.000207) test_keyword: .: (0.000242) test_reference: .: (0.000342) test_title: .: (0.000230) test_volume: .: (0.000214) Bio::TestBioNBRF: test_aalen: .: (0.000700) test_aaseq: .: (0.000188) test_entry: .: (0.000175) test_length: .: (0.000178) test_nalen: .: (0.000239) test_naseq: .: (0.000217) test_seq: .: (0.000219) test_seq_class: .: (0.000200) test_to_nbrf: .: (0.000214) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000338) test_to_newick_format_leaf: .: (0.000302) test_to_newick_format_leaf_NHX: .: (0.000216) Bio::TestBl2seqReport: test_db_len: .: (0.001270) test_db_num: .: (0.000448) test_new: .: (0.000339) test_undefed_methods: .: (0.000816) test_undefed_methods_for_iteration: .: (0.003769) Bio::TestBl2seqReportConstants: test_rs: .: (0.000197) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000360) test_hits: .: (0.000320) Bio::TestBlast: test_blast_reports_format0: .: (0.005171) test_blast_reports_format0_with_block: .: (0.000637) test_blast_reports_format7: .: (0.008110) test_blast_reports_format7_with_block: .: (0.006708) test_blast_reports_format7_with_parser: .: (0.009389) test_blast_reports_format7_with_parser_with_block: .: (0.006605) test_blast_reports_format8: .: (0.000929) test_blast_reports_format8_with_block: .: (0.000431) test_blast_reports_format8_with_parser: .: (0.000276) test_blast_reports_format8_with_parser_with_block: .: (0.000254) test_blast_reports_xml: .: (0.009334) test_blast_reports_xml_with_block: .: (0.006651) test_blastll: .: (0.000174) test_db: .: (0.000182) test_exec_genomenet: .: (0.000164) test_exec_local: .: (0.000161) test_exec_ncbi: .: (0.000162) test_filter: .: (0.000178) test_format: .: (0.000184) test_make_command_line: .: (0.000387) test_make_command_line_2: .: (0.000334) test_matrix: .: (0.000181) test_new: .: (0.000270) test_new_opt_string: .: (0.000268) test_option: .: (0.000204) test_option_set: .: (0.000268) test_option_set_m0: .: (0.000257) test_options: .: (0.000178) test_output: .: (0.000177) test_parse_result: .: (0.009052) test_parser: .: (0.000202) test_program: .: (0.000192) test_query: .: (0.000167) test_self_local: .: (0.000228) test_self_remote: .: (0.001586) test_server: .: (0.000172) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000306) test_delete: .: (0.000284) test_equal_equal: .: (0.000290) test_get: .: (0.000282) test_make_command_line_options: .: (0.000445) test_normalize!: .: (0.000207) test_parse: .: (0.000276) test_set: .: (0.000346) Bio::TestBlastReport: test_db: .: (0.006435) test_db_len: .: (0.008314) test_db_num: .: (0.006517) test_each_hit: .: (0.007476) test_each_iteration: .: (0.006345) test_eff_space: .: (0.007528) test_entrez_query: .: (0.006515) test_entropy: .: (0.007527) test_expect: .: (0.006337) test_filter: .: (0.007226) test_gap_extend: .: (0.006327) test_gap_open: .: (0.007240) test_hits: .: (0.006372) test_hsp_len: .: (0.007340) test_inclusion: .: (0.006332) test_iterations: .: (0.007440) test_kappa: .: (0.006328) test_lambda: .: (0.007143) test_matrix: .: (0.006380) test_message: .: (0.007155) test_parameters: .: (0.006464) test_pattern: .: (0.007174) test_program: .: (0.006329) test_query_def: .: (0.007205) test_query_id: .: (0.006314) test_query_len: .: (0.007131) test_reference: .: (0.006281) test_sc_match: .: (0.007211) test_sc_mismatch: .: (0.006402) test_statistics: .: (0.007068) test_version: .: (0.006260) Bio::TestBlastReportDefault: test_db: .: (0.000509) test_db_len: .: (0.000419) test_db_num: .: (0.000425) test_each_hit: .: (0.000424) test_each_iteration: .: (0.000369) test_eff_space: .: (0.000458) test_entropy: .: (0.000418) test_expect: .: (0.000434) test_gap_extend: .: (0.000427) test_gap_open: .: (0.000427) test_gapped_entropy: .: (0.000394) test_gapped_kappa: .: (0.000405) test_gapped_lambda: .: (0.000391) test_hits: .: (0.000387) test_iterations: .: (0.000370) test_kappa: .: (0.000390) test_lambda: .: (0.000391) test_matrix: .: (0.000428) test_message: .: (0.000366) test_pattern: .: (0.000361) test_program: .: (0.000398) test_query_def: .: (0.000390) test_query_len: .: (0.000369) test_reference: .: (0.000389) test_sc_match: .: (0.000411) test_sc_mismatch: .: (0.000423) test_version: .: (0.000360) Bio::TestBlastReportHit: test_Hit_accession: .: (0.008010) test_Hit_bit_score: .: (0.006571) test_Hit_definition: .: (0.007499) test_Hit_evalue: .: (0.006362) test_Hit_hit_id: .: (0.007759) test_Hit_hsps: .: (0.006303) test_Hit_identity: .: (0.007228) test_Hit_lap_at: .: (0.006250) test_Hit_len: .: (0.007060) test_Hit_midline: .: (0.006311) test_Hit_num: .: (0.007480) test_Hit_overlap: .: (0.006331) test_Hit_query_def: .: (0.007449) test_Hit_query_end: .: (0.006225) test_Hit_query_id: .: (0.007125) test_Hit_query_len: .: (0.006326) test_Hit_query_seq: .: (0.007115) test_Hit_query_start: .: (0.006290) test_Hit_taeget_def: .: (0.007096) test_Hit_target_end: .: (0.006286) test_Hit_target_id: .: (0.007025) test_Hit_target_len: .: (0.006257) test_Hit_target_seq: .: (0.007113) test_Hit_target_start: .: (0.006144) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000572) test_Hit_definition: .: (0.001355) test_Hit_evalue: .: (0.000419) test_Hit_hsps: .: (0.000389) test_Hit_identity: .: (0.000407) test_Hit_lap_at: .: (0.000755) test_Hit_len: .: (0.000431) test_Hit_midline: .: (0.000493) test_Hit_overlap: .: (0.000401) test_Hit_query_end: .: (0.000472) test_Hit_query_seq: .: (0.000490) test_Hit_query_start: .: (0.000663) test_Hit_taeget_def: .: (0.000401) test_Hit_target_end: .: (0.000487) test_Hit_target_id: .: (0.000403) test_Hit_target_len: .: (0.000396) test_Hit_target_seq: .: (0.000678) test_Hit_target_start: .: (0.000486) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.046878) test_Hit_bit_score: .: (0.019900) test_Hit_definition: .: (0.019298) test_Hit_evalue: .: (0.018430) test_Hit_hit_id: .: (0.018961) test_Hit_hsps: .: (0.019627) test_Hit_identity: .: (0.018641) test_Hit_lap_at: .: (0.018546) test_Hit_len: .: (0.018148) test_Hit_midline: .: (0.018134) test_Hit_num: .: (0.019225) test_Hit_overlap: .: (0.018648) test_Hit_query_def: .: (0.018527) test_Hit_query_end: .: (0.018233) test_Hit_query_id: .: (0.018070) test_Hit_query_len: .: (0.018707) test_Hit_query_seq: .: (0.018573) test_Hit_query_start: .: (0.018977) test_Hit_taeget_def: .: (0.018523) test_Hit_target_end: .: (0.019429) test_Hit_target_id: .: (0.018638) test_Hit_target_len: .: (0.018617) test_Hit_target_seq: .: (0.018305) test_Hit_target_start: .: (0.018451) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.018860) test_Hit_bit_score: .: (0.018715) test_Hit_definition: .: (0.018493) test_Hit_evalue: .: (0.018362) test_Hit_hit_id: .: (0.018982) test_Hit_hsps: .: (0.018393) test_Hit_identity: .: (0.018532) test_Hit_lap_at: .: (0.018485) test_Hit_len: .: (0.019025) test_Hit_midline: .: (0.018378) test_Hit_num: .: (0.018447) test_Hit_overlap: .: (0.018117) test_Hit_query_def: .: (0.018769) test_Hit_query_end: .: (0.018341) test_Hit_query_id: .: (0.018475) test_Hit_query_len: .: (0.018093) test_Hit_query_seq: .: (0.018806) test_Hit_query_start: .: (0.018286) test_Hit_taeget_def: .: (0.018515) test_Hit_target_end: .: (0.018162) test_Hit_target_id: .: (0.018851) test_Hit_target_len: .: (0.018508) test_Hit_target_seq: .: (0.018355) test_Hit_target_start: .: (0.018022) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.007165) test_Hit_bit_score: .: (0.006422) test_Hit_definition: .: (0.006617) test_Hit_evalue: .: (0.006544) test_Hit_hit_id: .: (0.006308) test_Hit_hsps: .: (0.006992) test_Hit_identity: .: (0.006500) test_Hit_lap_at: .: (0.005883) test_Hit_len: .: (0.007245) test_Hit_midline: .: (0.006220) test_Hit_num: .: (0.006965) test_Hit_overlap: .: (0.006475) test_Hit_query_def: .: (0.005860) test_Hit_query_end: .: (0.006987) test_Hit_query_id: .: (0.006450) test_Hit_query_len: .: (0.006924) test_Hit_query_seq: .: (0.006194) test_Hit_query_start: .: (0.006002) test_Hit_taeget_def: .: (0.007043) test_Hit_target_end: .: (0.006505) test_Hit_target_id: .: (0.006601) test_Hit_target_len: .: (0.006529) test_Hit_target_seq: .: (0.006254) test_Hit_target_start: .: (0.006951) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000339) test_Hit_bit_score: .: (0.000199) test_Hit_definition: .: (0.000182) test_Hit_evalue: .: (0.000181) test_Hit_hit_id: .: (0.000188) test_Hit_hsps: .: (0.000185) test_Hit_identity: .: (0.000183) test_Hit_lap_at: .: (0.000190) test_Hit_len: .: (0.000213) test_Hit_midline: .: (0.000258) test_Hit_num: .: (0.000189) test_Hit_overlap: .: (0.000187) test_Hit_query_def: .: (0.000191) test_Hit_query_end: .: (0.000183) test_Hit_query_id: .: (0.000187) test_Hit_query_len: .: (0.000177) test_Hit_query_seq: .: (0.000178) test_Hit_query_start: .: (0.000183) test_Hit_taeget_def: .: (0.000180) test_Hit_target_end: .: (0.000180) test_Hit_target_id: .: (0.000179) test_Hit_target_len: .: (0.000177) test_Hit_target_seq: .: (0.000176) test_Hit_target_start: .: (0.000180) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.006400) test_Hsp_bit_score: .: (0.007054) test_Hsp_density: .: (0.006557) test_Hsp_evalue: .: (0.005957) test_Hsp_gaps: .: (0.007151) test_Hsp_hit_frame: .: (0.006373) test_Hsp_hit_from: .: (0.007026) test_Hsp_hit_to: .: (0.006359) test_Hsp_hseq: .: (0.005891) test_Hsp_identity: .: (0.007198) test_Hsp_midline: .: (0.006443) test_Hsp_mismatch_count: .: (0.006932) test_Hsp_num: .: (0.006376) test_Hsp_pattern_from: .: (0.005825) test_Hsp_pattern_to: .: (0.007060) test_Hsp_percent_identity: .: (0.006361) test_Hsp_positive: .: (0.007298) test_Hsp_qseq: .: (0.006591) test_Hsp_query_frame: .: (0.005920) test_Hsp_query_from: .: (0.007486) test_Hsp_query_to: .: (0.006367) test_Hsp_score: .: (0.006963) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000562) test_Hsp_bit_score: .: (0.000409) test_Hsp_evalue: .: (0.000433) test_Hsp_gaps: .: (0.000410) test_Hsp_hit_frame: .: (0.000398) test_Hsp_hit_from: .: (0.000480) test_Hsp_hit_to: .: (0.000476) test_Hsp_hseq: .: (0.000565) test_Hsp_identity: .: (0.000403) test_Hsp_midline: .: (0.000487) test_Hsp_percent_identity: .: (0.000417) test_Hsp_positive: .: (0.000423) test_Hsp_qseq: .: (0.000488) test_Hsp_query_frame: .: (0.000400) test_Hsp_query_from: .: (0.000469) test_Hsp_query_to: .: (0.000485) test_Hsp_score: .: (0.000394) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.018650) test_Hsp_bit_score: .: (0.019298) test_Hsp_density: .: (0.018810) test_Hsp_evalue: .: (0.018188) test_Hsp_gaps: .: (0.019095) test_Hsp_hit_frame: .: (0.018382) test_Hsp_hit_from: .: (0.018266) test_Hsp_hit_to: .: (0.019256) test_Hsp_hseq: .: (0.018346) test_Hsp_identity: .: (0.018316) test_Hsp_midline: .: (0.019017) test_Hsp_mismatch_count: .: (0.018312) test_Hsp_num: .: (0.018169) test_Hsp_pattern_from: .: (0.019049) test_Hsp_pattern_to: .: (0.018316) test_Hsp_percent_identity: .: (0.018139) test_Hsp_positive: .: (0.018991) test_Hsp_qseq: .: (0.018331) test_Hsp_query_frame: .: (0.018176) test_Hsp_query_from: .: (0.019176) test_Hsp_query_to: .: (0.019033) test_Hsp_score: .: (0.018178) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.019149) test_Hsp_bit_score: .: (0.018388) test_Hsp_density: .: (0.018264) test_Hsp_evalue: .: (0.019159) test_Hsp_gaps: .: (0.018376) test_Hsp_hit_frame: .: (0.018264) test_Hsp_hit_from: .: (0.018961) test_Hsp_hit_to: .: (0.019195) test_Hsp_hseq: .: (0.018757) test_Hsp_identity: .: (0.018452) test_Hsp_midline: .: (0.018295) test_Hsp_mismatch_count: .: (0.018820) test_Hsp_num: .: (0.018642) test_Hsp_pattern_from: .: (0.018090) test_Hsp_pattern_to: .: (0.019089) test_Hsp_percent_identity: .: (0.018436) test_Hsp_positive: .: (0.018694) test_Hsp_qseq: .: (0.020359) test_Hsp_query_frame: .: (0.042248) test_Hsp_query_from: .: (0.018701) test_Hsp_query_to: .: (0.018605) test_Hsp_score: .: (0.018272) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.007121) test_Hsp_bit_score: .: (0.006396) test_Hsp_density: .: (0.006584) test_Hsp_evalue: .: (0.006737) test_Hsp_gaps: .: (0.006138) test_Hsp_hit_frame: .: (0.007076) test_Hsp_hit_from: .: (0.006341) test_Hsp_hit_to: .: (0.006144) test_Hsp_hseq: .: (0.007322) test_Hsp_identity: .: (0.006481) test_Hsp_midline: .: (0.006596) test_Hsp_mismatch_count: .: (0.006581) test_Hsp_num: .: (0.006286) test_Hsp_pattern_from: .: (0.006979) test_Hsp_pattern_to: .: (0.006277) test_Hsp_percent_identity: .: (0.006122) test_Hsp_positive: .: (0.007476) test_Hsp_qseq: .: (0.006585) test_Hsp_query_frame: .: (0.006904) test_Hsp_query_from: .: (0.006655) test_Hsp_query_to: .: (0.006267) test_Hsp_score: .: (0.007269) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000351) test_Hsp_bit_score: .: (0.000190) test_Hsp_density: .: (0.000252) test_Hsp_evalue: .: (0.000193) test_Hsp_gaps: .: (0.000186) test_Hsp_hit_frame: .: (0.000187) test_Hsp_hit_from: .: (0.000186) test_Hsp_hit_to: .: (0.000199) test_Hsp_hseq: .: (0.000185) test_Hsp_identity: .: (0.000182) test_Hsp_midline: .: (0.000179) test_Hsp_mismatch_count: .: (0.000177) test_Hsp_num: .: (0.000186) test_Hsp_pattern_from: .: (0.000179) test_Hsp_pattern_to: .: (0.000178) test_Hsp_percent_identity: .: (0.000178) test_Hsp_positive: .: (0.000177) test_Hsp_qseq: .: (0.000187) test_Hsp_query_frame: .: (0.000315) test_Hsp_query_from: .: (0.000178) test_Hsp_query_to: .: (0.000180) test_Hsp_score: .: (0.000177) Bio::TestBlastReportIteration: test_hits: .: (0.006437) test_message: .: (0.007465) test_num: .: (0.006453) test_statistics: .: (0.006030) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000475) test_message: .: (0.000375) test_num: .: (0.000372) Bio::TestBlastReportIterationMulti: test_each: .: (0.019535) test_hits: .: (0.019010) test_message: .: (0.018540) test_num: .: (0.018888) test_query_def: .: (0.018646) test_query_id: .: (0.018211) test_query_len: .: (0.018879) test_statistics: .: (0.018778) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.018270) test_hits: .: (0.018940) test_message: .: (0.018656) test_num: .: (0.018310) test_query_def: .: (0.019130) test_query_id: .: (0.018402) test_query_len: .: (0.018934) test_statistics: .: (0.018544) Bio::TestBlastReportIterationREXML: test_hits: .: (0.006495) test_message: .: (0.007105) test_num: .: (0.006328) test_statistics: .: (0.006562) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000311) test_message: .: (0.000189) test_num: .: (0.000198) test_statistics: .: (0.000193) Bio::TestBlastReportMulti: test_db: .: (0.018812) test_db_len: .: (0.018544) test_db_num: .: (0.019547) test_each_hit: .: (0.023737) test_each_iteration: .: (0.043103) test_eff_space: .: (0.019095) test_entropy: .: (0.018431) test_expect: .: (0.019175) test_filter: .: (0.018794) test_gap_extend: .: (0.018163) test_gap_open: .: (0.020203) test_hits: .: (0.020203) test_hsp_len: .: (0.019078) test_iterations: .: (0.019220) test_kappa: .: (0.018563) test_lambda: .: (0.018729) test_matrix: .: (0.020258) test_message: .: (0.019290) test_parameters: .: (0.019131) test_pattern: .: (0.018892) test_program: .: (0.046661) test_query_def: .: (0.018953) test_query_id: .: (0.018118) test_query_len: .: (0.020087) test_reference: .: (0.018501) test_reports: .: (0.017851) test_statistics: .: (0.018396) test_version: .: (0.017127) Bio::TestBlastReportMultiREXML: test_db: .: (0.019664) test_db_len: .: (0.018699) test_db_num: .: (0.017670) test_each_hit: .: (0.019309) test_each_iteration: .: (0.018245) test_eff_space: .: (0.018201) test_entropy: .: (0.019745) test_expect: .: (0.017873) test_filter: .: (0.020263) test_gap_extend: .: (0.019080) test_gap_open: .: (0.017078) test_hits: .: (0.020070) test_hsp_len: .: (0.019733) test_iterations: .: (0.017297) test_kappa: .: (0.019843) test_lambda: .: (0.019308) test_matrix: .: (0.017375) test_message: .: (0.019491) test_parameters: .: (0.019549) test_pattern: .: (0.017341) test_program: .: (0.020124) test_query_def: .: (0.020166) test_query_id: .: (0.017416) test_query_len: .: (0.019630) test_reference: .: (0.019495) test_reports: .: (0.018944) test_statistics: .: (0.019058) test_version: .: (0.019721) Bio::TestBlastReportREXML: test_db: .: (0.006670) test_db_len: .: (0.006006) test_db_num: .: (0.007958) test_each_hit: .: (0.006577) test_each_iteration: .: (0.006764) test_eff_space: .: (0.006740) test_entrez_query: .: (0.006298) test_entropy: .: (0.008332) test_expect: .: (0.006495) test_filter: .: (0.006299) test_gap_extend: .: (0.006490) test_gap_open: .: (0.007393) test_hits: .: (0.007168) test_hsp_len: .: (0.006549) test_inclusion: .: (0.006568) test_iterations: .: (0.005959) test_kappa: .: (0.008062) test_lambda: .: (0.006425) test_matrix: .: (0.006286) test_message: .: (0.006451) test_parameters: .: (0.007144) test_pattern: .: (0.006952) test_program: .: (0.006318) test_query_def: .: (0.006334) test_query_id: .: (0.006139) test_query_len: .: (0.007953) test_reference: .: (0.006545) test_sc_match: .: (0.006253) test_sc_mismatch: .: (0.006375) test_statistics: .: (0.006094) test_version: .: (0.008863) Bio::TestBlastReportTabular: test_db: .: (0.000302) test_db_len: .: (0.000186) test_db_num: .: (0.000188) test_each_hit: .: (0.000184) test_each_iteration: .: (0.000189) test_eff_space: .: (0.000181) test_entrez_query: .: (0.000192) test_entropy: .: (0.000184) test_expect: .: (0.000185) test_filter: .: (0.000178) test_gap_extend: .: (0.000178) test_gap_open: .: (0.000183) test_hits: .: (0.000213) test_hsp_len: .: (0.000179) test_inclusion: .: (0.000175) test_iterations: .: (0.000180) test_kappa: .: (0.000178) test_lambda: .: (0.000176) test_matrix: .: (0.000181) test_message: .: (0.000179) test_parameters: .: (0.000182) test_pattern: .: (0.000180) test_program: .: (0.000177) test_query_def: .: (0.000277) test_query_id: .: (0.000191) test_query_len: .: (0.000178) test_reference: .: (0.000178) test_sc_match: .: (0.000179) test_sc_mismatch: .: (0.000175) test_statistics: .: (0.000203) test_version: .: (0.000180) Bio::TestChain: test_aaseq: .: (0.000365) test_addLigand: .: (0.000144) test_addResidue: .: (0.000137) test_atom_seq: .: (0.000148) test_comp: .: (0.000165) test_each: .: (0.000147) test_each_heterogen: .: (0.000144) test_each_residue: .: (0.000140) test_get_heterogen_by_id: .: (0.000150) test_get_residue_by_id: .: (0.000245) test_inspect: .: (0.000170) test_rehash: .: (0.000140) test_rehash_heterogens: .: (0.000125) test_rehash_residues: .: (0.000123) test_square_brace: .: (0.000138) test_to_s: .: (0.000153) Bio::TestChainFinder: test_chains: .: (0.000319) test_each_chain: .: (0.000167) test_find_chain: .: (0.000151) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005252) test_header: .: (0.000439) test_match_line: .: (0.000616) test_sequence0: .: (0.000428) test_sequence1: .: (0.000630) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.004997) test_header: .: (0.000569) test_match_line: .: (0.000557) test_sequence0: .: (0.000559) test_sequence1: .: (0.000553) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.005490) test_header: .: (0.000434) test_match_line: .: (0.000420) test_sequence0: .: (0.000502) test_sequence1: .: (0.000434) Bio::TestCodonTable: test_Tables: .: (0.000249) test_accessor: .: (0.000164) test_definition: .: (0.000116) test_each: .: (0.000138) test_revtrans: .: (0.000185) test_self_accessor: .: (0.000127) test_self_copy: .: (0.000643) test_set_accessor: .: (0.049578) test_start: .: (0.000161) test_start_codon?: .: (0.000146) test_stop: .: (0.000120) test_stop_codon?: .: (0.000152) test_table: .: (0.000121) Bio::TestCodonTableConstants: test_Definitions: .: (0.000243) test_Starts: .: (0.000141) test_Tables: .: (0.000290) test_stops: .: (0.000130) Bio::TestColorScheme: test_buried: .: (0.000829) Bio::TestCommand: test_command_constants: .: (0.000204) test_escape_shell: .: (0.000185) test_escape_shell_unix: .: (0.000155) test_escape_shell_windows: .: (0.000168) test_make_cgi_params_by_array_of_array: .: (0.000327) test_make_cgi_params_by_array_of_hash: .: (0.000300) test_make_cgi_params_by_array_of_string: .: (0.000183) test_make_cgi_params_by_hash_in_string: .: (0.000371) test_make_cgi_params_by_hash_in_symbol: .: (0.000497) test_make_cgi_params_by_string: .: (0.000201) test_make_command_line: .: (0.000155) test_make_command_line_unix: .: (0.000147) test_make_command_line_windows: .: (0.000154) test_safe_command_line_array: .: (0.000163) test_safe_command_line_array_passthrough: .: (0.000148) Bio::TestContingencyTable: test_lite_example: .: (0.081005) Bio::TestDB: test_entry_id: .: (0.000329) test_exists: .: (0.000137) test_fetch: .: (0.000199) test_get: .: (0.000115) test_open: .: (0.000124) test_tags: .: (0.000121) Bio::TestDataType: test_const_like_method: .: (0.000679) test_pdb_achar: .: (0.000248) test_pdb_atom: .: (0.000229) test_pdb_character: .: (0.000233) test_pdb_date: .: (0.000235) test_pdb_idcode: .: (0.000231) test_pdb_integer: .: (0.000123) test_pdb_list: .: (0.000156) test_pdb_lstring: .: (0.000242) test_pdb_real: .: (0.000197) test_pdb_resudue_name: .: (0.000247) test_pdb_slist: .: (0.000131) test_pdb_string: .: (0.000253) test_pdb_stringrj: .: (0.000127) test_pdb_symop: .: (0.000242) test_specification_list: .: (0.000150) Bio::TestEMBL: test_ac: .: (0.001000) test_accession: .: (0.000299) test_cc: .: (0.000268) test_de: .: (0.000463) test_division: .: (0.000316) test_dr: .: (0.000272) test_dt: .: (0.000287) test_dt_created: .: (0.000282) test_dt_iterator: .: (0.000294) test_dt_updated: .: (0.000319) test_each_cds: .: (0.000426) test_each_gene: .: (0.000368) test_entry: .: (0.000328) test_fh: .: (0.000311) test_ft: .: (0.000391) test_ft_accessor: .: (0.000379) test_ft_iterator: .: (0.000403) test_id_line: .: (0.000311) test_id_line_data_class: .: (0.000311) test_id_line_division: .: (0.000317) test_id_line_entry_name: .: (0.000311) test_id_line_iterator: .: (0.000326) test_id_line_molecule_type: .: (0.000293) test_id_line_sequence_length: .: (0.000295) test_kw: .: (0.000319) test_molecule: .: (0.000240) test_oc: .: (0.000273) test_og: .: (0.000194) test_os: .: (0.000240) test_ref: .: (0.000291) test_references: .: (0.000388) test_seq: .: (0.000422) test_sequence_length: .: (0.000236) test_sq: .: (0.000234) test_sq_get: .: (0.000220) test_sv: .: (0.000215) test_version: .: (0.000211) Bio::TestEMBL89: test_ac: .: (0.000707) test_accession: .: (0.000218) test_cc: .: (0.000185) test_de: .: (0.000216) test_division: .: (0.000222) test_dr: .: (0.000181) test_dt: .: (0.000189) test_dt_created: .: (0.000188) test_dt_iterator: .: (0.000183) test_dt_updated: .: (0.000190) test_each_cds: .: (0.000288) test_each_gene: .: (0.000273) test_entry: .: (0.000241) test_fh: .: (0.000205) test_ft: .: (0.000316) test_ft_accessor: .: (0.000319) test_ft_iterator: .: (0.000314) test_id_line: .: (0.000228) test_id_line_data_class: .: (0.000234) test_id_line_division: .: (0.000231) test_id_line_entry_name: .: (0.000235) test_id_line_iterator: .: (0.000218) test_id_line_molecule_type: .: (0.000211) test_id_line_sequence_length: .: (0.000214) test_id_line_sequence_version: .: (0.000210) test_kw: .: (0.000196) test_molecule: .: (0.000218) test_oc: .: (0.000252) test_og: .: (0.000181) test_os: .: (0.000238) test_ref: .: (0.000265) test_references: .: (0.000341) test_seq: .: (0.000383) test_sequence_length: .: (0.000252) test_sq: .: (0.000344) test_sq_get: .: (0.000233) test_sv: .: (0.000250) test_version: .: (0.000230) Bio::TestEMBLAPI: test_ac: .: (0.000207) test_accessions: .: (0.000192) Bio::TestEMBLCommon: test_ac: .: (0.000156) test_accession: .: (0.000065) test_accessions: .: (0.000062) test_de: .: (0.000058) test_definition: .: (0.000059) test_description: .: (0.000059) test_dr: .: (0.000057) test_keywords: .: (0.000059) test_kw: .: (0.000077) test_oc: .: (0.000058) test_og: .: (0.000057) test_os: .: (0.000063) test_ref: .: (0.000060) test_references: .: (0.000062) Bio::TestEMBLDB: test_fetch: .: (0.000193) test_p_entry2hash: .: (0.000061) Bio::TestEMBLToBioSequence: test_classification: .: (0.002360) test_date_created: .: (0.000395) test_date_modified: .: (0.000337) test_definition: .: (0.000250) test_division: .: (0.000257) test_entry_id: .: (0.000250) test_entry_version: .: (0.000236) test_features: .: (0.000328) test_keywords: .: (0.000251) test_molecule_type: .: (0.000275) test_primary_accession: .: (0.003634) test_references: .: (0.000511) test_release_created: .: (0.000234) test_release_modified: .: (0.000222) test_secondary_accessions: .: (0.000228) test_sequence_version: .: (0.000260) test_species: .: (0.000224) test_topology: .: (0.001240) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002720) test_date_created: .: (0.001850) test_date_modified: .: (0.001746) test_definition: .: (0.001714) test_division: .: (0.001746) test_entry_id: .: (0.001788) test_entry_version: .: (0.001755) test_features: .: (0.001870) test_keywords: .: (0.001819) test_molecule_type: .: (0.001856) test_primary_accession: .: (0.001820) test_references: .: (0.001954) test_release_created: .: (0.002660) test_release_modified: .: (0.001661) test_secondary_accessions: .: (0.001597) test_sequence_version: .: (0.001654) test_species: .: (0.001622) test_topology: .: (0.001650) Bio::TestFasta: test_db: .: (0.000186) test_format: .: (0.000065) test_format_arg_integer: .: (0.000081) test_format_arg_str: .: (0.000068) test_ktup: .: (0.000066) test_matrix: .: (0.000063) test_option: .: (0.000125) test_options: .: (0.000070) test_output: .: (0.000057) test_program: .: (0.000065) test_server: .: (0.000063) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000173) test_accession: .: (0.000084) test_accessions: .: (0.000085) test_description: .: (0.000077) test_descriptions: .: (0.000075) test_entry_id: .: (0.000070) test_get_all_by_type: .: (0.000075) test_gi: .: (0.004329) test_id_strings: .: (0.000124) test_list_ids: .: (0.000079) test_locus: .: (0.000075) test_words: .: (0.000098) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000275) test_accession: .: (0.000092) test_accessions: .: (0.000130) test_description: .: (0.000079) test_descriptions: .: (0.000094) test_emb: .: (0.000093) test_entry_id: .: (0.000074) test_get_all_by_type: .: (0.000078) test_get_emb: .: (0.000082) test_gi: .: (0.000802) test_id_strings: .: (0.000122) test_list_ids: .: (0.000081) test_locus: .: (0.000080) test_words: .: (0.000106) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000282) test_accession: .: (0.000138) test_accessions: .: (0.000081) test_description: .: (0.000070) test_descriptions: .: (0.000069) test_entry_id: .: (0.000067) test_get_all_by_type: .: (0.000069) test_gi: .: (0.000070) test_id_strings: .: (0.000097) test_list_ids: .: (0.000070) test_locus: .: (0.000070) test_sp: .: (0.000079) test_words: .: (0.000094) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.001011) test_accession: .: (0.000117) test_accessions: .: (0.000110) test_description: .: (0.000093) test_descriptions: .: (0.000110) test_entry_id: .: (0.000092) test_get_all_by_type: .: (0.000092) test_gi: .: (0.000093) test_id_strings: .: (0.000169) test_list_ids: .: (0.000096) test_locus: .: (0.000096) test_words: .: (0.000172) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000164) test_accession: .: (0.000093) test_accessions: .: (0.000086) test_description: .: (0.000542) test_descriptions: .: (0.000089) test_entry_id: .: (0.000093) test_get_all_by_type: .: (0.000085) test_gi: .: (0.000082) test_id_strings: .: (0.000138) test_list_ids: .: (0.000088) test_locus: .: (0.000082) test_words: .: (0.000136) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000256) test_accession: .: (0.000075) test_accessions: .: (0.000068) test_description: .: (0.000065) test_descriptions: .: (0.000062) test_entry_id: .: (0.000072) test_get_all_by_type: .: (0.000069) test_gi: .: (0.000063) test_id_strings: .: (0.000086) test_list_ids: .: (0.000065) test_locus: .: (0.000063) test_words: .: (0.000079) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000143) test_accession: .: (0.000080) test_accessions: .: (0.000076) test_description: .: (0.000067) test_descriptions: .: (0.000069) test_entry_id: .: (0.000066) test_get: .: (0.000075) test_get_all_by_type: .: (0.000068) test_id_strings: .: (0.000116) test_list_ids: .: (0.000070) test_locus: .: (0.000068) test_sp: .: (0.000076) test_words: .: (0.000118) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000295) test_accession: .: (0.000085) test_accessions: .: (0.000077) test_description: .: (0.000070) test_descriptions: .: (0.000069) test_entry_id: .: (0.000068) test_get: .: (0.000077) test_get_all_by_type: .: (0.000069) test_id_strings: .: (0.000136) test_list_ids: .: (0.000070) test_locus: .: (0.000072) test_tr: .: (0.000080) test_words: .: (0.000152) Bio::TestFastaFirstName: test_first_name1: .: (0.000150) test_first_name_multi_identifier: .: (0.000226) test_first_name_single_worded_defintion: .: (0.000071) test_no_definition: .: (0.000063) test_space_before_first_name: .: (0.000066) test_tabbed_defintion: .: (0.000066) Bio::TestFastaFormat: test_aalen: .: (0.000170) test_aaseq: .: (0.000083) test_acc_version: .: (0.000109) test_accession: .: (0.000100) test_accessions: .: (0.000102) test_data: .: (0.000071) test_definition: .: (0.000067) test_entry: .: (0.000072) test_entry_id: .: (0.000091) test_entry_overrun: .: (0.000069) test_first_name: .: (0.000072) test_gi: .: (0.000098) test_identifiers: .: (0.000101) test_length: .: (0.000093) test_query: .: (0.000089) test_seq: .: (0.000076) Bio::TestFastaFormatConst: test_delimiter: .: (0.000131) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000178) test_data: .: (0.000079) test_definition: .: (0.000071) test_entry: .: (0.000071) test_entry_id: .: (0.000105) test_first_name: .: (0.000076) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000144) test_naseq: .: (0.000072) test_naseq_class: .: (0.000077) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000162) Bio::TestFastaInitialize: test_new_1: .: (0.000351) test_option: .: (0.000154) test_option_backward_compatibility: .: (0.000105) Bio::TestFastaNumericFormat: test_arg: .: (0.000181) test_data: .: (0.000101) test_definition: .: (0.000064) test_each: .: (0.000090) test_entry: .: (0.000063) test_entry_id: .: (0.000075) test_length: .: (0.000089) test_to_biosequence: .: (0.000669) Bio::TestFastaQuery: test_query: .: (0.000109) test_self_local: .: (0.000044) test_self_parser: .: (0.000040) test_self_remote: .: (0.000040) Bio::TestFastacmd: test_database: .: (0.000129) test_fastacmd: .: (0.000055) test_methods: .: (0.000071) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000867) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000619) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000673) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000660) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000714) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000643) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000697) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000733) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000770) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000751) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.001139) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001025) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000735) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000902) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000896) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000693) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000486) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000586) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.001964) test_error_probabilities_as_sanger: .: (0.002279) test_error_probabilities_as_solexa: .: (0.001725) test_quality_scores_as_illumina: .: (0.000229) test_quality_scores_as_sanger: .: (0.000213) test_quality_scores_as_solexa: .: (0.000227) test_validate_format: .: (0.000408) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000922) test_entry_id: .: (0.000593) test_error_probabilities: .: (0.045530) test_nalen: .: (0.000596) test_naseq: .: (0.000609) test_quality_scores: .: (0.001124) test_quality_string: .: (0.001972) test_roundtrip: .: (0.043192) test_seq: .: (0.000618) test_sequence_string: .: (0.000530) test_to_biosequence: .: (0.039666) test_to_biosequence_and_output: .: (0.003057) test_to_s: .: (0.000582) test_validate_format: .: (0.000724) test_validate_format_with_array: .: (0.000616) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000807) test_mask_20_with_empty_string: .: (0.000342) test_mask_20_with_longer_string: .: (0.000341) test_mask_20_with_x: .: (0.000332) test_mask_60: .: (0.000382) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.003192) test_error_probabilities_as_sanger: .: (0.002057) test_error_probabilities_as_solexa: .: (0.002221) test_quality_scores_as_illumina: .: (0.000329) test_quality_scores_as_sanger: .: (0.000295) test_quality_scores_as_solexa: .: (0.000357) test_validate_format: .: (0.000515) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.003083) test_error_probabilities_as_sanger: .: (0.002613) test_error_probabilities_as_solexa: .: (0.001864) test_quality_scores_as_illumina: .: (0.000347) test_quality_scores_as_sanger: .: (0.000319) test_quality_scores_as_solexa: .: (0.000319) test_validate_format: .: (0.000495) Bio::TestFeature: test_append: .: (0.000376) test_append_nil: .: (0.000133) test_assoc: .: (0.000142) test_each: .: (0.000118) test_feature: .: (0.000107) test_locations: .: (0.000197) test_new: .: (0.000116) test_position: .: (0.000113) test_qualifiers: .: (0.000110) Bio::TestFeatures: test_append: .: (0.000261) test_arg: .: (0.000136) test_each: .: (0.000130) test_features: .: (0.000134) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000816) test_aaindex2: .: (0.000253) test_blast: .: (0.000228) test_blastxml: .: (0.001339) test_embl: .: (0.000289) test_embl_oldrelease: .: (0.000272) test_fastaformat: .: (0.001052) test_fastanumericformat: .: (0.000183) test_fastq: .: (0.000210) test_genbank: .: (0.000240) test_genpept: .: (0.000259) test_hmmer: .: (0.000946) test_maxml_cluster: .: (0.002467) test_maxml_sequence: .: (0.000163) test_medline: .: (0.000182) test_prosite: .: (0.004186) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003348) test_transfac: .: (0.001172) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000257) test_auto_1arg_filename: .: (0.000356) test_auto_1arg_io: .: (0.000359) test_auto_1arg_io_with_block: .: (0.000556) test_auto_1arg_with_block: .: (0.000484) test_auto_2arg_filename_mode: .: (0.000325) test_auto_2arg_filename_mode_with_block: .: (0.000491) test_auto_3arg: .: (0.000306) test_auto_3arg_with_block: .: (0.000543) test_foreach: .: (0.000436) test_new_2arg_class: .: (0.000208) test_new_2arg_nil: .: (0.000299) test_open_0arg: .: (0.000159) test_open_1arg_class: .: (0.000167) test_open_1arg_filename: .: (0.000316) test_open_1arg_io: .: (0.000302) test_open_1arg_io_with_block: .: (0.000493) test_open_1arg_nil: .: (0.000195) test_open_1arg_with_block: .: (0.000480) test_open_2arg_autodetect: .: (0.000300) test_open_2arg_autodetect_io: .: (0.000302) test_open_2arg_autodetect_io_with_block: .: (0.000489) test_open_2arg_autodetect_with_block: .: (0.000495) test_open_2arg_class: .: (0.000212) test_open_2arg_class_io: .: (0.000206) test_open_2arg_class_io_with_block: .: (0.000439) test_open_2arg_class_with_block: .: (0.000390) test_open_2arg_filename_mode: .: (0.000312) test_open_2arg_filename_mode_with_block: .: (0.000487) test_open_3arg: .: (0.000543) test_open_3arg_with_block: .: (0.001139) test_open_4arg: .: (0.001501) test_to_a: .: (0.000475) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000387) test_close: .: (0.000185) test_dbclass: .: (0.000174) test_dbclass_eq: .: (0.000204) test_dbclass_nil: .: (0.000235) test_each: .: (0.000310) test_each_entry: .: (0.000405) test_ended_pos: .: (0.000270) test_entry_pos_flag: .: (0.000195) test_entry_raw: .: (0.000309) test_eof?: .: (0.000289) test_next_entry: .: (0.000347) test_path: .: (0.000182) test_pos: .: (0.000237) test_raw: .: (0.000301) test_rewind: .: (0.000250) test_start_pos: .: (0.000276) test_start_pos_ended_pos_not_recorded: .: (0.000317) test_to_io: .: (0.000195) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000292) test_simpleformat2: .: (0.000220) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000229) test_eof_false_after_prefetch: .: (0.000225) test_eof_false_first: .: (0.000148) test_eof_true: .: (0.000210) test_getc: .: (0.000153) test_getc_after_prefetch: .: (0.000153) test_gets: .: (0.000153) test_gets_equal_prefetch_gets: .: (0.000161) test_gets_paragraph_mode: .: (0.000211) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000380) test_gets_paragraph_mode_within_buffer: .: (0.000358) test_gets_rs: .: (0.000180) test_gets_rs_equal_prefetch_gets: .: (0.000186) test_gets_rs_within_buffer: .: (0.000276) test_pos: .: (0.000163) test_pos=: .: (0.000175) test_prefetch_buffer: .: (0.000153) test_prefetch_gets: .: (0.000165) test_prefetch_gets_with_arg: .: (0.000187) test_rewind: .: (0.000153) test_skip_spaces: .: (0.000165) test_to_io: .: (0.000157) test_ungetc: .: (0.000176) test_ungetc_after_prefetch: .: (0.000171) test_ungets: .: (0.000185) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000250) test_self_open_file: .: (0.000178) test_self_open_file_with_block: .: (0.032349) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000278) test_parse_file_open_arg_int_perm: .: (0.000134) test_parse_file_open_arg_int_perm_opt: .: (0.000126) test_parse_file_open_arg_integer: .: (0.000119) test_parse_file_open_arg_nil: .: (0.000117) test_parse_file_open_arg_opt: .: (0.000161) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000147) test_parse_file_open_arg_str: .: (0.000139) test_parse_file_open_arg_str_opt: .: (0.000151) test_parse_file_open_arg_str_perm: .: (0.000139) test_parse_file_open_arg_str_perm_opt: .: (0.000145) test_parse_file_open_arg_str_with_enc: .: (0.000145) test_parse_file_open_arg_str_with_ext_enc: .: (0.000140) test_parse_file_open_mode_integer: .: (0.000118) test_parse_file_open_mode_nil: .: (0.000132) test_parse_file_open_mode_str: .: (0.000128) test_parse_file_open_mode_str_with_enc: .: (0.000136) test_parse_file_open_mode_str_with_ext_enc: .: (0.000133) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000244) test_entry: .: (0.000143) test_entry_ended_pos: .: (0.000136) test_entry_pos_flag: .: (0.000155) test_entry_start_pos: .: (0.000129) test_get_entry: .: (0.000185) test_rewind: .: (0.000156) test_skip_leader: .: (0.000156) test_stream: .: (0.000121) test_stream_pos: .: (0.000159) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000260) test_delimiter_overrun: .: (0.000127) test_entry: .: (0.000178) test_entry_ended_pos: .: (0.000155) test_entry_ended_pos_default_nil: .: (0.000154) test_entry_start_pos: .: (0.000153) test_entry_start_pos_default_nil: .: (0.000143) test_get_entry: .: (0.000249) test_get_parsed_entry: .: (0.000271) test_header: .: (0.000130) test_skip_leader: .: (0.000178) test_skip_leader_without_header: .: (0.000175) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000339) test_entry_ended_pos: .: (0.000229) test_entry_start_pos: .: (0.000223) test_flag_to_fetch_header: .: (0.000212) test_get_entry: .: (0.000270) test_get_parsed_entry: .: (0.000290) test_rewind: .: (0.000254) test_skip_leader: .: (0.000169) Bio::TestGCGMsf: test_alignment: .: (0.000856) test_checksum: .: (0.000228) test_compcheck: .: (0.000229) test_date: .: (0.000228) test_description: .: (0.000233) test_entry_id: .: (0.000244) test_gap_length_weight: .: (0.000257) test_gap_weight: .: (0.000257) test_heading: .: (0.000260) test_length: .: (0.000245) test_seq_type: .: (0.000254) test_symbol_comparison_table: .: (0.003116) test_validate_checksum: .: (0.000838) Bio::TestGFF: test_record_class: .: (0.000429) test_records: .: (0.000312) Bio::TestGFF2: test_const_version: .: (0.001075) test_gff_version: .: (0.000343) test_metadata: .: (0.000352) test_metadata_size: .: (0.000673) test_records_size: .: (0.000338) test_to_s: .: (0.000524) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000229) test_attributes_case2: .: (0.000201) test_attributes_incompatible_backslash_semicolon: .: (0.000235) Bio::TestGFF2MetaData: test_data: .: (0.000202) test_directive: .: (0.000115) test_parse: .: (0.000132) Bio::TestGFF2Record: test_attribute: .: (0.000380) test_attribute_nonexistent: .: (0.000251) test_attributes: .: (0.000473) test_attributes_to_hash: .: (0.000283) test_comment_only?: .: (0.000267) test_delete_attribute: .: (0.000290) test_delete_attribute_multiple: .: (0.000300) test_delete_attribute_multiple2: .: (0.000515) test_delete_attribute_multiple_nil: .: (0.000275) test_delete_attribute_nil: .: (0.000270) test_delete_attribute_nonexistent: .: (0.000274) test_delete_attributes: .: (0.000468) test_delete_attributes_multiple: .: (0.000295) test_delete_attributes_nonexistent: .: (0.000269) test_end: .: (0.000256) test_eqeq: .: (0.000541) test_eqeq_false: .: (0.000625) test_feature: .: (0.000258) test_frame: .: (0.000246) test_get_attribute: .: (0.000306) test_get_attribute_nonexistent: .: (0.000240) test_get_attributes: .: (0.000446) test_get_attributes_nonexistent: .: (0.000245) test_replace_attributes: .: (0.000277) test_replace_attributes_multiple_multiple_over: .: (0.000280) test_replace_attributes_multiple_multiple_same: .: (0.000319) test_replace_attributes_multiple_multiple_two: .: (0.000438) test_replace_attributes_multiple_single: .: (0.000273) test_replace_attributes_nonexistent: .: (0.000275) test_replace_attributes_nonexistent_multiple: .: (0.000275) test_replace_attributes_single_multiple: .: (0.000288) test_score: .: (0.000449) test_self_parse: .: (0.000536) test_seqname: .: (0.000254) test_set_attribute: .: (0.000272) test_set_attribute_multiple: .: (0.000453) test_set_attribute_nonexistent: .: (0.000281) test_sort_attributes_by_tag!: .: (0.000320) test_sort_attributes_by_tag_bang_test2: .: (0.000305) test_sort_attributes_by_tag_bang_with_block: .: (0.000307) test_source: .: (0.000354) test_start: .: (0.000251) test_strand: .: (0.000248) test_to_s: .: (0.000354) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000236) test_comment_eq: .: (0.000130) test_comment_only?: .: (0.000133) test_comment_only_false: .: (0.000127) test_to_s: .: (0.000168) test_to_s_not_empty: .: (0.000195) Bio::TestGFF3: test_const_version: .: (0.000699) test_gff_version: .: (0.000372) test_records: .: (0.000633) test_sequence_regions: .: (0.000394) test_sequences: .: (0.000441) test_to_s: .: (0.000869) Bio::TestGFF3MetaData: test_data: .: (0.000188) test_directive: .: (0.000112) test_parse: .: (0.000136) Bio::TestGFF3Record: test_attributes: .: (0.000322) test_end: .: (0.000224) test_feature: .: (0.000220) test_frame: .: (0.000397) test_id: .: (0.000227) test_score: .: (0.000225) test_seqname: .: (0.000219) test_source: .: (0.000228) test_start: .: (0.000237) test_strand: .: (0.000261) test_to_s: .: (0.000553) test_to_s_attr_order_changed: .: (0.000371) Bio::TestGFF3RecordEscape: test_escape: .: (0.000236) test_escape_attribute: .: (0.000160) test_escape_seqid: .: (0.000163) test_unescape: .: (0.000164) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000326) test_eqeq: .: (0.000212) test_new_from_sequences_na: .: (0.000221) test_new_from_sequences_na_aa: .: (0.000284) test_new_from_sequences_na_aa_boundary_gap: .: (0.000363) test_new_from_sequences_na_aa_example: .: (0.000318) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000255) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000245) test_process_sequences_na: .: (0.000238) test_process_sequences_na_aa: .: (0.000230) test_process_sequences_na_aa_reverse_frameshift: .: (0.000230) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000240) test_process_sequences_na_aa_tooshort: .: (0.000348) test_process_sequences_na_tooshort: .: (0.000252) test_to_s: .: (0.000202) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000246) test_attributes_one: .: (0.000163) test_attributes_with_escaping: .: (0.000192) test_id_multiple: .: (0.000295) test_id_multiple2: .: (0.000270) test_id_replace: .: (0.000182) test_id_set: .: (0.000208) test_initialize_9: .: (0.000120) test_phase: .: (0.000182) test_score: .: (0.000167) test_to_s_void: .: (0.000152) Bio::TestGFF3RecordTarget: test_end: .: (0.000245) test_parse: .: (0.000221) test_start: .: (0.000134) test_strand: .: (0.000128) test_target_id: .: (0.000137) test_to_s: .: (0.000211) Bio::TestGFF3SequenceRegion: test_end: .: (0.000244) test_parse: .: (0.000225) test_seqid: .: (0.000162) test_start: .: (0.000134) test_to_s: .: (0.000207) Bio::TestGFFRecord: test_attributes: .: (0.000289) test_comment: .: (0.000163) test_end: .: (0.000157) test_feature: .: (0.000160) test_frame: .: (0.000160) test_score: .: (0.000162) test_seqname: .: (0.000160) test_source: .: (0.000161) test_start: .: (0.000161) test_strand: .: (0.000160) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000236) Bio::TestGeneAssociation: test_aspect: .: (0.000276) test_assigned_by: .: (0.000152) test_date: .: (0.000166) test_db: .: (0.000155) test_db_object_id: .: (0.000153) test_db_object_name: .: (0.000154) test_db_object_symbol: .: (0.000152) test_db_object_synonym: .: (0.000153) test_db_object_type: .: (0.000146) test_db_reference: .: (0.000153) test_evidence: .: (0.000152) test_goid: .: (0.000164) test_parser: .: (0.000833) test_qualifier: .: (0.000156) test_taxon: .: (0.000149) test_to_str: .: (0.000156) test_with: .: (0.000156) Bio::TestGenscanReport: test_date_run: .: (0.001171) test_gccontent: .: (0.000586) test_genscan_version: .: (0.000579) test_isochore: .: (0.000568) test_length: .: (0.000562) test_matrix: .: (0.000562) test_predictions_size: .: (0.000566) test_query_name: .: (0.000557) test_time: .: (0.000546) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000660) test_donor_score: .: (0.000557) test_exon_type: .: (0.000556) test_exon_type_long: .: (0.000577) test_first: .: (0.000562) test_initiation_score: .: (0.000571) test_last: .: (0.000564) test_number: .: (0.000597) test_p_value: .: (0.005185) test_phase: .: (0.000539) test_range: .: (0.000529) test_score: .: (0.000518) test_strand: .: (0.001314) test_t_score: .: (0.000523) test_termination_score: .: (0.000530) Bio::TestGenscanReportGene: test_aaseq: .: (0.000636) test_naseq: .: (0.001237) test_number: .: (0.000525) test_polyA: .: (0.000529) test_promoter: .: (0.000549) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000779) test_reports_ary_contents: .: (0.000578) Bio::TestHMMERReportConstants: test_rs: .: (0.000187) Bio::TestHMMERReportHit: test_accession: .: (0.000630) test_append_hsp: .: (0.000576) test_bit_score: .: (0.000725) test_definition: .: (0.000569) test_description: .: (0.000561) test_each: .: (0.000589) test_each_hsp: .: (0.000586) test_entry_id: .: (0.000567) test_evalue: .: (0.000863) test_hit: .: (0.000595) test_hit_id: .: (0.000571) test_hsps: .: (0.000575) test_num: .: (0.000561) test_score: .: (0.000568) test_target_def: .: (0.000592) test_target_id: .: (0.000802) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000638) test_each: .: (0.000838) test_each_hit: .: (0.001653) test_histogram: .: (0.000668) test_hits: .: (0.000587) test_hsps: .: (0.000595) test_parameter: .: (0.000606) test_program: .: (0.000630) test_query_info: .: (0.000610) test_statistical_detail: .: (0.000578) test_total_seq_searched: .: (0.000594) test_whole_seq_top_hits: .: (0.000579) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000769) test_histogram: .: (0.000679) test_statistical_detail: .: (0.000685) test_total_seq_searched: .: (0.000654) test_whole_seq_top_hit: .: (0.000687) Bio::TestHMMERReportHsp: test_accession: .: (0.000646) test_bit_score: .: (0.000589) test_csline: .: (0.000582) test_domain: .: (0.000576) test_evalue: .: (0.000573) test_flatseq: .: (0.000571) test_hmm_f: .: (0.000575) test_hmm_t: .: (0.000597) test_hmmseq: .: (0.000598) test_hsp: .: (0.005441) test_midline: .: (0.000687) test_query_frame: .: (0.000567) test_query_from: .: (0.000587) test_query_seq: .: (0.000566) test_query_to: .: (0.000559) test_rfline: .: (0.000564) test_score: .: (0.001222) test_seq_f: .: (0.000739) test_seq_ft: .: (0.000581) test_seq_t: .: (0.000570) test_set_alignment: .: (0.000550) test_targat_to: .: (0.000565) test_target_frame: .: (0.001036) test_target_from: .: (0.000696) test_target_seq: .: (0.000568) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000374) test_find_hetatm: .: (0.000233) test_hetatms: .: (0.000273) Bio::TestHeterogen: test_addAtom: .: (0.000296) test_each: .: (0.000219) test_each_hetatm: .: (0.000521) test_get_residue_id_from_atom: .: (0.000190) test_het_atom: .: (0.000167) test_iCode: .: (0.000207) test_inspect: .: (0.000250) test_resSeq: .: (0.000183) test_sort: .: (0.000258) test_square_bracket: .: (0.000211) test_to_s: .: (0.000282) test_update_resudue_id: .: (0.000188) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000480) test_find_heterogen: .: (0.000159) test_heterogens: .: (0.000170) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000269) test_match_description: .: (0.000177) test_match_evalue: .: (0.000175) test_match_ipr_description: .: (0.000172) test_match_ipr_id: .: (0.000180) test_match_match_end: .: (0.000176) test_match_match_start: .: (0.000168) test_match_method: .: (0.000172) test_matches_size: .: (0.000165) test_query_id: .: (0.000171) test_query_length: .: (0.000334) Bio::TestIprscanRawReport: test_entry_id: .: (0.001815) test_match_accession: .: (0.001219) test_match_crc64: .: (0.001380) test_match_date: .: (0.001250) test_match_description: .: (0.001587) test_match_evalue: .: (0.001494) test_match_go_terms: .: (0.001142) test_match_ipr_description: .: (0.001188) test_match_ipr_id: .: (0.001093) test_match_match_end: .: (0.001206) test_match_match_start: .: (0.001264) test_match_method: .: (0.007067) test_match_query_id: .: (0.001755) test_match_query_length: .: (0.001339) test_match_status: .: (0.001514) test_obj: .: (0.001281) test_query_id: .: (0.001250) test_query_length: .: (0.001408) test_self_reports_in_raw: .: (0.010052) Bio::TestIprscanReport: test_output_raw: .: (0.002605) test_to_raw: .: (0.001167) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.002090) test_match_accession: .: (0.003361) test_match_date: .: (0.001079) test_match_description: .: (0.001810) test_match_evalue: .: (0.001841) test_match_go_terms: .: (0.002621) test_match_ipr_description: .: (0.001473) test_match_ipr_id: .: (0.001932) test_match_match_end: .: (0.000747) test_match_match_start: .: (0.001548) test_match_method: .: (0.002157) test_match_status: .: (0.002937) test_matches_size: .: (0.001630) test_query_id: .: (0.002156) test_query_length: .: (0.000559) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000543) test_to_hash_match?: .: (0.000486) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.001996) Bio::TestKeggCompound: test_comment: .: (0.001063) test_dblinks_as_hash: .: (0.000342) test_dblinks_as_strings: .: (0.000284) test_entry_id: .: (0.000291) test_enzymes: .: (0.000491) test_formula: .: (0.000287) test_kcf: .: (0.000274) test_mass: .: (0.000288) test_name: .: (0.000508) test_names: .: (0.000289) test_pathways_as_hash: .: (0.000386) test_pathways_as_strings: .: (0.000309) test_reactions: .: (0.000490) test_remark: .: (0.000283) test_rpairs: .: (0.000283) Bio::TestKeggEnzyme: test_all_reac: .: (0.001059) test_classes: .: (0.000525) test_cofactors: .: (0.001164) test_comment: .: (0.000535) test_dblinks_as_hash: .: (0.000530) test_dblinks_as_strings: .: (0.000556) test_diseases: .: (0.000505) test_entry: .: (0.000518) test_entry_id: .: (0.000522) test_genes: .: (0.009607) test_genes_as_hash: .: (0.012573) test_genes_as_strings: .: (0.002406) test_inhibitors: .: (0.000406) test_iubmb_reactions: .: (0.000423) test_kegg_reactions: .: (0.000439) test_motifs: .: (0.000381) test_name: .: (0.000448) test_names: .: (0.000449) test_obsolete?: .: (0.000396) test_orthologs_as_hash: .: (0.000411) test_orthologs_as_strings: .: (0.000382) test_pathways_as_hash: .: (0.000515) test_pathways_as_strings: .: (0.000777) test_products: .: (0.000625) test_reaction: .: (0.000529) test_structures: .: (0.000647) test_substrates: .: (0.000531) test_sysname: .: (0.000522) Bio::TestKeggGenesDblinks: test_data: .: (0.000307) test_dblinks_0: .: (0.000219) test_dblinks_1: .: (0.000159) test_dblinks_2: .: (0.000160) Bio::TestKeggGenesStructure: test_data: .: (0.000255) test_ids: .: (0.000213) test_ids_in_array: .: (0.000187) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004619) test_graphics__size: .: (0.004183) test_id: .: (0.004168) test_link: .: (0.004202) test_name: .: (0.004312) test_reaction: .: (0.004270) test_type: .: (0.009870) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.005452) test_graphics__size: .: (0.004322) test_id: .: (0.004196) test_link: .: (0.004308) test_name: .: (0.004475) test_reaction: .: (0.004107) test_type: .: (0.004011) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.004276) test_category: .: (0.007715) test_entry_id: .: (0.005158) test_fgcolor=: .: (0.004406) test_height=: .: (0.004381) test_label=: .: (0.004404) test_shape=: .: (0.004497) test_width=: .: (0.004247) test_x=: .: (0.004169) test_y=: .: (0.008530) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.007652) test_graphics__size: .: (0.005161) test_id: .: (0.004375) test_link: .: (0.004297) test_name: .: (0.004887) test_reaction: .: (0.004697) test_type: .: (0.004844) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000283) test_graphics=: .: (0.000173) test_id=: .: (0.000203) test_link=: .: (0.000163) test_name=: .: (0.000148) test_reaction=: .: (0.000139) test_type=: .: (0.000136) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000267) test_category=: .: (0.000218) test_entry_id=: .: (0.000224) test_fgcolor=: .: (0.000208) test_height=: .: (0.000173) test_label=: .: (0.000177) test_pathway=: .: (0.000144) test_shape=: .: (0.000187) test_width=: .: (0.000211) test_x=: .: (0.000198) test_y=: .: (0.000164) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.005106) test_coords: .: (0.006556) test_fgcolor: .: (0.005766) test_height: .: (0.004875) test_name: .: (0.004532) test_type: .: (0.006677) test_width: .: (0.004771) test_x: .: (0.004399) test_y: .: (0.004229) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.004211) test_coords: .: (0.005934) test_fgcolor: .: (0.005428) test_height: .: (0.004786) test_name: .: (0.004504) test_type: .: (0.004579) test_width: .: (0.006213) test_x: .: (0.008704) test_y: .: (0.008254) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000445) test_coords=: .: (0.000236) test_fgcolor=: .: (0.000208) test_height=: .: (0.000206) test_name=: .: (0.000225) test_type=: .: (0.000206) test_width=: .: (0.000194) test_x=: .: (0.000208) test_y=: .: (0.000199) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.008286) test_entries__size: .: (0.006464) test_image: .: (0.004997) test_link: .: (0.004485) test_name: .: (0.004328) test_number: .: (0.004321) test_org: .: (0.004292) test_reactions=: .: (0.004192) test_reactions__size: .: (0.003966) test_relations=: .: (0.004152) test_relations__size: .: (0.006080) test_title: .: (0.005048) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.008697) test_name: .: (0.008663) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000223) test_initialize_0: .: (0.000114) test_initialize_1: .: (0.000128) test_initialize_2: .: (0.000130) test_name=: .: (0.000154) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.004138) test_name: .: (0.004090) test_products: .: (0.004361) test_substrates: .: (0.006387) test_type: .: (0.005199) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000256) test_name=: .: (0.000159) test_products=: .: (0.000150) test_substraces=: .: (0.000294) test_type=: .: (0.000153) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000263) test_entry_id=: .: (0.000174) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.004509) test_entry2: .: (0.004385) test_name: .: (0.004372) test_type: .: (0.004420) test_value: .: (0.004028) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000205) test_node1=: .: (0.000171) test_node2=: .: (0.000167) test_rel=: .: (0.000172) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000247) test_entry2=: .: (0.000148) test_name=: .: (0.000150) test_type=: .: (0.000148) test_value=: .: (0.000158) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.009998) test_name: .: (0.009442) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000234) test_initialize_0: .: (0.000116) test_initialize_1: .: (0.000118) test_initialize_2: .: (0.000243) test_name=: .: (0.000155) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000221) test_initialize_0: .: (0.000111) test_initialize_1: .: (0.000114) test_initialize_2: .: (0.000113) test_name=: .: (0.000147) Bio::TestKeggModule: test_compounds: .: (0.000732) test_compounds_as_hash: .: (0.000268) test_compounds_as_strings: .: (0.000241) test_definition: .: (0.000252) test_entry_id: .: (0.000235) test_keggclass: .: (0.000243) test_name: .: (0.000250) test_new: .: (0.000235) test_orthologs: .: (0.000429) test_orthologs_as_array: .: (0.000308) test_orthologs_as_hash: .: (0.000264) test_orthologs_as_strings: .: (0.000241) test_pathways: .: (0.000234) test_pathways_as_hash: .: (0.000232) test_pathways_as_strings: .: (0.000228) test_reactions: .: (0.000314) test_reactions_as_hash: .: (0.000259) test_reactions_as_strings: .: (0.000233) Bio::TestKeggOrthology: test_dblinks: .: (0.001032) test_dblinks_as_hash: .: (0.000435) test_dblinks_as_strings: .: (0.000367) test_definition: .: (0.000379) test_entry_id: .: (0.000371) test_genes_as_hash: .: (0.007095) test_genes_as_strings: .: (0.004211) test_keggclass: .: (0.001204) test_keggclasses: .: (0.000456) test_modules: .: (0.000362) test_modules_as_hash: .: (0.000351) test_modules_as_strings: .: (0.000360) test_name: .: (0.000371) test_names: .: (0.000366) test_pathways_as_strings: .: (0.000358) test_pathways_in_keggclass: .: (0.000439) test_references: .: (0.000545) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000599) test_compounds_as_strings: .: (0.000239) test_dblinks_as_hash: .: (0.000233) test_dblinks_as_strings: .: (0.000445) test_description: .: (0.000255) test_diseases_as_hash: .: (0.000229) test_diseases_as_strings: .: (0.000225) test_entry_id: .: (0.000251) test_enzymes_as_strings: .: (0.000240) test_genes_as_hash: .: (0.000246) test_genes_as_strings: .: (0.000241) test_keggclass: .: (0.000266) test_ko_pathway: .: (0.000261) test_modules_as_hash: .: (0.000313) test_modules_as_strings: .: (0.000244) test_name: .: (0.000242) test_organism: .: (0.000241) test_orthologs_as_hash: .: (0.000382) test_orthologs_as_strings: .: (0.000223) test_pathways_as_hash: .: (0.000236) test_pathways_as_strings: .: (0.000229) test_reactions_as_hash: .: (0.000230) test_reactions_as_strings: .: (0.000235) test_references: .: (0.000246) test_rel_pathways_as_hash: .: (0.000290) test_rel_pathways_as_strings: .: (0.000259) Bio::TestKeggReaction: test_definition: .: (0.000832) test_entry_id: .: (0.000264) test_enzymes: .: (0.000262) test_equation: .: (0.000256) test_name: .: (0.000441) test_orthologs_as_hash: .: (0.000294) test_orthologs_as_strings: .: (0.000249) test_pathways_as_hash: .: (0.000260) test_pathways_as_strings: .: (0.000243) test_rpairs_as_hash: .: (0.000294) test_rpairs_as_strings: .: (0.000271) test_rpairs_as_tokens: .: (0.000339) Bio::TestLasergene: test_methods: .: (0.004358) Bio::TestLocations: test_complement: .: (0.000276) test_hat: .: (0.000184) test_normal: .: (0.000176) test_replace_single_base: .: (0.000155) test_should_not_modify_argument: .: (0.000149) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002260) test_locations_to_s: .: (0.003681) Bio::TestMEDLINE: test_authors: .: (0.000618) test_authors_with_last_name_all_caps: .: (0.000157) test_authors_with_suffix: .: (0.000158) Bio::TestMEDLINE_20146148: test_ab: .: (0.000727) test_ad: .: (0.000302) test_au: .: (0.001039) test_authors: .: (0.000522) test_doi: .: (0.000311) test_dp: .: (0.000295) test_ip: .: (0.000296) test_mh: .: (0.000315) test_pages: .: (0.000327) test_pg: .: (0.000298) test_pii: .: (0.000829) test_pmid: .: (0.000460) test_pt: .: (0.000336) test_reference: .: (0.000450) test_self_new: .: (0.000311) test_so: .: (0.000290) test_ta: .: (0.000296) test_ti: .: (0.000497) test_ui: .: (0.000299) test_vi: .: (0.000284) test_year: .: (0.000293) Bio::TestMapSimple: test_attributes: .: (0.000259) Bio::TestMapping: test_add_mapping_as_map: .: (0.000333) test_add_mapping_as_marker: .: (0.000205) test_contains_marker?: .: (0.000171) test_mapped_to?: .: (0.000158) test_mapping_location_comparison: .: (0.000342) test_mappings_as_map_each: .: (0.000370) test_mappings_as_marker_each: .: (0.000208) test_mappings_on: .: (0.000200) test_multiple_mappings_between_same_marker_and_map: .: (0.000294) test_positions_on: .: (0.000221) test_raise_error_kind_of: .: (0.000339) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000318) test_check_options_with_invalid_opts: .: (0.000244) test_check_options_with_valid_opts: .: (0.000283) test_command_to_be_run: .: (0.000210) test_config_defaults: .: (0.000182) test_minimal_config: .: (0.000201) test_more_config: .: (0.000191) test_run: .: (0.000142) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000702) test_report_has_motifs: .: (0.000249) Bio::TestModel: test_addChain: .: (0.000216) test_comp: .: (0.000167) test_each: .: (0.000166) test_each_chain: .: (0.000145) test_inspect: .: (0.000141) test_rehash: .: (0.000123) test_square_brace: .: (0.000138) test_to_s: .: (0.000138) Bio::TestModelFinder: test_find_model: .: (0.000253) Bio::TestMotif: test_creation_and_attributes: .: (0.000266) test_length: .: (0.000115) Bio::TestMyGraph: test_cliquishness: .: (0.000368) Bio::TestNA: test_accessor: .: (0.000186) test_na: .: (0.000123) test_name: .: (0.000123) test_names: .: (0.000122) test_to_re: .: (0.000240) test_weight: .: (0.000140) test_weight_rna: .: (0.000131) Bio::TestNAConstants: test_NAMES: .: (0.000213) test_NAMES_1_to_name: .: (0.000123) test_WEIGHT: .: (0.000129) Bio::TestNATranslate: test_translate: .: (0.000378) test_translate_1: .: (0.000190) test_translate_2: .: (0.000145) test_translate_3: .: (0.000143) test_translate_4: .: (0.000202) test_translate_5: .: (0.000145) test_translate_6: .: (0.000140) Bio::TestNCBIDB: test_fetch: .: (0.000258) test_p_entry2hash: .: (0.000111) test_p_subtag2array: .: (0.000099) test_p_toptag2array: .: (0.000100) Bio::TestNewick: test_reparse: .: (0.000982) test_reparse_before_lazy_parsing: .: (0.000400) test_string_tree: .: (0.000585) Bio::TestNewick2: test_string_tree: .: (0.000510) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000206) test_parse_newick_leaf: .: (0.000204) test_parse_newick_tokenize: .: (0.000305) Bio::TestNexus: test_nexus: .: (0.006120) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000263) test_uncapitalized_letter_Q32725_9POAL: .: (0.000171) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000246) test_load_parameters: .: (0.000163) test_parameters: .: (0.000116) test_set_default_parameters: .: (0.000153) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.001716) test_expected_parameters_set_in_control_file: .: (0.001029) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000215) test_new_with_parameters: .: (0.000163) test_new_with_two_argument: .: (0.000159) test_new_without_argument: .: (0.000142) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.005020) test_rates_hundred_and_fiftieth_position: .: (0.000754) test_rates_last_position: .: (0.001748) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.001935) test_tree: .: (0.000557) test_tree_length: .: (0.000524) test_tree_log_likelihood: .: (0.000517) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000760) test_parameters_should_be_loaded_from_control: .: (0.000258) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001619) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000584) test_dN_dS: .: (0.000198) test_kappa: .: (0.000199) test_lnL: .: (0.000199) test_m3_classes: .: (0.000270) test_m3_lnL: .: (0.000204) test_m3_to_s: .: (0.000193) test_m3_tree: .: (0.000296) test_omega: .: (0.000200) test_to_s: .: (0.000192) test_tree: .: (0.000290) test_tree_length: .: (0.000202) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000662) test_p: .: (0.000329) test_position: .: (0.000320) test_probability: .: (0.000326) test_w: .: (0.000309) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000637) test_graph_omega: .: (0.000369) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000262) test_footer: .: (0.000193) test_header: .: (0.000188) test_initialize: .: (0.000200) test_models: .: (0.000215) test_nb_sites: .: (0.000516) test_num_codons: .: (0.000212) test_num_sequences: .: (0.000213) test_significant: .: (0.000401) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000666) test_nb_sites: .: (0.000268) test_significant: .: (0.000204) test_sites: .: (0.000722) Bio::TestPDB: test_accession: .: (0.001061) test_addModel: .: (0.000566) test_authors: .: (0.001407) test_bracket: .: (0.000576) test_classification: .: (0.000573) test_dbref: .: (0.000645) test_definition: .: (0.000565) test_each: .: (0.000641) test_each_model: .: (0.000584) test_entry_id: .: (0.000569) test_helix: .: (0.000621) test_inspect: .: (0.000587) test_jrnl: .: (0.000562) test_keywords: .: (0.000597) test_record: .: (0.000562) test_remark: .: (0.000713) test_seqres: .: (0.000765) test_sheet: .: (0.000762) test_ssbond: .: (0.000583) test_to_s: .: (0.000749) test_turn: .: (0.000597) test_version: .: (0.000586) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000280) test_U12: .: (0.000140) test_U13: .: (0.000165) test_U22: .: (0.000167) test_U23: .: (0.000168) test_U33: .: (0.000162) test_altLoc: .: (0.000165) test_chainID: .: (0.000162) test_charge: .: (0.000164) test_element: .: (0.000152) test_iCode: .: (0.000156) test_name: .: (0.000163) test_resName: .: (0.000162) test_resSeq: .: (0.000161) test_segID: .: (0.000164) test_serial: .: (0.000162) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000245) test_anisou: .: (0.000135) test_chainID: .: (0.000129) test_charge: .: (0.000130) test_comparable: .: (0.000162) test_do_parse: .: (0.000133) test_element: .: (0.000130) test_iCode: .: (0.000126) test_name: .: (0.000129) test_occupancy: .: (0.000161) test_original_data: .: (0.000133) test_record_name: .: (0.000128) test_resName: .: (0.000127) test_resSeq: .: (0.000128) test_residue: .: (0.000129) test_segID: .: (0.000126) test_serial: .: (0.000126) test_sigatm: .: (0.000128) test_tempFactor: .: (0.000145) test_ter: .: (0.000129) test_to_a: .: (0.000139) test_to_s: .: (0.000163) test_x: .: (0.000143) test_xyz: .: (0.000176) test_y: .: (0.000143) test_z: .: (0.000142) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000261) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000257) test_idcode: .: (0.000141) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000288) test_chainID2: .: (0.000184) test_icode1: .: (0.000178) test_icode2: .: (0.000159) test_measure: .: (0.000160) test_modNum: .: (0.000158) test_pep1: .: (0.000157) test_pep2: .: (0.000156) test_seqNum1: .: (0.000158) test_seqNum2: .: (0.000156) test_serNum: .: (0.000161) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000271) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000270) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000270) test_alpha: .: (0.000140) test_b: .: (0.000141) test_beta: .: (0.000137) test_c: .: (0.000136) test_gamma: .: (0.000158) test_sGroup: .: (0.000141) test_z: .: (0.000137) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000286) test_database: .: (0.000178) test_dbAccession: .: (0.000202) test_dbIdCode: .: (0.000172) test_dbseqBegin: .: (0.000120) test_dbseqEnd: .: (0.000092) test_idCode: .: (0.000095) test_idbnsBeg: .: (0.000094) test_insertBegin: .: (0.000092) test_insertEnd: .: (0.000093) test_seqBegin: .: (0.000091) test_seqEnd: .: (0.000088) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000153) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000140) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000147) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000135) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000145) test_depDate: .: (0.000081) test_idCode: .: (0.000076) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000171) test_hetID: .: (0.000080) test_iCode: .: (0.000080) test_numHetAtoms: .: (0.000080) test_seqNum: .: (0.000075) test_text: .: (0.000081) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000147) test_anisou: .: (0.000074) test_chainID: .: (0.000068) test_charge: .: (0.000065) test_comparable: .: (0.000086) test_do_parse: .: (0.000069) test_element: .: (0.000064) test_iCode: .: (0.000065) test_name: .: (0.000064) test_occupancy: .: (0.000080) test_original_data: .: (0.000070) test_record_name: .: (0.000064) test_resName: .: (0.000064) test_resSeq: .: (0.000064) test_residue: .: (0.000070) test_segID: .: (0.000065) test_serial: .: (0.000062) test_sigatm: .: (0.000065) test_tempFactor: .: (0.000075) test_ter: .: (0.000066) test_to_a: .: (0.000068) test_to_s: .: (0.000087) test_x: .: (0.000076) test_xyz: .: (0.000083) test_y: .: (0.000075) test_z: .: (0.000072) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000200) test_ChainH: .: (0.000109) test_ICode1: .: (0.000106) test_altLoc1: .: (0.000125) test_altLoc2: .: (0.000105) test_altLocH: .: (0.000103) test_chainID2: .: (0.000102) test_iCode2: .: (0.000107) test_iCodeH: .: (0.000106) test_name1: .: (0.000109) test_name2: .: (0.000103) test_nameH: .: (0.000102) test_resName1: .: (0.000105) test_resName2: .: (0.000107) test_resSeq1: .: (0.000107) test_resSeq2: .: (0.006133) test_resSeqH: .: (0.000109) test_sym1: .: (0.000101) test_sym2: .: (0.000114) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000167) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000177) test_altLoc2: .: (0.000095) test_chainID1: .: (0.000091) test_chainID2: .: (0.000087) test_iCode1: .: (0.000088) test_iCode2: .: (0.000090) test_name1: .: (0.000088) test_name2: .: (0.000088) test_resName1: .: (0.000086) test_resName2: .: (0.000086) test_resSeq1: .: (0.000109) test_resSeq2: .: (0.000089) test_sym1: .: (0.000087) test_sym2: .: (0.000085) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000165) test_numCoord: .: (0.000073) test_numHelix: .: (0.000067) test_numHet: .: (0.000066) test_numRemark: .: (0.000066) test_numSeq: .: (0.000064) test_numSheet: .: (0.000064) test_numSite: .: (0.000064) test_numTer: .: (0.000063) test_numTurn: .: (0.000066) test_numXform: .: (0.000064) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000137) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000163) test_comment: .: (0.000085) test_iCode: .: (0.000078) test_idCode: .: (0.000104) test_resName: .: (0.000081) test_seqNum: .: (0.000079) test_stdRes: .: (0.000077) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000166) test_Mn2: .: (0.000072) test_Mn3: .: (0.000064) test_Vn: .: (0.000063) test_iGiven: .: (0.000065) test_serial: .: (0.000059) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000142) test_Mn2: .: (0.000067) test_Mn3: .: (0.000062) test_Vn: .: (0.000067) test_iGiven: .: (0.000063) test_serial: .: (0.000061) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000138) test_Mn2: .: (0.000068) test_Mn3: .: (0.000064) test_Vn: .: (0.000080) test_iGiven: .: (0.000068) test_serial: .: (0.000068) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000159) test_rIdCode: .: (0.000078) test_repDate: .: (0.000070) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000147) test_On2: .: (0.000068) test_On3: .: (0.000062) test_Tn: .: (0.000061) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000149) test_modId: .: (0.000077) test_modNum: .: (0.000071) test_modType: .: (0.000069) test_record: .: (0.000073) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000134) test_text: .: (0.000067) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000477) test_Sn2: .: (0.000071) test_Sn3: .: (0.000063) test_Un: .: (0.000060) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000139) test_Sn2: .: (0.000065) test_Sn3: .: (0.000062) test_Un: .: (0.000059) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000136) test_Sn2: .: (0.000063) test_Sn3: .: (0.000062) test_Un: .: (0.000061) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000167) test_conflict: .: (0.000086) test_database: .: (0.000088) test_dbIdCode: .: (0.000081) test_dbRes: .: (0.000080) test_dbSeq: .: (0.000079) test_iCode: .: (0.000080) test_idCode: .: (0.000079) test_resName: .: (0.000079) test_seqNum: .: (0.000078) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000344) test_numRes: .: (0.000090) test_resName: .: (0.000089) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000180) test_curChainId: .: (0.000102) test_curICode: .: (0.000098) test_curResName: .: (0.000095) test_curResSeq: .: (0.000096) test_endChainID: .: (0.000096) test_endICode: .: (0.000097) test_endResName: .: (0.000095) test_endSeqNum: .: (0.000094) test_initChainID: .: (0.000096) test_initICode: .: (0.000095) test_initResName: .: (0.000095) test_initSeqNum: .: (0.000257) test_numStrands: .: (0.000099) test_prevAtom: .: (0.000096) test_prevChainId: .: (0.000092) test_prevICode: .: (0.000094) test_prevResName: .: (0.000096) test_prevResSeq: .: (0.000116) test_sense: .: (0.000097) test_sheetID: .: (0.000099) test_strand: .: (0.000096) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000192) test_chainID: .: (0.000090) test_charge: .: (0.000086) test_element: .: (0.000084) test_iCode: .: (0.000082) test_name: .: (0.000083) test_resName: .: (0.000084) test_resSeq: .: (0.000082) test_segID: .: (0.000083) test_serial: .: (0.000278) test_sigOcc: .: (0.000086) test_sigTemp: .: (0.000083) test_sigX: .: (0.000082) test_sigY: .: (0.000083) test_sigZ: .: (0.000082) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000184) test_SigmaU12: .: (0.000087) test_SigmaU13: .: (0.000084) test_SigmaU22: .: (0.000082) test_SigmaU23: .: (0.000082) test_SigmaU33: .: (0.000080) test_altLoc: .: (0.000083) test_chainID: .: (0.000082) test_charge: .: (0.002695) test_element: .: (0.000112) test_iCode: .: (0.000092) test_name: .: (0.001256) test_resName: .: (0.000109) test_resSeq: .: (0.001199) test_segID: .: (0.000099) test_serial: .: (0.000089) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.001165) test_chainID2: .: (0.000121) test_chainID3: .: (0.000102) test_chainID4: .: (0.000789) test_iCode1: .: (0.000103) test_iCode2: .: (0.001203) test_iCode3: .: (0.001214) test_iCode4: .: (0.000108) test_numRes: .: (0.000130) test_resName1: .: (0.000105) test_resName2: .: (0.001106) test_resName3: .: (0.000108) test_resName4: .: (0.000098) test_seq1: .: (0.001115) test_seq2: .: (0.000107) test_seq3: .: (0.001107) test_seq4: .: (0.000120) test_seqNum: .: (0.001186) test_siteID: .: (0.000110) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.001037) test_altLoc2: .: (0.000102) test_atom1: .: (0.000112) test_atom2: .: (0.000087) test_chainID1: .: (0.000988) test_chainID2: .: (0.000101) test_iCode1: .: (0.000090) test_iCode2: .: (0.000086) test_resName1: .: (0.000111) test_resName2: .: (0.000089) test_resSeq1: .: (0.000995) test_resSeq2: .: (0.001059) test_sym1: .: (0.000093) test_sym2: .: (0.000085) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.002149) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.001188) test_sIdCode: .: (0.000097) test_sprsdeDate: .: (0.001027) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000203) test_iCode: .: (0.000770) test_resName: .: (0.000106) test_resSeq: .: (0.000083) test_serial: .: (0.000076) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000183) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.001090) test_t1: .: (0.000106) test_t2: .: (0.000081) test_t3: .: (0.000106) test_text: .: (0.000081) Bio::TestPROSITE: test_ac: .: (0.005420) test_cc: .: (0.003204) test_de: .: (0.000770) test_division: .: (0.001720) test_dr: .: (0.013143) test_dt: .: (0.000691) test_false_neg: .: (0.000690) test_false_pos: .: (0.000679) test_false_positive_sequences: .: (0.000794) test_list_falsenegative: .: (0.015095) test_list_falsepositive: .: (0.013645) test_list_potentialhit: .: (0.011239) test_list_truepositive: .: (0.012847) test_list_unknown: .: (0.011668) test_list_xref: .: (0.009730) test_ma: .: (0.000639) test_max_repeat: .: (0.000670) test_name: .: (0.000613) test_nr: .: (0.000667) test_pa: .: (0.000655) test_pa2re: .: (0.000665) test_partial: .: (0.000694) test_pdb_xref: .: (0.000637) test_pdoc_xref: .: (0.000621) test_positive: .: (0.000772) test_positive_hits: .: (0.000843) test_positive_sequences: .: (0.000975) test_release: .: (0.000865) test_ru: .: (0.000834) test_self_pa2re: .: (0.000860) test_site: .: (0.000838) test_skip_flag: .: (0.000867) test_swissprot_release_number: .: (0.001053) test_swissprot_release_sequences: .: (0.000932) test_taxon_range: .: (0.003351) test_total: .: (0.000907) test_total_hits: .: (0.000858) test_total_sequences: .: (0.001636) test_unknown: .: (0.000786) test_unknown_hits: .: (0.001885) test_unknown_sequences: .: (0.000869) Bio::TestPROSITEConst: test_delimiter: .: (0.000190) test_tagsize: .: (0.000060) Bio::TestPTS1: test_function_set: .: (0.000161) test_function_set_number_1: .: (0.000080) test_function_set_number_2: .: (0.000884) test_function_set_number_3: .: (0.000072) test_function_show: .: (0.000061) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000132) Bio::TestPTS1New: test_fungi: .: (0.000401) test_general: .: (0.000070) test_metazoa: .: (0.000065) Bio::TestQualifier: test_qualifier: .: (0.000154) test_value: .: (0.000057) Bio::TestREBASE: test_methods: .: (0.001319) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001216) test_bit_score: .: (0.000449) test_evalue: .: (0.000433) test_gaps: .: (0.000457) test_hit_from: .: (0.000462) test_hit_to: .: (0.000456) test_hseq: .: (0.000459) test_identity: .: (0.000440) test_midline: .: (0.000458) test_percent_identity: .: (0.000438) test_positive: .: (0.000539) test_qseq: .: (0.000468) test_query_from: .: (0.000439) test_query_to: .: (0.000436) test_score: .: (0.000414) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000470) test_hits_size: .: (0.000929) test_iterations_size: .: (0.000895) test_program: .: (0.000392) test_query_def: .: (0.000869) test_query_len: .: (0.000870) test_version: .: (0.000377) test_version_date: .: (0.000367) test_version_number: .: (0.000365) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000560) test_definition: .: (0.000463) test_evalue: .: (0.000457) test_hsps_size: .: (0.000413) test_identity: .: (0.000451) test_lap_at: .: (0.000487) test_len: .: (0.000905) test_midline: .: (0.000507) test_overlap: .: (0.000457) test_query_end: .: (0.000470) test_query_seq: .: (0.000472) test_query_start: .: (0.000478) test_target_def: .: (0.000440) test_target_end: .: (0.000459) test_target_len: .: (0.000508) test_target_seq: .: (0.000512) test_target_start: .: (0.000519) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000422) test_get_entry: .: (0.000348) test_rewind: .: (0.000112) test_skip_leader: .: (0.000174) Bio::TestReference: test_abstract: .: (0.000160) test_affiliations: .: (0.000066) test_authors: .: (0.000060) test_format_bibitem: .: (0.000125) test_format_bibtex: .: (0.000163) test_format_bibtex_with_arguments: .: (0.000177) test_format_cell: .: (0.000100) test_format_current: .: (0.000082) test_format_endnote: .: (0.000095) test_format_general: .: (0.000085) test_format_genome_biol: .: (0.000079) test_format_genome_res: .: (0.000091) test_format_nar: .: (0.000078) test_format_nature: .: (0.000117) test_format_rd: .: (0.000091) test_format_science: .: (0.000126) test_format_trends: .: (0.000070) test_issue: .: (0.000058) test_journal: .: (0.000056) test_mesh: .: (0.000058) test_pages: .: (0.000068) test_pubmed: .: (0.000060) test_pubmed_url: .: (0.000061) test_url: .: (0.000070) test_volume: .: (0.000056) test_year: .: (0.000054) Bio::TestReference_noURL: test_format_endnote: .: (0.000229) test_url: .: (0.000091) Bio::TestReferences: test_append: .: (0.000189) test_each: .: (0.000079) Bio::TestRelation: test_comparison_operator: .: (0.000180) test_uniq: .: (0.000088) Bio::TestResidue: test_addAtom: .: (0.000255) test_each: .: (0.000171) test_each_atom: .: (0.000155) test_get_residue_id_from_atom: .: (0.000147) test_het_atom: .: (0.000108) test_iCode: .: (0.000101) test_inspect: .: (0.000112) test_resSeq: .: (0.000100) test_sort: .: (0.000170) test_square_bracket: .: (0.000115) test_to_s: .: (0.000192) test_update_resudue_id: .: (0.000116) Bio::TestResidueFinder: test_each_residue: .: (0.000230) test_find_residue: .: (0.000114) test_residues: .: (0.000100) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.124496) test_cut_from_bio_sequence_na: .: (0.026795) test_cut_without_permutations: .: (0.019194) test_view_ranges: .: (0.015787) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000929) test_cuts_after_remove_incomplete_cuts: .: (0.000427) test_strands_for_display: .: (0.001608) test_strands_for_display_current: .: (0.000451) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000418) test_fragments_for_display_1: .: (0.000555) test_fragments_for_display_10: .: (0.000612) test_fragments_for_display_2: .: (0.000530) test_fragments_for_display_3: .: (0.000734) test_fragments_for_display_4: .: (0.000632) test_fragments_for_display_5: .: (0.000447) test_fragments_for_display_6: .: (0.000474) test_fragments_for_display_7: .: (0.000475) test_fragments_for_display_8: .: (0.003522) test_fragments_for_display_9: .: (0.000424) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000331) test_obj_3: .: (0.000166) test_obj_7: .: (0.000371) test_obj_z: .: (0.000188) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000270) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000188) test_bracket_eq: .: (0.000160) test_concat: .: (0.000093) test_delete: .: (0.000090) test_dup: .: (0.000114) test_each: .: (0.000137) test_eqeq: .: (0.000279) test_eqeq_false: .: (0.000074) test_eqeq_other: .: (0.000064) test_eqeq_self: .: (0.000061) test_include?: .: (0.000097) test_internal_data: .: (0.000068) test_internal_data_eq: .: (0.000117) test_length: .: (0.000069) test_ltlt: .: (0.000074) test_ltlt_larger: .: (0.000073) test_ltlt_middle: .: (0.000072) test_plus: .: (0.000123) test_plus_error: .: (0.000100) test_push: .: (0.000079) test_reverse_each: .: (0.000099) test_self_bracket: .: (0.000083) test_self_new: .: (0.000083) test_size: .: (0.000104) test_sort!: .: (0.000064) test_to_a: .: (0.000067) test_uniq!: .: (0.000061) test_unshift: .: (0.000122) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003769) test_complement: .: (0.003002) test_complement_with_cut_symbols: .: (0.003380) test_cut_locations: .: (0.003164) test_cut_locations_in_enzyme_notation: .: (0.003075) test_primary: .: (0.002953) test_primary_with_cut_symbols: .: (0.002872) test_to_re: .: (0.002755) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000777) test_align_with_cuts: .: (0.000537) test_argument_error: .: (0.000806) test_ds: .: (0.000582) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000374) test_complement: .: (0.000136) test_contents: .: (0.000175) test_primary: .: (0.000122) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000324) test_complement: .: (0.000161) test_contents: .: (0.000171) test_primary: .: (0.000142) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000310) test_contents: .: (0.000104) test_primary: .: (0.000139) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000235) test_complement_to_array_index: .: (0.000203) test_complement_to_array_index_class: .: (0.000146) test_contents: .: (0.000103) test_primary: .: (0.000133) test_primary_to_array_index: .: (0.000483) test_primary_to_array_index_class: .: (0.000149) test_to_array_index: .: (0.000318) test_to_array_index_class: .: (0.000253) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000315) test_rebase: .: (0.000141) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000904) test_creation_with_no_cuts: .: (0.000354) test_cut_locations: .: (0.000305) test_cut_locations_in_enzyme_notation: .: (0.000336) test_orientation: .: (0.000621) test_pattern: .: (0.000349) test_pattern_palindromic?: .: (0.000396) test_stripped: .: (0.000275) test_to_re: .: (0.000532) test_with_cut_symbols: .: (0.000304) test_with_spaces: .: (0.000381) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000820) test_creation_with_no_cuts: .: (0.000379) test_cut_locations: .: (0.000332) test_cut_locations_in_enzyme_notation: .: (0.000545) test_orientation: .: (0.000325) test_pattern: .: (0.000327) test_pattern_palindromic?: .: (0.000404) test_stripped: .: (0.000515) test_to_re: .: (0.000313) test_with_cut_symbols: .: (0.000298) test_with_spaces: .: (0.000354) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000533) test_initialize_with_pattern: .: (0.000214) test_max: .: (0.000094) test_min: .: (0.000123) test_to_array_index: .: (0.000106) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000203) test_bracket_eq: .: (0.000106) test_concat: .: (0.000080) test_delete: .: (0.000068) test_dup: .: (0.000106) test_each: .: (0.000106) test_eqeq: .: (0.000071) test_eqeq_false: .: (0.000327) test_eqeq_other: .: (0.000067) test_eqeq_self: .: (0.000083) test_include?: .: (0.000066) test_internal_data_hash: .: (0.000064) test_internal_data_hash_eq: .: (0.000102) test_length: .: (0.000061) test_ltlt: .: (0.000068) test_ltlt_noeffect: .: (0.000068) test_plus: .: (0.000069) test_plus_error: .: (0.000129) test_private_push_element: .: (0.000070) test_private_push_element_intermediate: .: (0.000069) test_private_push_element_last: .: (0.000067) test_private_push_element_noeffect: .: (0.000107) test_private_sorted_keys: .: (0.000063) test_private_unshift_element: .: (0.000066) test_private_unshift_element_first: .: (0.000071) test_private_unshift_element_intermediate: .: (0.000067) test_private_unshift_element_noeffect: .: (0.000099) test_push: .: (0.000091) test_reverse_each: .: (0.000100) test_self_bracket: .: (0.000061) test_self_new: .: (0.000102) test_size: .: (0.000063) test_sort!: .: (0.000072) test_to_a: .: (0.000061) test_uniq!: .: (0.000058) test_unshift: .: (0.000068) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000179) test_left_padding: .: (0.000087) test_right_padding: .: (0.000082) test_strip_padding: .: (0.000102) Bio::TestSOFT: test_dataset: .: (0.005994) test_series: .: (0.009058) Bio::TestSOSUIReport: test_entry_id: .: (0.000289) test_prediction: .: (0.000109) test_tmh: .: (0.000099) test_tmhs: .: (0.000115) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000130) test_rs: .: (0.000092) Bio::TestSOSUITMH: test_grade: .: (0.000214) test_range: .: (0.000128) test_sequence: .: (0.000105) Bio::TestSampleGraph: test_bellman_ford: .: (0.000829) test_bfs_shortest_path: .: (0.000136) test_breadth_first_search: .: (0.000111) test_depth_first_search: .: (0.000244) test_dijkstra: .: (0.000161) test_dump_list: .: (0.000199) test_dump_matrix: .: (0.000256) test_extract_subgraph_by_label: .: (0.000158) test_extract_subgraph_by_list: .: (0.000166) test_extract_subgraph_retains_disconnected_nodes: .: (0.000109) test_small_world_aka_node_degree_histogram: .: (0.000112) test_to_matrix: .: (0.000266) test_to_matrix_fixed_index: .: (0.000204) test_undirected_cliquishness: .: (0.000199) Bio::TestScf_version_2: test_complement: .: (0.006577) test_seq: .: (0.005499) test_to_biosequence: .: (0.005162) Bio::TestScf_version_3: test_complement: .: (0.014597) test_seq: .: (0.013520) test_to_biosequence: .: (0.013457) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000216) test_AA_new_sequence_all_legal_symbols: .: (0.000082) test_AA_new_sequence_removes_whitespace: .: (0.000081) test_AA_new_sequence_upcases_symbols: .: (0.000075) test_DNA_new_blank_sequence: .: (0.000072) test_DNA_new_sequence_downcases_symbols: .: (0.000094) test_DNA_new_sequence_removes_whitespace: .: (0.000087) test_NA_randomize_with_counts: .: (0.000589) test_NA_randomize_with_counts_and_block: .: (0.008735) test_RNA_new_sequence: .: (0.001399) test_ambiguous_dna_sequence_complement: .: (0.000095) test_ambiguous_rna_sequence_complement: .: (0.000080) test_amino_acid_codes: .: (0.000129) test_amino_acid_molecular_weight: .: (0.000178) test_amino_acid_names: .: (0.000134) test_amino_acid_randomize_can_be_chained: .: (0.011241) test_amino_acid_randomize_has_same_composition: .: (0.004733) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.005852) test_dna_composition: .: (0.000139) test_dna_gc_percent: .: (0.000125) test_dna_molecular_weight: .: (0.001354) test_dna_pikachu: .: (0.000141) test_dna_sequence_complement: .: (0.000096) test_dna_sequence_translate: .: (0.001536) test_dna_to_re: .: (0.000170) test_element_reference_operator_with_one_argument: .: (0.001114) test_element_reference_operator_with_two_arguments: .: (0.000075) test_invalid_nucleic_acid_illegal_bases: .: (0.000104) test_invalid_nucleic_acid_illegal_bases_more: .: (0.002427) test_nucleic_acid_names: .: (0.000140) test_randomize_dna_can_be_chained: .: (0.002042) test_randomize_dna_retains_composition: .: (0.001562) test_randomize_dna_with_block: .: (0.000246) test_rna_composition: .: (0.000087) test_rna_gc_percent: .: (0.000088) test_rna_molecular_weight: .: (0.000116) test_rna_pikachu: .: (0.000076) test_rna_sequence_complement: .: (0.000066) test_rna_sequence_translate: .: (0.000306) test_rna_to_re: .: (0.000126) test_total: .: (0.000080) test_two_consecutive_dna_randomizations_not_equal: .: (0.000197) test_valid_dna_sequence_illegal_bases: .: (0.000720) Bio::TestSequenceAA: test_codes: .: (0.000220) test_molecular_weight: .: (0.000096) test_names: .: (0.000079) test_to_re: .: (0.000108) test_to_s: .: (0.000076) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000178) Bio::TestSequenceAANew: test_new: .: (0.000146) test_new_n: .: (0.000064) test_new_r: .: (0.000057) test_new_t: .: (0.000057) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000159) test_concat: .: (0.000065) test_push: .: (0.000054) test_seq: .: (0.000054) test_splicing: .: (0.000191) test_sum: .: (0.000061) test_to_s: .: (0.000075) test_to_str: .: (0.000058) test_total: .: (0.000062) test_window_search: .: (0.000167) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000229) test_normalize_A: .: (0.000092) test_normalize_a: .: (0.000061) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.001190) test_randomize_with_block: .: (0.003751) test_randomize_with_hash: .: (0.000926) test_randomize_with_hash_block: .: (0.003270) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:325:in `test_randomize_equiprobability' =============================================================================== : (0.001027) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:331:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.000521) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000189) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000103) test_subseq_returns_subsequence: .: (0.000074) test_to_s_returns_self_as_string: .: (0.000080) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000520) test_window_search_with_width_3_step_two_with_residual: .: (0.000098) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000185) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000121) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000216) test_na_self_randomize: .: (0.000115) Bio::TestSequenceDBLink: test_database: .: (0.000186) test_id: .: (0.000060) test_secondary_ids: .: (0.000057) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000196) test_parse_uniprot_DR_line: .: (0.000094) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000887) test_output_width_35: .: (0.000204) test_output_width_nil: .: (0.000255) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000538) test_output_after_adding_sequence: .: (0.000280) test_output_after_truncating_sequence: .: (0.000142) test_output_from_error_probabilities: .: (0.001819) test_output_width45: .: (0.000163) test_output_with_converting_score_phred2solexa: .: (0.000429) test_output_with_converting_score_solexa2phred: .: (0.000258) test_output_with_default_score: .: (0.000187) Bio::TestSequenceMasker: test_mask: .: (0.000247) test_mask_with_enumerator: .: (0.000126) test_mask_with_enumerator_empty_mask_char: .: (0.000108) test_mask_with_enumerator_excess: .: (0.000335) test_mask_with_enumerator_longer_mask_char: .: (0.000106) test_mask_with_enumerator_shorter: .: (0.000180) test_mask_with_error_probability: .: (0.000101) test_mask_with_quality_score: .: (0.000094) Bio::TestSequenceNA: test_at_content: .: (0.000271) test_at_skew: .: (0.000208) test_codon_usage: .: (0.000108) test_complement: .: (0.000088) test_dna: .: (0.000081) test_dna!: .: (0.000109) test_forward_complement: .: (0.000115) test_gc_content: .: (0.000162) test_gc_percent: .: (0.000172) test_gc_skew: .: (0.000214) test_iliegal_bases: .: (0.000077) test_molecular_weight: .: (0.000135) test_names: .: (0.000184) test_reverse_complement: .: (0.000114) test_rna: .: (0.000083) test_rna!: .: (0.000072) test_splicing: .: (0.000136) test_to_re: .: (0.000159) test_to_s: .: (0.000066) Bio::TestSequenceNACommon: test_composition: .: (0.000181) test_concat: .: (0.000078) test_push: .: (0.000063) test_seq: .: (0.000064) test_splicing: .: (0.000115) test_sum: .: (0.000130) test_to_s: .: (0.000065) test_to_str: .: (0.000062) test_total: .: (0.000068) test_window_search: .: (0.000199) Bio::TestSequenceNANew: test_new: .: (0.000144) test_new_n: .: (0.000070) test_new_r: .: (0.000064) test_new_t: .: (0.000067) Bio::TestSequenceNATranslation: test_translate: .: (0.000415) test_translate_0: .: (0.000610) test_translate_1: .: (0.000189) test_translate_2: .: (0.000223) test_translate_3: .: (0.000187) test_translate_4: .: (0.000203) test_translate_5: .: (0.000168) test_translate_6: .: (0.000164) test_translate_7: .: (0.000455) test_translate_given_codon_table: .: (0.033222) test_translate_n1: .: (0.000477) test_translate_n2: .: (0.000406) test_translate_n3: .: (0.000393) test_translate_unknown_o: .: (0.000180) test_translate_unknown_x: .: (0.000218) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000218) test_convert_scores_from_phred_to_solexa: .: (0.000266) test_convert_scores_from_solexa_to_phred: .: (0.000109) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000148) test_convert_scores_from_phred: .: (0.000064) test_convert_scores_from_phred_to_solexa: .: (0.000270) test_convert_scores_from_solexa: .: (0.000109) test_convert_scores_from_solexa_to_phred: .: (0.000100) test_convert_scores_to_phred: .: (0.000059) test_convert_scores_to_solexa: .: (0.000248) test_p2q: .: (0.000103) test_phred_p2q: .: (0.000115) test_phred_q2p: .: (0.001238) test_q2p: .: (0.001202) test_quality_score_type: .: (0.000074) test_self_convert_scores_to_solexa: .: (0.000241) test_self_p2q: .: (0.000104) test_self_q2p: .: (0.001246) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000190) test_convert_scores_from_phred: .: (0.000276) test_convert_scores_from_phred_to_solexa: .: (0.000276) test_convert_scores_from_solexa: .: (0.000061) test_convert_scores_from_solexa_to_phred: .: (0.000107) test_convert_scores_to_phred: .: (0.000137) test_convert_scores_to_solexa: .: (0.000077) test_p2q: .: (0.000136) test_q2p: .: (0.001407) test_quality_score_type: .: (0.000066) test_self_convert_scores_to_phred: .: (0.000151) test_self_p2q: .: (0.000141) test_self_q2p: .: (0.001404) test_solexa_p2q: .: (0.000142) test_solexa_q2p: .: (0.005402) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000228) test_center: .: (0.000085) test_chomp: .: (0.000092) test_chop: .: (0.000089) test_delete: .: (0.000527) test_delete_prefix: .: (0.000084) test_delete_suffix: .: (0.000074) test_downcase: .: (0.000098) test_each_char: .: (0.000145) test_each_char_enum: .: (0.000124) test_each_grapheme_cluster: .: (0.000380) test_each_grapheme_cluster_enum: .: (0.000111) test_each_line: .: (0.000110) test_each_line_enum: .: (0.000129) test_gsub: .: (0.000094) test_gsub_with_block: .: (0.000336) test_ljust: .: (0.000518) test_lstrip: .: (0.000081) test_multiply: .: (0.000068) test_next: .: (0.000066) test_reverse: .: (0.000073) test_rjust: .: (0.000110) test_rstrip: .: (0.000076) test_slice: .: (0.000074) test_slice2: .: (0.000068) test_split: .: (0.000122) test_squeeze: .: (0.000078) test_strip: .: (0.000070) test_sub: .: (0.000079) test_sub_with_block: .: (0.000209) test_succ: .: (0.000074) test_swapcase: .: (0.000073) test_tr: .: (0.000664) test_tr_s: .: (0.000105) test_upcase: .: (0.000073) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000211) test_partition_nomatch: .: (0.000096) test_partition_sep_TSeq: .: (0.000084) test_partition_sep_regexp: .: (0.000089) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000212) test_rpartition_nomatch: .: (0.000089) test_rpartition_sep_TSeq: .: (0.000085) test_rpartition_sep_regexp: .: (0.000128) Bio::TestShRNA: test_blocK_it: .: (0.018886) test_blocK_it_: .: (0.015787) test_blocK_it_BLOCK_IT: .: (0.014770) test_blocK_it_BLOCK_iT: .: (0.014547) test_blocK_it_piGene: .: (0.014594) test_bottom_strand: .: (0.013777) test_bottom_strand_class: .: (0.015649) test_bottom_strand_nil: .: (0.014938) test_design: .: (0.014525) test_design_BLOCK_IT: .: (0.014493) test_report: .: (0.013406) test_report_before_design: .: (0.014196) test_top_strand: .: (0.013432) test_top_strand_class: .: (0.012911) test_top_strand_nil: .: (0.012892) Bio::TestShRNANew: test_new: .: (0.000472) Bio::TestSiRNA: test_antisense_size: .: (0.000145) test_design: .: (0.013922) test_design_reynolds: .: (0.017084) test_design_uitei: .: (0.013694) test_max_gc_percent: .: (0.000077) test_min_gc_percent: .: (0.000063) test_reynolds: .: (0.017056) test_reynolds?: .: (0.000105) test_uitei: .: (0.013183) test_uitei?: .: (0.000090) Bio::TestSiRNANew: test_new: .: (0.000597) Bio::TestSiRNAPair: test_antisense: .: (0.014793) test_gc_percent: .: (0.013540) test_report: .: (0.014067) test_rule: .: (0.013209) test_sense: .: (0.013752) test_start: .: (0.014330) test_stop: .: (0.014455) test_target: .: (0.015835) Bio::TestSiRNAPairNew: test_new: .: (0.000349) Bio::TestSim4Report: test_all_hits: .: (0.000929) test_each: .: (0.000176) test_each_hit: .: (0.000147) test_hits: .: (0.000152) test_num_hits: .: (0.000306) test_query_def: .: (0.000141) test_query_id: .: (0.000151) test_query_len: .: (0.000138) test_seq1: .: (0.000166) Bio::TestSim4Report2: test_all_hits: .: (0.000615) test_each: .: (0.000154) test_each_hit: .: (0.000143) test_hits: .: (0.000141) test_num_hits: .: (0.000122) test_query_def: .: (0.000121) test_query_id: .: (0.000124) test_query_len: .: (0.000119) test_seq1: .: (0.000149) Bio::TestSim4Report4: test_all_hits: .: (0.000454) test_each: .: (0.000157) test_each_hit: .: (0.000611) test_hits: .: (0.000371) test_num_hits: .: (0.000137) test_query_def: .: (0.000132) test_query_id: .: (0.000130) test_query_len: .: (0.000128) test_seq1: .: (0.000160) Bio::TestSim4ReportHit: test_align: .: (0.000281) test_complement?: .: (0.000131) test_definition: .: (0.000128) test_each: .: (0.000258) test_exons: .: (0.000225) test_hit_id: .: (0.000136) test_hsps: .: (0.000580) test_introns: .: (0.000337) test_len: .: (0.000137) test_query_def: .: (0.000128) test_query_id: .: (0.000119) test_query_len: .: (0.000137) test_segmentpairs: .: (0.000226) test_seq1: .: (0.000161) test_seq2: .: (0.000156) test_target_def: .: (0.000124) test_target_id: .: (0.000129) test_target_len: .: (0.000126) Bio::TestSim4ReportHit2: test_align: .: (0.000260) test_complement?: .: (0.000129) test_definition: .: (0.000134) test_each: .: (0.000215) test_exons: .: (0.000226) test_hit_id: .: (0.000127) test_hsps: .: (0.000202) test_introns: .: (0.000196) test_len: .: (0.000123) test_query_def: .: (0.000119) test_query_id: .: (0.000118) test_query_len: .: (0.000119) test_segmentpairs: .: (0.000205) test_seq1: .: (0.000168) test_seq2: .: (0.000195) test_target_def: .: (0.000123) test_target_id: .: (0.000118) test_target_len: .: (0.000117) Bio::TestSim4ReportHit4: test_align: .: (0.000293) test_complement?: .: (0.000136) test_definition: .: (0.000128) test_each: .: (0.000276) test_exons: .: (0.000273) test_hit_id: .: (0.000137) test_hsps: .: (0.000323) test_introns: .: (0.000266) test_len: .: (0.000136) test_query_def: .: (0.000130) test_query_id: .: (0.000127) test_query_len: .: (0.000126) test_segmentpairs: .: (0.000275) test_seq1: .: (0.000167) test_seq2: .: (0.000174) test_target_def: .: (0.000130) test_target_id: .: (0.000129) test_target_len: .: (0.000127) Bio::TestSim4ReportSegment: test_from: .: (0.000133) test_self_new: .: (0.000148) test_seq: .: (0.000060) test_to: .: (0.000053) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000270) test_direction: .: (0.000193) test_hit_from: .: (0.000189) test_hit_to: .: (0.000182) test_hseq: .: (0.000182) test_midline: .: (0.000177) test_percent_identity: .: (0.000178) test_qseq: .: (0.000177) test_query_from: .: (0.000177) test_query_to: .: (0.000245) test_seq1: .: (0.000224) test_seq2: .: (0.000218) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000289) test_direction: .: (0.000190) test_hit_from: .: (0.000182) test_hit_to: .: (0.000179) test_hseq: .: (0.000177) test_midline: .: (0.000175) test_percent_identity: .: (0.000177) test_qseq: .: (0.000196) test_query_from: .: (0.000183) test_query_to: .: (0.000180) test_seq1: .: (0.000206) test_seq2: .: (0.000203) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000310) test_direction: .: (0.000235) test_hit_from: .: (0.000228) test_hit_to: .: (0.000244) test_hseq: .: (0.000349) test_midline: .: (0.000230) test_percent_identity: .: (0.000224) test_qseq: .: (0.000226) test_query_from: .: (0.000225) test_query_to: .: (0.000229) test_seq1: .: (0.000261) test_seq2: .: (0.000264) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000313) test_direction: .: (0.000340) test_hit_from: .: (0.000233) test_hit_to: .: (0.000271) test_hseq: .: (0.000229) test_midline: .: (0.000243) test_percent_identity: .: (0.000225) test_qseq: .: (0.000226) test_query_from: .: (0.000223) test_query_to: .: (0.000222) test_seq1: .: (0.000246) test_seq2: .: (0.000251) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000307) test_direction: .: (0.000243) test_hit_from: .: (0.000230) test_hit_to: .: (0.000226) test_hseq: .: (0.000223) test_midline: .: (0.000222) test_percent_identity: .: (0.000220) test_qseq: .: (0.000223) test_query_from: .: (0.000243) test_query_to: .: (0.000221) test_seq1: .: (0.000257) test_seq2: .: (0.000252) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000261) test_direction: .: (0.000189) test_hit_from: .: (0.000181) test_hit_to: .: (0.000181) test_hseq: .: (0.000180) test_midline: .: (0.000177) test_percent_identity: .: (0.000180) test_qseq: .: (0.000179) test_query_from: .: (0.000178) test_query_to: .: (0.000173) test_seq1: .: (0.000205) test_seq2: .: (0.000199) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000278) test_direction: .: (0.000191) test_hit_from: .: (0.000182) test_hit_to: .: (0.000186) test_hseq: .: (0.000180) test_midline: .: (0.000178) test_percent_identity: .: (0.000178) test_qseq: .: (0.000178) test_query_from: .: (0.000175) test_query_to: .: (0.000174) test_seq1: .: (0.000199) test_seq2: .: (0.000199) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000145) test_entry_id: .: (0.000071) test_filename: .: (0.000065) test_len: .: (0.000065) test_self_new: .: (0.000078) test_self_parse: .: (0.000094) Bio::TestTMHMMReport: test_entry_id: .: (0.000324) test_exp_aas_in_tmhs: .: (0.000211) test_exp_first_60aa: .: (0.000197) test_helix: .: (0.000244) test_predicted_tmhs: .: (0.000209) test_query_len: .: (0.000193) test_tmhs: .: (0.000210) test_to_s: .: (0.000284) test_total_prob_of_N_in: .: (0.000213) Bio::TestTMHMMReport_reports: test_reports: .: (0.000165) Bio::TestTMHMMTMH: test_entry_id: .: (0.000310) test_pos: .: (0.000245) test_range: .: (0.002293) test_status: .: (0.000208) test_version: .: (0.000194) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000250) test_cutoff: .: (0.000148) test_entry_id: .: (0.000137) test_length: .: (0.000134) test_loc: .: (0.000131) test_name: .: (0.000129) test_networks: .: (0.000127) test_prediction: .: (0.000139) test_query_len: .: (0.000131) test_query_sequences: .: (0.000716) test_rc: .: (0.000144) test_version: .: (0.000136) Bio::TestTargetPReportConst: test_delimiter: .: (0.000242) test_rs: .: (0.000061) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000122) test_togows_access_wait: .: (2.000644) Bio::TestTogoWSREST: test_debug: .: (0.000952) test_debug_default: .: (0.000343) test_internal_http: .: (0.000329) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000340) test_entry: .: (0.000191) test_entry_database_list: .: (0.000187) test_new: .: (0.000548) test_new_with_uri_object: .: (0.000364) test_new_with_uri_string: .: (0.000334) test_retrieve: .: (0.000183) test_search: .: (0.000183) test_search_database_list: .: (0.000176) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000492) test_prepare_return_value: .: (0.000356) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000537) Bio::TestTree: test_get_edge_distance: .: (0.000448) test_get_edge_distance_string: .: (0.000284) test_get_node_name: .: (0.000203) test_initialize: .: (0.001721) test_options: .: (0.000202) test_root: .: (0.000173) test_root=: .: (0.000213) Bio::TestTree2: test_add_edge: .: (0.000542) test_add_node: .: (0.000359) test_adjacency_matrix: .: (0.000378) test_adjacency_matrix_with_block: .: (0.000350) test_adjacent_nodes: .: (0.000363) test_adjacent_nodes_nonexistent: .: (0.000317) test_ancestors: .: (0.000352) test_children: .: (0.000266) test_clear: .: (0.000282) test_clear_node: .: (0.000316) test_clear_node_nonexistent: .: (0.000480) test_collect_edge!: .: (0.000403) test_collect_node!: .: (0.000454) test_concat: .: (0.000414) test_descendents: .: (0.000307) test_distance_matrix: .: (0.000646) test_each_edge: .: (0.000333) test_each_node: .: (0.000318) test_each_out_edge: .: (0.000298) test_each_out_edge_chimpanzee: .: (0.000291) test_each_out_edge_human: .: (0.000372) test_each_out_edge_mammals: .: (0.000542) test_each_out_edge_nonexistent: .: (0.000122) test_each_out_edge_primates: .: (0.000151) test_each_out_edge_rat: .: (0.000118) test_each_out_edge_rodents: .: (0.000150) test_edges: .: (0.000122) test_get_edge: .: (0.000212) test_get_edge_indirect: .: (0.000103) test_get_edge_merged: .: (0.000116) test_get_edge_nonexistent: .: (0.000107) test_get_node_bootstrap: .: (0.000106) test_get_node_bootstrap_string=: .: (0.000109) test_get_node_by_name: .: (0.000146) test_get_node_by_name_noexistent: .: (0.000095) test_include?: .: (0.000400) test_include_nonexistent: .: (0.000105) test_insert_node: .: (0.000171) test_leaves: .: (0.000145) test_leaves_noargs: .: (0.000115) test_lowest_common_ancestor: .: (0.000154) test_nodes: .: (0.000110) test_number_of_edges: .: (0.000096) test_number_of_nodes: .: (0.000100) test_out_degree: .: (0.000123) test_out_degree_nonexistent: .: (0.000125) test_out_edges: .: (0.000126) test_out_edges_mammals: .: (0.000139) test_out_edges_nonexistent: .: (0.000102) test_out_edges_primates: .: (0.000366) test_out_edges_rodents: .: (0.000156) test_parent: .: (0.000129) test_path: .: (0.000118) test_remove_edge: .: (0.000116) test_remove_edge_if: .: (0.000127) test_remove_edge_if_nothing_removed: .: (0.000137) test_remove_edge_nonexistent: .: (0.000156) test_remove_node: .: (0.000140) test_remove_node_if: .: (0.000111) test_remove_node_if_false: .: (0.000121) test_remove_node_nonexistent: .: (0.000123) test_remove_nonsense_nodes: .: (0.000135) test_subtree: .: (0.000437) test_subtree_with_all_paths: .: (0.000225) test_total_distance: .: (0.000112) Bio::TestTreeEdge: test_distance: .: (0.000165) test_distance=: .: (0.000085) test_distance_string: .: (0.000059) test_distance_string=: .: (0.000076) test_initialize: .: (0.000084) test_inspect: .: (0.000058) test_to_s: .: (0.000059) Bio::TestTreeNode: test_bootstrap: .: (0.000124) test_bootstrap=: .: (0.000083) test_bootstrap_string: .: (0.000051) test_bootstrap_string=: .: (0.000086) test_initialize: .: (0.000075) test_inspect: .: (0.000311) test_name: .: (0.000068) test_to_s: .: (0.000055) Bio::TestUniProt: test_gene_name: .: (0.002209) Bio::TestUniProtKB: test_ac: .: (0.002180) test_accession: .: (0.001701) test_cc: .: (0.002746) test_cc_alternative_products: .: (0.002882) test_cc_database: .: (0.006431) test_cc_mass_spectrometry: .: (0.003281) test_de: .: (0.002804) test_dr: .: (0.002942) test_dr_with_key: .: (0.003202) test_dr_with_key_empty: .: (0.005673) test_dt: .: (0.002752) test_dt_annotation: .: (0.002131) test_dt_created: .: (0.001787) test_dt_sequence: .: (0.001549) test_entry: .: (0.001617) test_ft: .: (0.008185) test_gene_name: .: (0.002631) test_gene_names: .: (0.002317) test_gn: .: (0.001859) test_gn_old_parser: .: (0.001775) test_gn_uniprot_parser: .: (0.001674) test_id_line: .: (0.001790) test_id_line_data_class: .: (0.012278) test_id_line_entry_name: .: (0.012640) test_id_line_molecule_type: .: (0.014029) test_id_line_sequence_length: .: (0.004281) test_kw: .: (0.003101) test_molecule: .: (0.002159) test_oc: .: (0.001926) test_og_1: .: (0.001880) test_og_2: .: (0.001674) test_og_3: .: (0.001902) test_og_4: .: (0.001815) test_og_5: .: (0.001570) test_og_6: .: (0.001534) test_os: .: (0.001566) test_os_access: .: (0.001625) test_os_access2: .: (0.003963) test_ox: .: (0.002811) test_protein_name: .: (0.002273) test_ref: .: (0.004952) test_seq: .: (0.001915) test_sequence_length: .: (0.001468) test_sq: .: (0.001476) test_sq_crc64: .: (0.001461) test_sq_len: .: (0.001500) test_sq_mw: .: (0.001609) test_synonyms: .: (0.003655) Bio::TestUniProtKB_CC: test_allergen: .: (0.000243) test_alternative_products_access_as_hash: .: (0.000164) test_alternative_products_ai: .: (0.000206) test_alternative_products_apu: .: (0.000819) test_alternative_products_as: .: (0.000351) test_alternative_products_rf: .: (0.000072) test_biophysicochemical_properties: .: (0.000296) test_biotechnology: .: (0.000185) test_catalytic_activity: .: (0.000136) test_caution: .: (0.000152) test_cofactor: .: (0.000133) test_developmental_stage: .: (0.000147) test_disease: .: (0.000213) test_domain: .: (0.000231) test_enzyme_regulation: .: (0.000140) test_function: .: (0.000885) test_induction: .: (0.000136) test_interaction: .: (0.000177) test_mass_spectrometry: .: (0.000193) test_miscellaneous: .: (0.000125) test_pathway: .: (0.000162) test_pharmaceutical: .: (0.000145) test_polymorphism: .: (0.000203) test_ptm: .: (0.000128) test_rna_editing: .: (0.000217) test_similarity: .: (0.000134) test_subcellular_location: .: (0.000159) test_subunit: .: (0.000110) test_tissue_specificity: .: (0.000152) test_toxic_dose: .: (0.000586) test_web_resource: .: (0.000247) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000420) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000403) test_protein_name: .: (0.000211) test_synonyms: .: (0.000239) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000285) test_entry: .: (0.000084) test_entry_id: .: (0.000077) test_entry_name: .: (0.000072) test_id_line: .: (0.000077) test_molecule: .: (0.000096) test_sequence_length: .: (0.000073) Bio::TestUniProtKB_P03589: test_ac: .: (0.000763) test_accession: .: (0.000269) test_cc: .: (0.000417) test_cc_alternative_products: .: (0.000557) test_cc_database: .: (0.000418) test_cc_mass_spectrometry: .: (0.000404) test_de: .: (0.000285) test_dr: .: (0.000454) test_dr_with_key: .: (0.000577) test_dr_with_key_empty: .: (0.000400) test_dt: .: (0.000248) test_dt_annotation: .: (0.000244) test_dt_created: .: (0.000239) test_dt_sequence: .: (0.000239) test_entry: .: (0.000403) test_ft: .: (0.000401) test_gene_name: .: (0.000291) test_gene_names: .: (0.000273) test_gn: .: (0.000273) test_gn_old_parser: .: (0.000323) test_gn_uniprot_parser: .: (0.000289) test_id_line: .: (0.000373) test_id_line_data_class: .: (0.000249) test_id_line_entry_name: .: (0.000241) test_id_line_sequence_length: .: (0.000244) test_kw: .: (0.000295) test_oc: .: (0.000280) test_oh: .: (0.000584) test_os: .: (0.000269) test_os_access: .: (0.000271) test_os_access2: .: (0.000265) test_ox: .: (0.000282) test_protein_name: .: (0.000403) test_protein_name_after_calling_de: .: (0.000290) test_ref: .: (0.000297) test_seq: .: (0.000487) test_sequence_length: .: (0.000260) test_sq: .: (0.000272) test_sq_crc64: .: (0.000318) test_sq_len: .: (0.000282) test_sq_mw: .: (0.000275) test_synonyms: .: (0.000284) Bio::TestUniProtKB_P28907: test_ac: .: (0.001153) test_accession: .: (0.000639) test_cc: .: (0.001017) test_cc_alternative_products: .: (0.001062) test_cc_database: .: (0.001026) test_cc_mass_spectrometry: .: (0.001196) test_de: .: (0.000693) test_dr: .: (0.004065) test_dr_with_key: .: (0.002508) test_dr_with_key_empty: .: (0.003216) test_dt: .: (0.000904) test_dt_annotation: .: (0.000696) test_dt_created: .: (0.001127) test_dt_sequence: .: (0.000631) test_entry: .: (0.000798) test_ft: .: (0.008513) test_gene_name: .: (0.004022) test_gene_names: .: (0.003145) test_gn: .: (0.004001) test_gn_old_parser: .: (0.003556) test_gn_uniprot_parser: .: (0.004765) test_id_line: .: (0.003372) test_id_line_data_class: .: (0.003094) test_id_line_entry_name: .: (0.004329) test_id_line_sequence_length: .: (0.001766) test_kw: .: (0.001792) test_oc: .: (0.001334) test_os: .: (0.000641) test_os_access: .: (0.001215) test_os_access2: .: (0.000674) test_ox: .: (0.001341) test_protein_name: .: (0.001340) test_protein_name_after_calling_de: .: (0.000819) test_ref: .: (0.001430) test_seq: .: (0.000981) test_sequence_length: .: (0.000630) test_sq: .: (0.000773) test_sq_crc64: .: (0.000650) test_sq_len: .: (0.000808) test_sq_mw: .: (0.000827) test_synonyms: .: (0.000723) test_synonyms_after_calling_de: .: (0.000951) Bio::TestUniProtKB_P49144: test_ac: .: (0.000887) test_accession: .: (0.000364) test_cc: .: (0.000668) test_cc_alternative_products: .: (0.000939) test_cc_database: .: (0.000650) test_cc_mass_spectrometry: .: (0.000675) test_de: .: (0.000398) test_dr: .: (0.000666) test_dr_with_key: .: (0.000654) test_dr_with_key_empty: .: (0.000637) test_dt: .: (0.000339) test_dt_annotation: .: (0.000332) test_dt_created: .: (0.000344) test_dt_sequence: .: (0.000347) test_entry: .: (0.000341) test_ft: .: (0.000882) test_gene_name: .: (0.000384) test_gene_names: .: (0.000365) test_gn: .: (0.000359) test_gn_old_parser: .: (0.000394) test_gn_uniprot_parser: .: (0.000379) test_id_line: .: (0.000364) test_id_line_data_class: .: (0.000348) test_id_line_entry_name: .: (0.000344) test_id_line_sequence_length: .: (0.000349) test_kw: .: (0.002225) test_oc: .: (0.000408) test_os: .: (0.000392) test_os_access: .: (0.000360) test_os_access2: .: (0.001025) test_ox: .: (0.000376) test_protein_name: .: (0.000394) test_protein_name_after_calling_de: .: (0.000893) test_ref: .: (0.000608) test_seq: .: (0.000441) test_sequence_length: .: (0.000346) test_sq: .: (0.001012) test_sq_crc64: .: (0.000365) test_sq_len: .: (0.000363) test_sq_mw: .: (0.001104) test_synonyms: .: (0.000404) test_synonyms_after_calling_de: .: (0.000393) Bio::TestUniProtKB_Ref: test_RA: .: (0.000268) test_RC: .: (0.000334) test_RG: .: (0.000166) test_RL: .: (0.000161) test_RN: .: (0.000156) test_RP: .: (0.000157) test_RT: .: (0.000154) test_RX: .: (0.000156) test_ref: .: (0.000162) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000172) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000321) test_alternative_products_with_ft: .: (0.000643) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000228) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000206) test_RL_lines: .: (0.000094) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000365) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000161) test_RG_line: .: (0.000100) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000475) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000212) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000151) test_RL_line: .: (0.000095) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000473) test_RP_line: .: (0.000160) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000101) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000329) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000157) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000133) test_CC_interaction_isoform: .: (0.000126) test_CC_interaction_no_gene_name: .: (0.000123) test_CC_interaction_self_association: .: (0.000142) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000175) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000201) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000260) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000342) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000203) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000177) test_DT_line: .: (0.000112) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.002379) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000428) test_CC_web_resource: .: (0.000074) test_FT_VER_SEQ: .: (0.000132) test_OH_line_exception: .: (0.000175) test_OH_lines: .: (0.000483) Bio::TestUtils: test_centreOfGravity: .: (0.000333) test_dihedral_angle: .: (0.000257) test_distance: .: (0.000259) test_geometricCentre: .: (0.000170) test_rad2deg: .: (0.000111) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000208) test_dijkstra_on_weighted_graph: .: (0.000097) Finished in 9.708279187 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 405.94 tests/s, 2225.01 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.6' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.6-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.6-1_amd64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.6-1_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/4191131 and its subdirectories I: Current time: Wed Oct 22 02:17:39 -12 2025 I: pbuilder-time-stamp: 1761142659 Wed Oct 22 14:17:40 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Oct 22 14:17:40 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Oct 22 14:19:56 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Oct 22 14:19:57 UTC 2025 I: ruby-bio_2.0.6-1_amd64.changes: Format: 1.8 Date: Fri, 26 Sep 2025 16:59:33 +0530 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1 Distribution: unstable Urgency: medium Maintainer: Debian Ruby Team Changed-By: Nilesh Patra Description: ruby-bio - Ruby tools for computational molecular biology Closes: 1116111 Changes: ruby-bio (2.0.6-1) unstable; urgency=medium . * Team Upload. . [ Lucas Nussbaum ] * debian/gbp.conf: Add for DEP-14 * debian/gbp.conf: remove trailing empty lines * debian/.gitattributes: remove * debian/salsa-ci.yml: use team-specific include . [ Nilesh Patra ] * New upstream version 2.0.6 * Change Recommends from blast2 => ncbi-blast+-legacy Closes: #1116111 * Bump Standards-Version to 4.7.2 (no changes needed) * Drop myself from uploaders Checksums-Sha1: 68b9d38780c52e4778cb2da4df127794d40c30cb 705580 ruby-bio_2.0.6-1_all.deb 8f083fd8c0436b91a88e009499ae96c1e97eb2fd 7506 ruby-bio_2.0.6-1_amd64.buildinfo Checksums-Sha256: 11173dfaa9e46e2e4888606f2e352d1c63c63f5edf863c011dae91ece002230c 705580 ruby-bio_2.0.6-1_all.deb b89c8cc0e69227a0761afcc31e8ae7de9d499dd239ab996ea4b6ef5d57d51642 7506 ruby-bio_2.0.6-1_amd64.buildinfo Files: 828bb6ced0347bf22572590ac7cb273f 705580 ruby optional ruby-bio_2.0.6-1_all.deb 60e3d20f9221a58ed26d09ed6e41eccf 7506 ruby optional ruby-bio_2.0.6-1_amd64.buildinfo Wed Oct 22 14:19:57 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_5-60007.service; invocation ID: 8762c7ddd66f414992a359b0f3abbf9a # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/ruby-bio_2.0.6-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/ruby-bio_2.0.6-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/ruby-bio_2.0.6-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/b1/ruby-bio_2.0.6-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.KNRqlf20/b2/ruby-bio_2.0.6-1_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 217ms CPU time consumed: 166ms Memory peak: 17M (swap: 0B) Wed Oct 22 14:20:09 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Wed Oct 22 14:20:09 UTC 2025 I: ruby-bio from forky built successfully and reproducibly on amd64. Wed Oct 22 14:20:10 UTC 2025 I: Removing signed ruby-bio_2.0.6-1_amd64.buildinfo.asc files: removed './b1/ruby-bio_2.0.6-1_amd64.buildinfo.asc' removed './b2/ruby-bio_2.0.6-1_amd64.buildinfo.asc'