I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 7 10:57:32 +14 2025 I: pbuilder-time-stamp: 1738875452 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ruby-bio_2.0.5-1.dsc] I: copying [./ruby-bio_2.0.5.orig.tar.gz] I: copying [./ruby-bio_2.0.5-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.5-1.dsc: unsupported subcommand dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.5 dpkg-source: info: unpacking ruby-bio_2.0.5.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable_tests_using_chi2.patch dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 6 20:57 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4c75dbc372ad4229b518ee2786f96588 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3036177 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lg5EDUjY/pbuilderrc_sgqr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lg5EDUjY/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19920 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} gpgv{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libb-hooks-op-check-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libffi8{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgcrypt20{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls30t64{a} libgpg-error0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libidn2-0{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap2{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libp11-kit0{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libruby3.3{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-quote-perl{a} libtasn1-6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunistring5{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-did-you-mean{a} ruby-libxml{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} ruby3.3{a} ruby3.3-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} sopv-gpgv{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato gnupg-utils gpg-wks-client libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpg-error-l10n libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc ruby3.3-doc strace unzip wget zip 0 packages upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 56.0 MB of archives. After unpacking 230 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libassuan9 arm64 3.0.1-2 [58.1 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.46-1+b1 [115 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-2 [22.8 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.46-1+b1 [344 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.46-1 [702 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.46-1+b1 [481 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.46-1+b1 [231 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.46-1+b1 [232 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.46-1 [376 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 gpgv arm64 2.2.46-1+b1 [200 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 sopv-gpgv all 0.1.1-1 [10.7 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 71 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 74 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 102 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-7 [121 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.25.2 [1058 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 docbook all 4.5-11 [126 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libosp5 arm64 1.5.2-15.1 [922 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 opensp arm64 1.5.2-15.1 [441 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 docbook-to-man arm64 1:2.0.0-47+b1 [71.4 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 rubygems-integration all 1.19 [5488 B] Get: 119 http://deb.debian.org/debian unstable/main arm64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libruby arm64 1:3.3~3.2 [5084 B] Get: 124 http://deb.debian.org/debian unstable/main arm64 ruby-sdbm arm64 1.0.0-5+b6 [17.9 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250125-2 [96.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libruby3.1t64 arm64 3.1.2-8.5 [5267 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 ruby-minitest all 5.25.4-1 [66.2 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libruby3.3 arm64 3.3.7-1 [6122 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 ruby3.3 arm64 3.3.7-1 [828 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 ruby-rubygems all 3.6.3-1 [406 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 ruby arm64 1:3.3~3.2 [6200 B] Get: 136 http://deb.debian.org/debian unstable/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 gem2deb-test-runner arm64 2.2.5 [17.9 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 ruby3.3-dev arm64 3.3.7-1 [1038 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 ruby3.1 arm64 3.1.2-8.5 [664 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 ruby3.1-dev arm64 3.1.2-8.5 [1007 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 ruby-all-dev arm64 1:3.3~3.2 [6180 B] Get: 144 http://deb.debian.org/debian unstable/main arm64 gem2deb arm64 2.2.5 [48.0 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 ruby-libxml arm64 5.0.3-1+b2 [95.7 kB] Fetched 56.0 MB in 0s (159 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19920 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20254 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21264 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_arm64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.4.0-2_arm64.deb ... Unpacking openssl (3.4.0-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../025-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../027-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../034-libgpg-error0_1.51-3_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-3) ... Selecting previously unselected package libassuan9:arm64. Preparing to unpack .../035-libassuan9_3.0.1-2_arm64.deb ... Unpacking libassuan9:arm64 (3.0.1-2) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../036-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../037-gpgconf_2.2.46-1+b1_arm64.deb ... Unpacking gpgconf (2.2.46-1+b1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../038-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../039-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../040-libtasn1-6_4.19.0-3+b3_arm64.deb ... Unpacking libtasn1-6:arm64 (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../041-libgnutls30t64_3.8.8-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.8-2) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../042-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../043-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../044-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../045-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../046-libnpth0t64_1.8-2_arm64.deb ... Unpacking libnpth0t64:arm64 (1.8-2) ... Selecting previously unselected package dirmngr. Preparing to unpack .../047-dirmngr_2.2.46-1+b1_arm64.deb ... Unpacking dirmngr (2.2.46-1+b1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../048-gnupg-l10n_2.2.46-1_all.deb ... Unpacking gnupg-l10n (2.2.46-1) ... Selecting previously unselected package gpg. Preparing to unpack .../049-gpg_2.2.46-1+b1_arm64.deb ... Unpacking gpg (2.2.46-1+b1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../050-pinentry-curses_1.3.1-2_arm64.deb ... Unpacking pinentry-curses (1.3.1-2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../051-gpg-agent_2.2.46-1+b1_arm64.deb ... Unpacking gpg-agent (2.2.46-1+b1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../052-gpgsm_2.2.46-1+b1_arm64.deb ... Unpacking gpgsm (2.2.46-1+b1) ... Selecting previously unselected package gnupg. Preparing to unpack .../053-gnupg_2.2.46-1_all.deb ... Unpacking gnupg (2.2.46-1) ... Selecting previously unselected package gpgv. Preparing to unpack .../054-gpgv_2.2.46-1+b1_arm64.deb ... Unpacking gpgv (2.2.46-1+b1) ... Selecting previously unselected package sopv-gpgv. Preparing to unpack .../055-sopv-gpgv_0.1.1-1_all.deb ... Unpacking sopv-gpgv (0.1.1-1) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../056-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../057-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../058-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../059-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../060-libio-pty-perl_1%3a1.20-1+b2_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../061-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../062-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../063-libclass-xsaccessor-perl_1.19-4+b4_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b4) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../064-libb-hooks-op-check-perl_0.22-3+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../065-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../066-libdevel-callchecker-perl_0.009-1+b1_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../067-libparams-classify-perl_0.015-2+b4_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../068-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../069-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../070-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../071-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../072-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../073-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../074-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../075-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../076-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../077-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../078-liburi-perl_5.30-1_all.deb ... Unpacking liburi-perl (5.30-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../079-libhtml-parser-perl_3.83-1+b2_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1+b2) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../080-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../081-libclone-perl_0.47-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.47-1+b1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../082-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 .../083-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 .../084-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 .../085-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 .../086-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../087-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../088-libnet-ssleay-perl_1.94-2_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-2) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../089-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../090-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../091-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../092-libtry-tiny-perl_0.32-1_all.deb ... Unpacking libtry-tiny-perl (0.32-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../093-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../094-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../095-patchutils_0.4.2-1+b1_arm64.deb ... Unpacking patchutils (0.4.2-1+b1) ... Selecting previously unselected package wdiff. Preparing to unpack .../096-wdiff_1.2.2-7_arm64.deb ... Unpacking wdiff (1.2.2-7) ... Selecting previously unselected package devscripts. Preparing to unpack .../097-devscripts_2.25.2_all.deb ... Unpacking devscripts (2.25.2) ... Selecting previously unselected package xml-core. Preparing to unpack .../098-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../099-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../100-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../101-libosp5_1.5.2-15.1_arm64.deb ... Unpacking libosp5 (1.5.2-15.1) ... Selecting previously unselected package opensp. Preparing to unpack .../102-opensp_1.5.2-15.1_arm64.deb ... Unpacking opensp (1.5.2-15.1) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../103-docbook-to-man_1%3a2.0.0-47+b1_arm64.deb ... Unpacking docbook-to-man (1:2.0.0-47+b1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../104-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../105-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 .../106-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../107-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../108-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../109-libruby_1%3a3.3~3.2_arm64.deb ... Unpacking libruby:arm64 (1:3.3~3.2) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../110-ruby-sdbm_1.0.0-5+b6_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b6) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../111-libedit2_3.1-20250104-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20250104-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../112-libncurses6_6.5+20250125-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5+20250125-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../113-libyaml-0-2_0.2.5-2_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-2) ... Selecting previously unselected package libruby3.1t64:arm64. Preparing to unpack .../114-libruby3.1t64_3.1.2-8.5_arm64.deb ... Unpacking libruby3.1t64:arm64 (3.1.2-8.5) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../115-ruby-minitest_5.25.4-1_all.deb ... Unpacking ruby-minitest (5.25.4-1) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../116-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 .../117-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package libruby3.3:arm64. Preparing to unpack .../118-libruby3.3_3.3.7-1_arm64.deb ... Unpacking libruby3.3:arm64 (3.3.7-1) ... Selecting previously unselected package ruby3.3. Preparing to unpack .../119-ruby3.3_3.3.7-1_arm64.deb ... Unpacking ruby3.3 (3.3.7-1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../120-ruby-rubygems_3.6.3-1_all.deb ... Unpacking ruby-rubygems (3.6.3-1) ... Selecting previously unselected package ruby. Preparing to unpack .../121-ruby_1%3a3.3~3.2_arm64.deb ... Unpacking ruby (1:3.3~3.2) ... Selecting previously unselected package rake. Preparing to unpack .../122-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../123-gem2deb-test-runner_2.2.5_arm64.deb ... Unpacking gem2deb-test-runner (2.2.5) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../124-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../125-libgmp-dev_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package ruby3.3-dev:arm64. Preparing to unpack .../126-ruby3.3-dev_3.3.7-1_arm64.deb ... Unpacking ruby3.3-dev:arm64 (3.3.7-1) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../127-ruby3.1_3.1.2-8.5_arm64.deb ... Unpacking ruby3.1 (3.1.2-8.5) ... Selecting previously unselected package ruby3.1-dev:arm64. Preparing to unpack .../128-ruby3.1-dev_3.1.2-8.5_arm64.deb ... Unpacking ruby3.1-dev:arm64 (3.1.2-8.5) ... Selecting previously unselected package ruby-all-dev:arm64. Preparing to unpack .../129-ruby-all-dev_1%3a3.3~3.2_arm64.deb ... Unpacking ruby-all-dev:arm64 (1:3.3~3.2) ... Selecting previously unselected package gem2deb. Preparing to unpack .../130-gem2deb_2.2.5_arm64.deb ... Unpacking gem2deb (2.2.5) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../131-ruby-rd_0.6.38-4.1_all.deb ... Unpacking ruby-rd (0.6.38-4.1) ... Selecting previously unselected package rdtool. Preparing to unpack .../132-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:arm64. Preparing to unpack .../133-ruby-libxml_5.0.3-1+b2_arm64.deb ... Unpacking ruby-libxml:arm64 (5.0.3-1+b2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up wdiff (1.2.2-7) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:arm64 (1.8-2) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libgpg-error0:arm64 (1.51-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libedit2:arm64 (3.1-20250104-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up libosp5 (1.5.2-15.1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Feb 6 20:58:04 UTC 2025. Universal Time is now: Thu Feb 6 20:58:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ruby-minitest (5.25.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up gnupg-l10n (2.2.46-1) ... Setting up libncurses6:arm64 (6.5+20250125-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.23.1-1) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up gpgv (2.2.46-1+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libassuan9:arm64 (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up 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 (3.4.0-2) ... Setting up readline-common (8.2-6) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:arm64 (1.94-2) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:arm64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.1-2) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.5.4-3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up opensp (1.5.2-15.1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.2.46-1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.46-1+b1) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.46-1+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up gpgsm (2.2.46-1+b1) ... Setting up python3 (3.13.1-2) ... Setting up rubygems-integration (1.19) ... Setting up sopv-gpgv (0.1.1-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.46-1+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gnupg (2.2.46-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.24.1) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libruby:arm64 (1:3.3~3.2) ... Setting up libwww-perl (6.77-1) ... Setting up libruby3.3:arm64 (3.3.7-1) ... Setting up ruby (1:3.3~3.2) ... Setting up devscripts (2.25.2) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby3.3-dev:arm64 (3.3.7-1) ... Setting up ruby3.3 (3.3.7-1) ... Setting up ruby-libxml:arm64 (5.0.3-1+b2) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b6) ... Setting up ruby-rubygems (3.6.3-1) ... Setting up gem2deb-test-runner (2.2.5) ... Setting up libruby3.1t64:arm64 (3.1.2-8.5) ... Setting up ruby3.1 (3.1.2-8.5) ... Setting up ruby3.1-dev:arm64 (3.1.2-8.5) ... Setting up ruby-all-dev:arm64 (1:3.3~3.2) ... Setting up gem2deb (2.2.5) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-47+b1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lucas Nussbaum dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.5.gemspec /usr/bin/ruby3.3 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.3 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.3.0:/var/lib/gems/3.3.0:/usr/local/lib/ruby/gems/3.3.0:/usr/lib/ruby/gems/3.3.0:/usr/lib/aarch64-linux-gnu/ruby/gems/3.3.0:/usr/share/rubygems-integration/3.3.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.3.0 ruby3.3 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.3 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000405) test_dbs: .: (0.000114) test_go_ids: .: (0.000102) test_go_terms: .: (0.000097) test_parser: .: (0.000294) test_set_date: .: (0.000122) test_set_desc: .: (0.000103) test_to_str: .: (0.000112) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000828) test_mktmpdir_without_block: .: (0.000370) test_remove_entry_secure: .: (0.000265) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.008021) test_call_command_fork: .: (0.000124) test_call_command_open3: .: (0.022761) test_call_command_popen: .: (0.003985) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.003882) test_call_command_fork: .: (0.000119) test_call_command_open3: .: (0.019737) test_call_command_popen: .: (0.007977) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.015905) test_call_command_fork: .: (0.000117) test_call_command_open3: .: (0.035761) test_call_command_popen: .: (0.021403) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.010401) test_call_command_fork_chdir: .: (0.000366) test_call_command_popen_chdir: .: (0.007504) test_query_command_chdir: .: (0.011923) test_query_command_fork_chdir: .: (0.000243) test_query_command_popen_chdir: .: (0.004668) Bio::FuncTestCommandQuery: test_query_command: .: (0.027743) test_query_command_fork: .: (0.004516) test_query_command_open3: .: (0.078516) test_query_command_popen: .: (0.024632) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000632) test_initialize: .: (0.000238) test_path: .: (0.000130) test_path_after_close: .: (0.000258) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.007276) test_output_fasta: .: (0.030109) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000329) test_accession: .: (0.000089) test_accessions: .: (0.000085) test_comment: .: (0.000065) test_common_name: .: (0.000099) test_definition: .: (0.000637) test_features: .: (0.000245) test_gi: .: (0.000086) test_keywords: .: (0.000072) test_locus: .: (0.000048) test_nid: .: (0.000072) test_organism: .: (0.000090) test_origin: .: (0.000066) test_references: .: (0.000371) test_segment: .: (0.000313) test_source: .: (0.000162) test_taxonomy: .: (0.000320) test_version: .: (0.000098) test_versions: .: (0.000075) Bio::TestAA: test_13: .: (0.000165) test_1n: .: (0.000040) test_name2one: .: (0.000084) test_name2three: .: (0.000046) test_one2name: .: (0.000040) test_one2three: .: (0.000035) test_three2name: .: (0.000034) test_three2one: .: (0.000044) test_to_1_1: .: (0.000036) test_to_1_3: .: (0.000045) test_to_1_name: .: (0.000043) test_to_3_1: .: (0.000037) test_to_3_3: .: (0.000031) test_to_3_name: .: (0.000044) test_to_re: .: (0.000079) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000118) Bio::TestAAindex: test_api: .: (0.000078) test_auto_aax1: .: (0.000202) test_auto_aax2: .: (0.000120) Bio::TestAAindex1: test_author: .: (0.000193) test_comment: .: (0.000119) test_correlation_coefficient: .: (0.000234) test_dblinks: .: (0.000113) test_definition: .: (0.000104) test_entry_id: .: (0.000100) test_index: .: (0.000176) test_journal: .: (0.000134) test_title: .: (0.000118) Bio::TestAAindex2: test_access_A_R: .: (0.000552) test_access_R_A: .: (0.008761) test_author: .: (0.000240) test_cols: .: (0.000125) test_comment: .: (0.000113) test_dblinks: .: (0.000099) test_definition: .: (0.000102) test_entry_id: .: (0.000095) test_journal: .: (0.000111) test_matrix: .: (0.000391) test_matrix_1_2: .: (0.000368) test_matrix_2_2: .: (0.000366) test_matrix_A_R: .: (0.000390) test_matrix_R_A: .: (0.000387) test_matrix_determinant: .: (0.001326) test_matrix_rank: .: (0.001275) test_matrix_transpose: .: (0.000490) test_rows: .: (0.000146) test_title: .: (0.000127) Bio::TestAAindexConstant: test_delimiter: .: (0.000152) test_tagsize: .: (0.000044) Bio::TestAbif: test_complement: .: (0.017979) test_seq: .: (0.017524) test_to_biosequence: .: (0.030599) Bio::TestActsLikeMap: test_mixin: .: (0.000242) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000213) Bio::TestActsLikeMarker: test_mixin: .: (0.000870) Bio::TestAlignment: test_add_seq_no_key: .: (0.000244) test_add_seq_using_seq_with_aaseq_method: .: (0.000087) test_add_seq_using_seq_with_definition_method: .: (0.000054) test_add_seq_using_seq_with_entry_id_method: .: (0.000063) test_add_seq_using_seq_with_naseq_method: .: (0.000097) test_add_seq_using_seq_with_seq_method: .: (0.000062) test_consensus_iupac_gap_modes: .: (0.000279) test_consensus_iupac_missing_char: .: (0.000098) test_consensus_iupac_missing_char_option: .: (0.000101) test_consensus_iupac_no_gaps: .: (0.000367) test_consensus_iupac_of_ambiguous_bases: .: (0.000191) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.010785) test_consensus_opt_gap_mode: .: (0.000561) test_consensus_opt_missing_char: .: (0.000166) test_consensus_string_no_gaps: .: (0.000110) test_consensus_threshold_four_sequences: .: (0.000158) test_consensus_threshold_two_sequences: .: (0.001428) test_convert_match: .: (0.001507) test_convert_unmatch: .: (0.001440) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000125) test_convert_unmatch_different_match_char: .: (0.015615) test_convert_unmatch_multiple_sequences: .: (0.000231) test_default_gap_char: .: (0.000161) test_default_gap_regexp_matches_default_gap_char: .: (0.000062) test_default_missing_char: .: (0.000053) test_each_site_equal_length: .: (0.001607) test_each_site_unequal_length: .: (0.000126) test_equals: .: (0.001576) test_match_line_protein: .: (0.010265) test_normalizebang_extends_sequences_with_gaps: .: (0.001540) test_seq_length_is_max_seq_length: .: (0.000200) test_seq_length_when_one_sequence: .: (0.000058) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.001508) test_seqclass_when_seqclass_set: .: (0.000135) test_seqclass_when_sequence_used: .: (0.000061) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.001598) test_set_and_get_gap_char: .: (0.000124) test_store_cannot_override_key: .: (0.000070) test_store_with_default_keys_and_user_defined_keys: .: (0.000067) test_store_with_nil_key_uses_next_number_for_key: .: (0.000172) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.001097) test_alignment_concat: .: (0.000103) test_alignment_length: .: (0.001186) test_alignment_lstrip!: .: (0.000165) test_alignment_lstrip_nil: .: (0.001600) test_alignment_normalize!: .: (0.000061) test_alignment_rstrip!: .: (0.001003) test_alignment_rstrip_nil: .: (0.000983) test_alignment_site: .: (0.008234) test_alignment_slice: .: (0.000146) test_alignment_strip!: .: (0.002338) test_alignment_strip_nil: .: (0.002484) test_alignment_subseq: .: (0.002990) test_alignment_window: .: (0.000736) test_collect_each_site: .: (0.000176) test_consensus_each_site_default: .: (0.000157) test_consensus_each_site_gap_mode_1: .: (0.000094) test_consensus_each_site_gap_mode_minus1: .: (0.000081) test_consensus_iupac: .: (0.000216) test_consensus_string_default: .: (0.000090) test_consensus_string_half: .: (0.000069) test_convert_match: .: (0.000169) test_convert_unmatch: .: (0.000072) test_each_seq: .: (0.000067) test_each_site: .: (0.000486) test_each_site_step: .: (0.000081) test_each_window: .: (0.000096) test_match_line: .: (0.000579) test_match_line_amino: .: (0.001137) test_match_line_nuc: .: (0.000106) test_private_alignment_site: .: (0.000061) test_remove_all_gaps!: .: (0.000070) test_seqclass: .: (0.000058) test_seqclass=: .: (0.000071) test_seqclass_default: .: (0.000040) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002779) test_determine_seq_method: .: (0.001453) test_entries: .: (0.000553) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000236) test_avoid_same_name_numbering: .: (0.000072) test_clustal_have_same_name_true: .: (0.000051) test_have_same_name_false: .: (0.000048) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000112) test_gap_char_default: .: (0.000043) test_gap_char_never_nil: .: (0.000035) test_gap_regexp: .: (0.000039) test_gap_regexp=: .: (0.000039) test_gap_regexp_never_nil: .: (0.000037) test_get_all_property_default: .: (0.000039) test_get_all_property_nodefault: .: (0.000050) test_is_gap_default_false: .: (0.000045) test_is_gap_default_true: .: (0.000039) test_is_gap_nodefault_false: .: (0.000037) test_is_gap_nodefault_true: .: (0.000036) test_missing_char=: .: (0.000038) test_missing_char_default: .: (0.000035) test_missing_char_never_nil: .: (0.000034) test_seqclass=: .: (0.000039) test_seqclass_default: .: (0.000037) test_seqclass_never_nil: .: (0.000034) test_set_all_property: .: (0.000046) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000309) test_consensus_string_50percent: .: (0.000057) test_consensus_string_50percent_nil: .: (0.000047) test_consensus_string_default: .: (0.000037) test_consensus_string_default_nil: .: (0.000039) test_has_gap_false: .: (0.000042) test_has_gap_true: .: (0.000066) test_match_line_amino_100percent: .: (0.000070) test_match_line_amino_missing: .: (0.000090) test_match_line_amino_strong: .: (0.000055) test_match_line_amino_weak: .: (0.000069) test_match_line_nuc_100percent: .: (0.000055) test_match_line_nuc_missing: .: (0.000051) test_remove_gaps!: .: (0.000048) test_remove_gaps_bang_not_removed: .: (0.000038) Bio::TestAtomFinder: test_atoms: .: (0.018730) test_each_atom: .: (0.000130) test_find_atom: .: (0.000092) Bio::TestBioFastaDefline: test_acc_version: .: (0.000487) test_accession: .: (0.000263) test_accessions: .: (0.000182) test_description: .: (0.000153) test_descriptions: .: (0.000459) test_entry_id: .: (0.000164) test_get: .: (0.000183) test_get_all_by_type: .: (0.000285) test_get_by_type: .: (0.000139) test_gi: .: (0.000124) test_id_strings: .: (0.000427) test_locus: .: (0.000151) test_method_missing: .: (0.000191) test_to_s: .: (0.000181) test_words: .: (0.000408) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000686) test_goid2term: .: (0.000220) test_parse_goids: .: (0.000529) Bio::TestBioGenBank: test_basecount: .: (0.000311) test_circular: .: (0.000156) test_classification: .: (0.000194) test_date: .: (0.000140) test_date_modified: .: (0.000474) test_division: .: (0.000155) test_each_cds_feature: .: (0.000487) test_each_cds_qualifiers: .: (0.000505) test_each_gene: .: (0.000493) test_entry_id: .: (0.000162) test_length: .: (0.000143) test_locus_circular: .: (0.000474) test_locus_class: .: (0.000213) test_locus_date: .: (0.000173) test_locus_division: .: (0.000162) test_locus_entry_id: .: (0.000137) test_locus_length: .: (0.000131) test_locus_natype: .: (0.000130) test_locus_strand: .: (0.005540) test_natype: .: (0.000268) test_seq: .: (0.000207) test_seq_len: .: (0.000167) test_strand: .: (0.000424) test_strandedness: .: (0.000225) test_to_biosequence: .: (0.002164) Bio::TestBioGenPept: test_circular: .: (0.000356) test_date: .: (0.000126) test_dbsource: .: (0.000108) test_division: .: (0.000103) test_entry_id: .: (0.000097) test_length: .: (0.000097) test_locus: .: (0.000112) test_seq: .: (0.000228) test_seq_len: .: (0.000139) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000510) test_aaseq: .: (0.000281) test_chromosome: .: (0.000162) test_codon_usage: .: (0.000218) test_cu_list: .: (0.000110) test_dblinks_as_hash: .: (0.000157) test_dblinks_as_strings: .: (0.000142) test_definition: .: (0.000157) test_division: .: (0.000126) test_eclinks: .: (0.000398) test_entry: .: (0.000138) test_entry_id: .: (0.000103) test_gbposition: .: (0.000123) test_gene: .: (0.000120) test_genes: .: (0.000113) test_keggclass: .: (0.000570) test_keggclasses: .: (0.000208) test_locations: .: (0.000250) test_motifs_as_hash: .: (0.000170) test_motifs_as_strings: .: (0.000109) test_name: .: (0.000116) test_names_as_array: .: (0.000151) test_new: .: (0.000131) test_ntlen: .: (0.000171) test_ntseq: .: (0.000206) test_organism: .: (0.000107) test_orthologs_as_hash: .: (0.000134) test_orthologs_as_strings: .: (0.000107) test_pathway: .: (0.000127) test_pathway_after_pathways_as_strings: .: (0.000156) test_pathway_before_pathways_as_strings: .: (0.000193) test_pathways_as_hash: .: (0.000145) test_pathways_as_strings: .: (0.000113) test_position: .: (0.000125) test_structure: .: (0.000123) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001148) test_comment: .: (0.000250) test_data_source: .: (0.000277) test_definition: .: (0.000211) test_disease: .: (0.000203) test_entry_id: .: (0.000191) test_lineage: .: (0.000241) test_nalen: .: (0.000232) test_name: .: (0.000234) test_new: .: (0.000224) test_num_gene: .: (0.000243) test_num_rna: .: (0.000231) test_original_databases: .: (0.000226) test_original_db: .: (0.000528) test_plasmids: .: (0.000339) test_references: .: (0.001622) test_statistics: .: (0.000302) test_taxid: .: (0.000253) test_taxonomy: .: (0.000290) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000315) test_comment: .: (0.000398) test_data_source: .: (0.000244) test_definition: .: (0.000136) test_disease: .: (0.000108) test_entry_id: .: (0.000107) test_lineage: .: (0.000129) test_nalen: .: (0.000125) test_name: .: (0.000122) test_new: .: (0.000116) test_num_gene: .: (0.000175) test_num_rna: .: (0.000189) test_original_databases: .: (0.000125) test_original_db: .: (0.000167) test_plasmids: .: (0.000190) test_references: .: (0.000224) test_statistics: .: (0.000119) test_taxid: .: (0.000150) test_taxonomy: .: (0.000135) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000285) test_compounds_as_strings: .: (0.000119) test_dblinks_as_hash: .: (0.000090) test_dblinks_as_strings: .: (0.000076) test_description: .: (0.000400) test_diseases_as_hash: .: (0.000144) test_diseases_as_strings: .: (0.000090) test_entry_id: .: (0.000103) test_enzymes_as_strings: .: (0.000167) test_genes_as_hash: .: (0.000140) test_genes_as_strings: .: (0.000086) test_keggclass: .: (0.000101) test_ko_pathway: .: (0.000092) test_modules_as_hash: .: (0.000168) test_modules_as_strings: .: (0.000100) test_name: .: (0.000099) test_new: .: (0.000112) test_organism: .: (0.000096) test_orthologs_as_hash: .: (0.000087) test_orthologs_as_strings: .: (0.000076) test_pathways_as_hash: .: (0.006521) test_pathways_as_strings: .: (0.000385) test_reactions_as_hash: .: (0.000122) test_reactions_as_strings: .: (0.000162) test_references: .: (0.000129) test_rel_pathways_as_hash: .: (0.000143) test_rel_pathways_as_strings: .: (0.000109) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000406) test_compounds_as_strings: .: (0.000184) test_dblinks_as_hash: .: (0.000126) test_dblinks_as_strings: .: (0.000136) test_description: .: (0.000160) test_diseases_as_hash: .: (0.000140) test_diseases_as_strings: .: (0.001234) test_entry_id: .: (0.000191) test_enzymes_as_strings: .: (0.000115) test_genes_as_hash: .: (0.000169) test_genes_as_strings: .: (0.000127) test_keggclass: .: (0.000185) test_ko_pathway: .: (0.000140) test_modules_as_hash: .: (0.000135) test_modules_as_strings: .: (0.000112) test_name: .: (0.000132) test_new: .: (0.000144) test_organism: .: (0.000121) test_orthologs_as_hash: .: (0.000104) test_orthologs_as_strings: .: (0.000426) test_pathways_as_hash: .: (0.000150) test_pathways_as_strings: .: (0.000109) test_reactions_as_hash: .: (0.000103) test_reactions_as_strings: .: (0.000098) test_references: .: (0.000098) test_rel_pathways_as_hash: .: (0.000129) test_rel_pathways_as_strings: .: (0.000112) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000308) test_compounds_as_strings: .: (0.000116) test_dblinks_as_hash: .: (0.000093) test_dblinks_as_strings: .: (0.000081) test_description: .: (0.000119) test_diseases_as_hash: .: (0.000093) test_diseases_as_strings: .: (0.000299) test_entry_id: .: (0.000250) test_enzymes_as_strings: .: (0.000100) test_genes_as_hash: .: (0.000087) test_genes_as_strings: .: (0.000083) test_keggclass: .: (0.000104) test_ko_pathway: .: (0.000097) test_modules_as_hash: .: (0.000088) test_modules_as_strings: .: (0.000083) test_name: .: (0.000095) test_new: .: (0.000106) test_organism: .: (0.000098) test_orthologs_as_hash: .: (0.000162) test_orthologs_as_strings: .: (0.000111) test_pathways_as_hash: .: (0.000101) test_pathways_as_strings: .: (0.000089) test_reactions_as_hash: .: (0.000092) test_reactions_as_strings: .: (0.000081) test_references: .: (0.000087) test_rel_pathways_as_hash: .: (0.000093) test_rel_pathways_as_strings: .: (0.000086) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000310) test_compounds_as_strings: .: (0.000351) test_dblinks_as_hash: .: (0.000172) test_dblinks_as_strings: .: (0.000111) test_description: .: (0.000273) test_diseases_as_hash: .: (0.000144) test_diseases_as_strings: .: (0.000108) test_entry_id: .: (0.000124) test_enzymes_as_strings: .: (0.000106) test_genes_as_hash: .: (0.000186) test_genes_as_strings: .: (0.000122) test_keggclass: .: (0.000132) test_ko_pathway: .: (0.000118) test_modules_as_hash: .: (0.000562) test_modules_as_strings: .: (0.000198) test_name: .: (0.000138) test_new: .: (0.000133) test_organism: .: (0.000485) test_orthologs_as_hash: .: (0.000145) test_orthologs_as_strings: .: (0.000105) test_pathways_as_hash: .: (0.000201) test_pathways_as_strings: .: (0.000130) test_reactions_as_hash: .: (0.000131) test_reactions_as_strings: .: (0.000104) test_references: .: (0.000569) test_rel_pathways_as_hash: .: (0.000335) test_rel_pathways_as_strings: .: (0.000118) Bio::TestBioKeggDRUG: test_activity: .: (0.000302) test_comment: .: (0.000154) test_dblinks_as_hash: .: (0.000179) test_dblinks_as_strings: .: (0.000132) test_entry_id: .: (0.000134) test_formula: .: (0.000122) test_kcf: .: (0.000111) test_mass: .: (0.000119) test_name: .: (0.000448) test_names: .: (0.000226) test_pathways_as_hash: .: (0.000160) test_pathways_as_strings: .: (0.000112) test_products: .: (0.000130) test_remark: .: (0.000126) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000271) test_composition: .: (0.000142) test_compounds: .: (0.000112) test_dblinks_as_hash: .: (0.000239) test_dblinks_as_strings: .: (0.000134) test_entry_id: .: (0.000108) test_enzymes: .: (0.000119) test_kcf: .: (0.000096) test_keggclass: .: (0.000109) test_mass: .: (0.000134) test_name: .: (0.000129) test_orthologs_as_hash: .: (0.000169) test_orthologs_as_strings: .: (0.000133) test_pathways_as_hash: .: (0.000124) test_pathways_as_strings: .: (0.000113) test_reactions: .: (0.000125) test_references: .: (0.000453) test_remark: .: (0.000231) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000252) test_composition: .: (0.000128) test_compounds: .: (0.000107) test_dblinks_as_hash: .: (0.000136) test_dblinks_as_strings: .: (0.000092) test_entry_id: .: (0.007027) test_enzymes: .: (0.000540) test_kcf: .: (0.000123) test_keggclass: .: (0.000118) test_mass: .: (0.000116) test_name: .: (0.000113) test_orthologs_as_hash: .: (0.000106) test_orthologs_as_strings: .: (0.000097) test_pathways_as_hash: .: (0.000100) test_pathways_as_strings: .: (0.000824) test_reactions: .: (0.000170) test_references: .: (0.000100) test_remark: .: (0.000113) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000396) test_compounds_as_strings: .: (0.000539) test_dblinks_as_hash: .: (0.000204) test_dblinks_as_strings: .: (0.000136) test_description: .: (0.000168) test_diseases_as_hash: .: (0.000151) test_diseases_as_strings: .: (0.000133) test_entry_id: .: (0.000145) test_enzymes_as_strings: .: (0.000181) test_genes_as_hash: .: (0.000157) test_genes_as_strings: .: (0.000131) test_keggclass: .: (0.000146) test_ko_pathway: .: (0.000138) test_modules_as_hash: .: (0.000196) test_modules_as_strings: .: (0.000397) test_name: .: (0.000154) test_new: .: (0.000141) test_organism: .: (0.000137) test_orthologs_as_hash: .: (0.000123) test_orthologs_as_strings: .: (0.000112) test_pathways_as_hash: .: (0.000126) test_pathways_as_strings: .: (0.000511) test_reactions_as_hash: .: (0.000435) test_reactions_as_strings: .: (0.000234) test_references: .: (0.000359) test_rel_pathways_as_hash: .: (0.000225) test_rel_pathways_as_strings: .: (0.000160) Bio::TestBioLITDB: test_author: .: (0.000588) test_entry_id: .: (0.000111) test_field: .: (0.000452) test_journal: .: (0.000123) test_keyword: .: (0.000133) test_reference: .: (0.000246) test_title: .: (0.000694) test_volume: .: (0.000169) Bio::TestBioNBRF: test_aalen: .: (0.000259) test_aaseq: .: (0.000090) test_entry: .: (0.000076) test_length: .: (0.000070) test_nalen: .: (0.000126) test_naseq: .: (0.000092) test_seq: .: (0.000077) test_seq_class: .: (0.000069) test_to_nbrf: .: (0.000181) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000220) test_to_newick_format_leaf: .: (0.000153) test_to_newick_format_leaf_NHX: .: (0.000121) Bio::TestBl2seqReport: test_db_len: .: (0.000610) test_db_num: .: (0.000298) test_new: .: (0.000187) test_undefed_methods: .: (0.001013) test_undefed_methods_for_iteration: .: (0.000625) Bio::TestBl2seqReportConstants: test_rs: .: (0.000219) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000271) test_hits: .: (0.000177) Bio::TestBlast: test_blast_reports_format0: .: (0.004839) test_blast_reports_format0_with_block: .: (0.000942) test_blast_reports_format7: .: (0.015765) test_blast_reports_format7_with_block: .: (0.026950) test_blast_reports_format7_with_parser: .: (0.028398) test_blast_reports_format7_with_parser_with_block: .: (0.007605) test_blast_reports_format8: .: (0.000678) test_blast_reports_format8_with_block: .: (0.000543) test_blast_reports_format8_with_parser: .: (0.000209) test_blast_reports_format8_with_parser_with_block: .: (0.000141) test_blast_reports_xml: .: (0.007088) test_blast_reports_xml_with_block: .: (0.011394) test_blastll: .: (0.000698) test_db: .: (0.000153) test_exec_genomenet: .: (0.000071) test_exec_local: .: (0.000061) test_exec_ncbi: .: (0.000065) test_filter: .: (0.000235) test_format: .: (0.000084) test_make_command_line: .: (0.000338) test_make_command_line_2: .: (0.000248) test_matrix: .: (0.000077) test_new: .: (0.000132) test_new_opt_string: .: (0.000127) test_option: .: (0.000284) test_option_set: .: (0.000147) test_option_set_m0: .: (0.000108) test_options: .: (0.000089) test_output: .: (0.000070) test_parse_result: .: (0.007021) test_parser: .: (0.000158) test_program: .: (0.000071) test_query: .: (0.000057) test_self_local: .: (0.000103) test_self_remote: .: (0.001648) test_server: .: (0.000172) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000290) test_delete: .: (0.000187) test_equal_equal: .: (0.000196) test_get: .: (0.000224) test_make_command_line_options: .: (0.000172) test_normalize!: .: (0.000101) test_parse: .: (0.000130) test_set: .: (0.000230) Bio::TestBlastReport: test_db: .: (0.006658) test_db_len: .: (0.011578) test_db_num: .: (0.007114) test_each_hit: .: (0.006888) test_each_iteration: .: (0.008501) test_eff_space: .: (0.008202) test_entrez_query: .: (0.007021) test_entropy: .: (0.006470) test_expect: .: (0.009517) test_filter: .: (0.007198) test_gap_extend: .: (0.006641) test_gap_open: .: (0.008466) test_hits: .: (0.008390) test_hsp_len: .: (0.006995) test_inclusion: .: (0.006651) test_iterations: .: (0.009057) test_kappa: .: (0.007040) test_lambda: .: (0.006673) test_matrix: .: (0.008194) test_message: .: (0.007902) test_parameters: .: (0.007176) test_pattern: .: (0.006415) test_program: .: (0.008963) test_query_def: .: (0.007030) test_query_id: .: (0.006822) test_query_len: .: (0.008142) test_reference: .: (0.007880) test_sc_match: .: (0.006989) test_sc_mismatch: .: (0.006409) test_statistics: .: (0.009033) test_version: .: (0.007149) Bio::TestBlastReportDefault: test_db: .: (0.000590) test_db_len: .: (0.000375) test_db_num: .: (0.000283) test_each_hit: .: (0.000293) test_each_iteration: .: (0.000263) test_eff_space: .: (0.000353) test_entropy: .: (0.000304) test_expect: .: (0.000650) test_gap_extend: .: (0.000371) test_gap_open: .: (0.000302) test_gapped_entropy: .: (0.000281) test_gapped_kappa: .: (0.000263) test_gapped_lambda: .: (0.000264) test_hits: .: (0.000271) test_iterations: .: (0.000440) test_kappa: .: (0.000316) test_lambda: .: (0.000278) test_matrix: .: (0.000325) test_message: .: (0.000241) test_pattern: .: (0.000504) test_program: .: (0.000284) test_query_def: .: (0.000271) test_query_len: .: (0.000246) test_reference: .: (0.000331) test_sc_match: .: (0.000332) test_sc_mismatch: .: (0.000292) test_version: .: (0.000249) Bio::TestBlastReportHit: test_Hit_accession: .: (0.006526) test_Hit_bit_score: .: (0.009795) test_Hit_definition: .: (0.007122) test_Hit_evalue: .: (0.006793) test_Hit_hit_id: .: (0.009621) test_Hit_hsps: .: (0.007004) test_Hit_identity: .: (0.006807) test_Hit_lap_at: .: (0.008690) test_Hit_len: .: (0.008030) test_Hit_midline: .: (0.006880) test_Hit_num: .: (0.006508) test_Hit_overlap: .: (0.009229) test_Hit_query_def: .: (0.007127) test_Hit_query_end: .: (0.006891) test_Hit_query_id: .: (0.008741) test_Hit_query_len: .: (0.007082) test_Hit_query_seq: .: (0.006722) test_Hit_query_start: .: (0.008182) test_Hit_taeget_def: .: (0.007946) test_Hit_target_end: .: (0.007009) test_Hit_target_id: .: (0.006533) test_Hit_target_len: .: (0.009106) test_Hit_target_seq: .: (0.007099) test_Hit_target_start: .: (0.006631) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000567) test_Hit_definition: .: (0.000333) test_Hit_evalue: .: (0.000296) test_Hit_hsps: .: (0.000258) test_Hit_identity: .: (0.000607) test_Hit_lap_at: .: (0.000432) test_Hit_len: .: (0.000282) test_Hit_midline: .: (0.000370) test_Hit_overlap: .: (0.000274) test_Hit_query_end: .: (0.000414) test_Hit_query_seq: .: (0.000378) test_Hit_query_start: .: (0.000372) test_Hit_taeget_def: .: (0.000284) test_Hit_target_end: .: (0.000357) test_Hit_target_id: .: (0.000665) test_Hit_target_len: .: (0.000312) test_Hit_target_seq: .: (0.000364) test_Hit_target_start: .: (0.000349) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.021712) test_Hit_bit_score: .: (0.020836) test_Hit_definition: .: (0.020681) test_Hit_evalue: .: (0.020502) test_Hit_hit_id: .: (0.020293) test_Hit_hsps: .: (0.021867) test_Hit_identity: .: (0.020451) test_Hit_lap_at: .: (0.020339) test_Hit_len: .: (0.019826) test_Hit_midline: .: (0.020089) test_Hit_num: .: (0.020584) test_Hit_overlap: .: (0.020296) test_Hit_query_def: .: (0.020400) test_Hit_query_end: .: (0.020228) test_Hit_query_id: .: (0.020287) test_Hit_query_len: .: (0.019958) test_Hit_query_seq: .: (0.020830) test_Hit_query_start: .: (0.020717) test_Hit_taeget_def: .: (0.021914) test_Hit_target_end: .: (0.020701) test_Hit_target_id: .: (0.020281) test_Hit_target_len: .: (0.021464) test_Hit_target_seq: .: (0.021552) test_Hit_target_start: .: (0.020866) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.019925) test_Hit_bit_score: .: (0.020528) test_Hit_definition: .: (0.021775) test_Hit_evalue: .: (0.020427) test_Hit_hit_id: .: (0.020816) test_Hit_hsps: .: (0.020145) test_Hit_identity: .: (0.019972) test_Hit_lap_at: .: (0.020803) test_Hit_len: .: (0.020356) test_Hit_midline: .: (0.022878) test_Hit_num: .: (0.020380) test_Hit_overlap: .: (0.020026) test_Hit_query_def: .: (0.020013) test_Hit_query_end: .: (0.031042) test_Hit_query_id: .: (0.020510) test_Hit_query_len: .: (0.020267) test_Hit_query_seq: .: (0.020345) test_Hit_query_start: .: (0.020386) test_Hit_taeget_def: .: (0.020075) test_Hit_target_end: .: (0.020259) test_Hit_target_id: .: (0.020238) test_Hit_target_len: .: (0.021019) test_Hit_target_seq: .: (0.020660) test_Hit_target_start: .: (0.020251) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.008995) test_Hit_bit_score: .: (0.015056) test_Hit_definition: .: (0.007021) test_Hit_evalue: .: (0.009110) test_Hit_hit_id: .: (0.006921) test_Hit_hsps: .: (0.006872) test_Hit_identity: .: (0.008911) test_Hit_lap_at: .: (0.006938) test_Hit_len: .: (0.006841) test_Hit_midline: .: (0.009164) test_Hit_num: .: (0.006999) test_Hit_overlap: .: (0.007055) test_Hit_query_def: .: (0.009102) test_Hit_query_end: .: (0.006938) test_Hit_query_id: .: (0.006837) test_Hit_query_len: .: (0.008887) test_Hit_query_seq: .: (0.006995) test_Hit_query_start: .: (0.006780) test_Hit_taeget_def: .: (0.009084) test_Hit_target_end: .: (0.007056) test_Hit_target_id: .: (0.007656) test_Hit_target_len: .: (0.012140) test_Hit_target_seq: .: (0.006926) test_Hit_target_start: .: (0.007006) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000309) test_Hit_bit_score: .: (0.000094) test_Hit_definition: .: (0.000075) test_Hit_evalue: .: (0.000076) test_Hit_hit_id: .: (0.000078) test_Hit_hsps: .: (0.000077) test_Hit_identity: .: (0.000067) test_Hit_lap_at: .: (0.000080) test_Hit_len: .: (0.000066) test_Hit_midline: .: (0.000065) test_Hit_num: .: (0.000069) test_Hit_overlap: .: (0.000071) test_Hit_query_def: .: (0.000075) test_Hit_query_end: .: (0.000069) test_Hit_query_id: .: (0.000067) test_Hit_query_len: .: (0.000069) test_Hit_query_seq: .: (0.000068) test_Hit_query_start: .: (0.000069) test_Hit_taeget_def: .: (0.000068) test_Hit_target_end: .: (0.000063) test_Hit_target_id: .: (0.000063) test_Hit_target_len: .: (0.000063) test_Hit_target_seq: .: (0.000063) test_Hit_target_start: .: (0.000061) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.009426) test_Hsp_bit_score: .: (0.007112) test_Hsp_density: .: (0.006894) test_Hsp_evalue: .: (0.009556) test_Hsp_gaps: .: (0.007500) test_Hsp_hit_frame: .: (0.006883) test_Hsp_hit_from: .: (0.009105) test_Hsp_hit_to: .: (0.006989) test_Hsp_hseq: .: (0.006982) test_Hsp_identity: .: (0.009099) test_Hsp_midline: .: (0.006840) test_Hsp_mismatch_count: .: (0.006882) test_Hsp_num: .: (0.009109) test_Hsp_pattern_from: .: (0.007163) test_Hsp_pattern_to: .: (0.006761) test_Hsp_percent_identity: .: (0.009158) test_Hsp_positive: .: (0.007120) test_Hsp_qseq: .: (0.007005) test_Hsp_query_frame: .: (0.009208) test_Hsp_query_from: .: (0.006754) test_Hsp_query_to: .: (0.006720) test_Hsp_score: .: (0.009004) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.001132) test_Hsp_bit_score: .: (0.000395) test_Hsp_evalue: .: (0.000294) test_Hsp_gaps: .: (0.000427) test_Hsp_hit_frame: .: (0.000333) test_Hsp_hit_from: .: (0.000360) test_Hsp_hit_to: .: (0.000548) test_Hsp_hseq: .: (0.000393) test_Hsp_identity: .: (0.000278) test_Hsp_midline: .: (0.000692) test_Hsp_percent_identity: .: (0.000327) test_Hsp_positive: .: (0.000290) test_Hsp_qseq: .: (0.000608) test_Hsp_query_frame: .: (0.000308) test_Hsp_query_from: .: (0.000347) test_Hsp_query_to: .: (0.000332) test_Hsp_score: .: (0.000289) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.021333) test_Hsp_bit_score: .: (0.020736) test_Hsp_density: .: (0.020892) test_Hsp_evalue: .: (0.020494) test_Hsp_gaps: .: (0.020953) test_Hsp_hit_frame: .: (0.021202) test_Hsp_hit_from: .: (0.021340) test_Hsp_hit_to: .: (0.021007) test_Hsp_hseq: .: (0.021689) test_Hsp_identity: .: (0.020509) test_Hsp_midline: .: (0.020103) test_Hsp_mismatch_count: .: (0.021684) test_Hsp_num: .: (0.020782) test_Hsp_pattern_from: .: (0.021939) test_Hsp_pattern_to: .: (0.020427) test_Hsp_percent_identity: .: (0.020160) test_Hsp_positive: .: (0.020272) test_Hsp_qseq: .: (0.020644) test_Hsp_query_frame: .: (0.020347) test_Hsp_query_from: .: (0.021215) test_Hsp_query_to: .: (0.020939) test_Hsp_score: .: (0.027895) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.023092) test_Hsp_bit_score: .: (0.025619) test_Hsp_density: .: (0.020836) test_Hsp_evalue: .: (0.020455) test_Hsp_gaps: .: (0.020286) test_Hsp_hit_frame: .: (0.020449) test_Hsp_hit_from: .: (0.020069) test_Hsp_hit_to: .: (0.019904) test_Hsp_hseq: .: (0.020579) test_Hsp_identity: .: (0.020566) test_Hsp_midline: .: (0.020051) test_Hsp_mismatch_count: .: (0.020016) test_Hsp_num: .: (0.019884) test_Hsp_pattern_from: .: (0.020621) test_Hsp_pattern_to: .: (0.020080) test_Hsp_percent_identity: .: (0.021616) test_Hsp_positive: .: (0.020209) test_Hsp_qseq: .: (0.020512) test_Hsp_query_frame: .: (0.020234) test_Hsp_query_from: .: (0.020900) test_Hsp_query_to: .: (0.020738) test_Hsp_score: .: (0.019813) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.010204) test_Hsp_bit_score: .: (0.007414) test_Hsp_density: .: (0.006705) test_Hsp_evalue: .: (0.008998) test_Hsp_gaps: .: (0.006981) test_Hsp_hit_frame: .: (0.006566) test_Hsp_hit_from: .: (0.008866) test_Hsp_hit_to: .: (0.007357) test_Hsp_hseq: .: (0.006473) test_Hsp_identity: .: (0.008840) test_Hsp_midline: .: (0.006989) test_Hsp_mismatch_count: .: (0.006568) test_Hsp_num: .: (0.008998) test_Hsp_pattern_from: .: (0.006894) test_Hsp_pattern_to: .: (0.008080) test_Hsp_percent_identity: .: (0.009155) test_Hsp_positive: .: (0.007163) test_Hsp_qseq: .: (0.006914) test_Hsp_query_frame: .: (0.009318) test_Hsp_query_from: .: (0.007393) test_Hsp_query_to: .: (0.006728) test_Hsp_score: .: (0.009210) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000406) test_Hsp_bit_score: .: (0.000090) test_Hsp_density: .: (0.000083) test_Hsp_evalue: .: (0.000074) test_Hsp_gaps: .: (0.000074) test_Hsp_hit_frame: .: (0.000065) test_Hsp_hit_from: .: (0.000071) test_Hsp_hit_to: .: (0.000065) test_Hsp_hseq: .: (0.000065) test_Hsp_identity: .: (0.000068) test_Hsp_midline: .: (0.000095) test_Hsp_mismatch_count: .: (0.000086) test_Hsp_num: .: (0.000074) test_Hsp_pattern_from: .: (0.000069) test_Hsp_pattern_to: .: (0.000068) test_Hsp_percent_identity: .: (0.000064) test_Hsp_positive: .: (0.000066) test_Hsp_qseq: .: (0.000066) test_Hsp_query_frame: .: (0.000077) test_Hsp_query_from: .: (0.000075) test_Hsp_query_to: .: (0.000075) test_Hsp_score: .: (0.000368) Bio::TestBlastReportIteration: test_hits: .: (0.006922) test_message: .: (0.008100) test_num: .: (0.007923) test_statistics: .: (0.007093) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000517) test_message: .: (0.000289) test_num: .: (0.000248) Bio::TestBlastReportIterationMulti: test_each: .: (0.020896) test_hits: .: (0.021981) test_message: .: (0.021319) test_num: .: (0.020307) test_query_def: .: (0.021373) test_query_id: .: (0.021958) test_query_len: .: (0.023473) test_statistics: .: (0.021894) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.022171) test_hits: .: (0.022076) test_message: .: (0.020410) test_num: .: (0.021736) test_query_def: .: (0.020146) test_query_id: .: (0.021553) test_query_len: .: (0.021048) test_statistics: .: (0.020214) Bio::TestBlastReportIterationREXML: test_hits: .: (0.006561) test_message: .: (0.009159) test_num: .: (0.006940) test_statistics: .: (0.007059) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000278) test_message: .: (0.000088) test_num: .: (0.000078) test_statistics: .: (0.000076) Bio::TestBlastReportMulti: test_db: .: (0.022681) test_db_len: .: (0.021522) test_db_num: .: (0.028821) test_each_hit: .: (0.043056) test_each_iteration: .: (0.020841) test_eff_space: .: (0.024261) test_entropy: .: (0.021915) test_expect: .: (0.020559) test_filter: .: (0.020434) test_gap_extend: .: (0.022441) test_gap_open: .: (0.020803) test_hits: .: (0.020141) test_hsp_len: .: (0.019872) test_iterations: .: (0.021734) test_kappa: .: (0.020967) test_lambda: .: (0.059000) test_matrix: .: (0.020495) test_message: .: (0.020052) test_parameters: .: (0.020230) test_pattern: .: (0.019817) test_program: .: (0.020124) test_query_def: .: (0.020467) test_query_id: .: (0.019826) test_query_len: .: (0.019777) test_reference: .: (0.020223) test_reports: .: (0.019800) test_statistics: .: (0.020076) test_version: .: (0.020273) Bio::TestBlastReportMultiREXML: test_db: .: (0.020323) test_db_len: .: (0.020404) test_db_num: .: (0.020104) test_each_hit: .: (0.019927) test_each_iteration: .: (0.020321) test_eff_space: .: (0.021932) test_entropy: .: (0.022800) test_expect: .: (0.021082) test_filter: .: (0.021332) test_gap_extend: .: (0.020386) test_gap_open: .: (0.020658) test_hits: .: (0.020434) test_hsp_len: .: (0.021636) test_iterations: .: (0.022119) test_kappa: .: (0.021770) test_lambda: .: (0.020279) test_matrix: .: (0.019880) test_message: .: (0.021288) test_parameters: .: (0.021435) test_pattern: .: (0.020486) test_program: .: (0.020904) test_query_def: .: (0.022336) test_query_id: .: (0.022173) test_query_len: .: (0.020930) test_reference: .: (0.020106) test_reports: .: (0.023553) test_statistics: .: (0.022158) test_version: .: (0.021090) Bio::TestBlastReportREXML: test_db: .: (0.009984) test_db_len: .: (0.007009) test_db_num: .: (0.008931) test_each_hit: .: (0.007751) test_each_iteration: .: (0.006789) test_eff_space: .: (0.009277) test_entrez_query: .: (0.006954) test_entropy: .: (0.008839) test_expect: .: (0.015392) test_filter: .: (0.012058) test_gap_extend: .: (0.015819) test_gap_open: .: (0.015112) test_hits: .: (0.016947) test_hsp_len: .: (0.012011) test_inclusion: .: (0.008884) test_iterations: .: (0.008252) test_kappa: .: (0.007126) test_lambda: .: (0.008947) test_matrix: .: (0.007141) test_message: .: (0.009928) test_parameters: .: (0.007279) test_pattern: .: (0.007618) test_program: .: (0.009610) test_query_def: .: (0.007371) test_query_id: .: (0.009015) test_query_len: .: (0.007328) test_reference: .: (0.007903) test_sc_match: .: (0.008162) test_sc_mismatch: .: (0.006961) test_statistics: .: (0.009537) test_version: .: (0.006944) Bio::TestBlastReportTabular: test_db: .: (0.000284) test_db_len: .: (0.000083) test_db_num: .: (0.000075) test_each_hit: .: (0.000076) test_each_iteration: .: (0.000069) test_eff_space: .: (0.000666) test_entrez_query: .: (0.000114) test_entropy: .: (0.000082) test_expect: .: (0.000068) test_filter: .: (0.000070) test_gap_extend: .: (0.000067) test_gap_open: .: (0.000066) test_hits: .: (0.000075) test_hsp_len: .: (0.000117) test_inclusion: .: (0.000101) test_iterations: .: (0.000076) test_kappa: .: (0.000068) test_lambda: .: (0.000066) test_matrix: .: (0.000066) test_message: .: (0.000067) test_parameters: .: (0.000068) test_pattern: .: (0.000064) test_program: .: (0.000062) test_query_def: .: (0.000072) test_query_id: .: (0.000064) test_query_len: .: (0.000063) test_reference: .: (0.000064) test_sc_match: .: (0.000066) test_sc_mismatch: .: (0.000065) test_statistics: .: (0.000065) test_version: .: (0.000060) Bio::TestChain: test_aaseq: .: (0.000285) test_addLigand: .: (0.000054) test_addResidue: .: (0.000045) test_atom_seq: .: (0.000051) test_comp: .: (0.000074) test_each: .: (0.000052) test_each_heterogen: .: (0.000054) test_each_residue: .: (0.000050) test_get_heterogen_by_id: .: (0.000048) test_get_residue_by_id: .: (0.000046) test_inspect: .: (0.000069) test_rehash: .: (0.000481) test_rehash_heterogens: .: (0.000069) test_rehash_residues: .: (0.000044) test_square_brace: .: (0.000069) test_to_s: .: (0.000069) Bio::TestChainFinder: test_chains: .: (0.000199) test_each_chain: .: (0.000068) test_find_chain: .: (0.000058) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.007820) test_header: .: (0.000640) test_match_line: .: (0.000369) test_sequence0: .: (0.000527) test_sequence1: .: (0.000390) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.005361) test_header: .: (0.000642) test_match_line: .: (0.000799) test_sequence0: .: (0.000570) test_sequence1: .: (0.000726) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.005957) test_header: .: (0.000475) test_match_line: .: (0.000354) test_sequence0: .: (0.000383) test_sequence1: .: (0.000377) Bio::TestCodonTable: test_Tables: .: (0.000206) test_accessor: .: (0.000142) test_definition: .: (0.000041) test_each: .: (0.000058) test_revtrans: .: (0.000379) test_self_accessor: .: (0.000070) test_self_copy: .: (0.000481) test_set_accessor: .: (0.048311) test_start: .: (0.000087) test_start_codon?: .: (0.000060) test_stop: .: (0.000038) test_stop_codon?: .: (0.000045) test_table: .: (0.000098) Bio::TestCodonTableConstants: test_Definitions: .: (0.000173) test_Starts: .: (0.000053) test_Tables: .: (0.000035) test_stops: .: (0.000041) Bio::TestColorScheme: test_buried: .: (0.000756) Bio::TestCommand: test_command_constants: .: (0.000157) test_escape_shell: .: (0.000166) test_escape_shell_unix: .: (0.000056) test_escape_shell_windows: .: (0.000066) test_make_cgi_params_by_array_of_array: .: (0.000209) test_make_cgi_params_by_array_of_hash: .: (0.000155) test_make_cgi_params_by_array_of_string: .: (0.000148) test_make_cgi_params_by_hash_in_string: .: (0.000349) test_make_cgi_params_by_hash_in_symbol: .: (0.000250) test_make_cgi_params_by_string: .: (0.000102) test_make_command_line: .: (0.000073) test_make_command_line_unix: .: (0.000049) test_make_command_line_windows: .: (0.000057) test_safe_command_line_array: .: (0.000064) test_safe_command_line_array_passthrough: .: (0.000054) Bio::TestContingencyTable: test_lite_example: .: (0.115677) Bio::TestDB: test_entry_id: .: (0.000422) test_exists: .: (0.005413) test_fetch: .: (0.000339) test_get: .: (0.000318) test_open: .: (0.000220) test_tags: .: (0.000159) Bio::TestDataType: test_const_like_method: .: (0.000570) test_pdb_achar: .: (0.000286) test_pdb_atom: .: (0.000243) test_pdb_character: .: (0.000262) test_pdb_date: .: (0.000241) test_pdb_idcode: .: (0.000242) test_pdb_integer: .: (0.000129) test_pdb_list: .: (0.000139) test_pdb_lstring: .: (0.000294) test_pdb_real: .: (0.000213) test_pdb_resudue_name: .: (0.000238) test_pdb_slist: .: (0.000133) test_pdb_string: .: (0.000278) test_pdb_stringrj: .: (0.000139) test_pdb_symop: .: (0.000229) test_specification_list: .: (0.004176) Bio::TestEMBL: test_ac: .: (0.000582) test_accession: .: (0.000426) test_cc: .: (0.000291) test_de: .: (0.000327) test_division: .: (0.000477) test_dr: .: (0.000512) test_dt: .: (0.000448) test_dt_created: .: (0.000419) test_dt_iterator: .: (0.000409) test_dt_updated: .: (0.005924) test_each_cds: .: (0.000629) test_each_gene: .: (0.000520) test_entry: .: (0.000472) test_fh: .: (0.000506) test_ft: .: (0.000535) test_ft_accessor: .: (0.000509) test_ft_iterator: .: (0.000625) test_id_line: .: (0.000445) test_id_line_data_class: .: (0.000363) test_id_line_division: .: (0.000820) test_id_line_entry_name: .: (0.000511) test_id_line_iterator: .: (0.000475) test_id_line_molecule_type: .: (0.000467) test_id_line_sequence_length: .: (0.000454) test_kw: .: (0.007819) test_molecule: .: (0.000542) test_oc: .: (0.000515) test_og: .: (0.000415) test_os: .: (0.000453) test_ref: .: (0.000481) test_references: .: (0.000945) test_seq: .: (0.000585) test_sequence_length: .: (0.000458) test_sq: .: (0.005443) test_sq_get: .: (0.000573) test_sv: .: (0.000692) test_version: .: (0.000447) Bio::TestEMBL89: test_ac: .: (0.000622) test_accession: .: (0.000442) test_cc: .: (0.000393) test_de: .: (0.000421) test_division: .: (0.000433) test_dr: .: (0.000376) test_dt: .: (0.000555) test_dt_created: .: (0.000637) test_dt_iterator: .: (0.000448) test_dt_updated: .: (0.000401) test_each_cds: .: (0.000516) test_each_gene: .: (0.000429) test_entry: .: (0.000545) test_fh: .: (0.000363) test_ft: .: (0.000531) test_ft_accessor: .: (0.006470) test_ft_iterator: .: (0.000563) test_id_line: .: (0.000562) test_id_line_data_class: .: (0.000375) test_id_line_division: .: (0.000333) test_id_line_entry_name: .: (0.000379) test_id_line_iterator: .: (0.000344) test_id_line_molecule_type: .: (0.000368) test_id_line_sequence_length: .: (0.000514) test_id_line_sequence_version: .: (0.000314) test_kw: .: (0.000311) test_molecule: .: (0.000330) test_oc: .: (0.000367) test_og: .: (0.000312) test_os: .: (0.000463) test_ref: .: (0.004230) test_references: .: (0.000589) test_seq: .: (0.001929) test_sequence_length: .: (0.000768) test_sq: .: (0.004008) test_sq_get: .: (0.000458) test_sv: .: (0.000418) test_version: .: (0.000386) Bio::TestEMBLAPI: test_ac: .: (0.000360) test_accessions: .: (0.000182) Bio::TestEMBLCommon: test_ac: .: (0.000291) test_accession: .: (0.000127) test_accessions: .: (0.000159) test_de: .: (0.000132) test_definition: .: (0.000130) test_description: .: (0.000127) test_dr: .: (0.000131) test_keywords: .: (0.006910) test_kw: .: (0.000234) test_oc: .: (0.000137) test_og: .: (0.000125) test_os: .: (0.000133) test_ref: .: (0.000128) test_references: .: (0.000142) Bio::TestEMBLDB: test_fetch: .: (0.000363) test_p_entry2hash: .: (0.000119) Bio::TestEMBLToBioSequence: test_classification: .: (0.002512) test_date_created: .: (0.000545) test_date_modified: .: (0.000442) test_definition: .: (0.000390) test_division: .: (0.000395) test_entry_id: .: (0.000380) test_entry_version: .: (0.003404) test_features: .: (0.000671) test_keywords: .: (0.000477) test_molecule_type: .: (0.000488) test_primary_accession: .: (0.000499) test_references: .: (0.000665) test_release_created: .: (0.003595) test_release_modified: .: (0.000570) test_secondary_accessions: .: (0.000521) test_sequence_version: .: (0.000540) test_species: .: (0.000496) test_topology: .: (0.000520) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.015481) test_date_created: .: (0.007655) test_date_modified: .: (0.007584) test_definition: .: (0.002420) test_division: .: (0.008921) test_entry_id: .: (0.002569) test_entry_version: .: (0.008785) test_features: .: (0.002466) test_keywords: .: (0.002257) test_molecule_type: .: (0.014629) test_primary_accession: .: (0.007890) test_references: .: (0.007316) test_release_created: .: (0.002456) test_release_modified: .: (0.008901) test_secondary_accessions: .: (0.002547) test_sequence_version: .: (0.002489) test_species: .: (0.006085) test_topology: .: (0.002361) Bio::TestFasta: test_db: .: (0.000382) test_format: .: (0.000202) test_format_arg_integer: .: (0.000216) test_format_arg_str: .: (0.000243) test_ktup: .: (0.000193) test_matrix: .: (0.000205) test_option: .: (0.000258) test_options: .: (0.000201) test_output: .: (0.000185) test_program: .: (0.000184) test_server: .: (0.000226) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000349) test_accession: .: (0.000220) test_accessions: .: (0.000227) test_description: .: (0.000209) test_descriptions: .: (0.000238) test_entry_id: .: (0.000224) test_get_all_by_type: .: (0.000217) test_gi: .: (0.000210) test_id_strings: .: (0.000278) test_list_ids: .: (0.000213) test_locus: .: (0.000241) test_words: .: (0.000391) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000413) test_accession: .: (0.000262) test_accessions: .: (0.000257) test_description: .: (0.000246) test_descriptions: .: (0.000237) test_emb: .: (0.000270) test_entry_id: .: (0.000225) test_get_all_by_type: .: (0.000221) test_get_emb: .: (0.000231) test_gi: .: (0.000235) test_id_strings: .: (0.000313) test_list_ids: .: (0.000268) test_locus: .: (0.000258) test_words: .: (0.000329) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000383) test_accession: .: (0.000260) test_accessions: .: (0.000282) test_description: .: (0.000248) test_descriptions: .: (0.000245) test_entry_id: .: (0.004800) test_get_all_by_type: .: (0.000296) test_gi: .: (0.000242) test_id_strings: .: (0.010660) test_list_ids: .: (0.000373) test_locus: .: (0.000322) test_sp: .: (0.000305) test_words: .: (0.000319) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000481) test_accession: .: (0.000326) test_accessions: .: (0.000306) test_description: .: (0.000264) test_descriptions: .: (0.000279) test_entry_id: .: (0.000275) test_get_all_by_type: .: (0.000276) test_gi: .: (0.000287) test_id_strings: .: (0.000596) test_list_ids: .: (0.000300) test_locus: .: (0.000287) test_words: .: (0.000385) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000518) test_accession: .: (0.000337) test_accessions: .: (0.000307) test_description: .: (0.000242) test_descriptions: .: (0.006383) test_entry_id: .: (0.000364) test_get_all_by_type: .: (0.000328) test_gi: .: (0.000292) test_id_strings: .: (0.000519) test_list_ids: .: (0.000299) test_locus: .: (0.000278) test_words: .: (0.000399) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000365) test_accession: .: (0.000228) test_accessions: .: (0.000214) test_description: .: (0.000210) test_descriptions: .: (0.000229) test_entry_id: .: (0.000209) test_get_all_by_type: .: (0.000214) test_gi: .: (0.000216) test_id_strings: .: (0.000253) test_list_ids: .: (0.000204) test_locus: .: (0.000211) test_words: .: (0.000281) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000411) test_accession: .: (0.000288) test_accessions: .: (0.000307) test_description: .: (0.000235) test_descriptions: .: (0.000270) test_entry_id: .: (0.000258) test_get: .: (0.000434) test_get_all_by_type: .: (0.000250) test_id_strings: .: (0.000297) test_list_ids: .: (0.000214) test_locus: .: (0.000220) test_sp: .: (0.000234) test_words: .: (0.000289) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000358) test_accession: .: (0.000242) test_accessions: .: (0.000231) test_description: .: (0.000216) test_descriptions: .: (0.000219) test_entry_id: .: (0.000219) test_get: .: (0.000227) test_get_all_by_type: .: (0.000221) test_id_strings: .: (0.000379) test_list_ids: .: (0.000218) test_locus: .: (0.000341) test_tr: .: (0.000373) test_words: .: (0.000450) Bio::TestFastaFirstName: test_first_name1: .: (0.000657) test_first_name_multi_identifier: .: (0.000273) test_first_name_single_worded_defintion: .: (0.000255) test_no_definition: .: (0.000230) test_space_before_first_name: .: (0.000245) test_tabbed_defintion: .: (0.000245) Bio::TestFastaFormat: test_aalen: .: (0.000402) test_aaseq: .: (0.000246) test_acc_version: .: (0.000359) test_accession: .: (0.000368) test_accessions: .: (0.000320) test_data: .: (0.000243) test_definition: .: (0.000223) test_entry: .: (0.000219) test_entry_id: .: (0.000275) test_entry_overrun: .: (0.000247) test_first_name: .: (0.000229) test_gi: .: (0.000315) test_identifiers: .: (0.000196) test_length: .: (0.000105) test_query: .: (0.000081) test_seq: .: (0.000056) Bio::TestFastaFormatConst: test_delimiter: .: (0.000146) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000214) test_data: .: (0.000067) test_definition: .: (0.000051) test_entry: .: (0.000091) test_entry_id: .: (0.000119) test_first_name: .: (0.000068) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000138) test_naseq: .: (0.000090) test_naseq_class: .: (0.000062) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000199) Bio::TestFastaInitialize: test_new_1: .: (0.000392) test_option: .: (0.000057) test_option_backward_compatibility: .: (0.000074) Bio::TestFastaNumericFormat: test_arg: .: (0.000207) test_data: .: (0.000101) test_definition: .: (0.000044) test_each: .: (0.000069) test_entry: .: (0.002264) test_entry_id: .: (0.000299) test_length: .: (0.000287) test_to_biosequence: .: (0.002276) Bio::TestFastaQuery: test_query: .: (0.001449) test_self_local: .: (0.000235) test_self_parser: .: (0.000183) test_self_remote: .: (0.000177) Bio::TestFastacmd: test_database: .: (0.001461) test_fastacmd: .: (0.000251) test_methods: .: (0.000232) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.003418) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.002677) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001705) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.002580) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.002572) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.002765) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.003355) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.003494) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.002658) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001782) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.001622) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001890) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.001280) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.005260) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.004894) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.002956) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001680) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000984) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.003677) test_error_probabilities_as_sanger: .: (0.002148) test_error_probabilities_as_solexa: .: (0.002674) test_quality_scores_as_illumina: .: (0.000591) test_quality_scores_as_sanger: .: (0.000416) test_quality_scores_as_solexa: .: (0.000412) test_validate_format: .: (0.000549) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000822) test_entry_id: .: (0.001049) test_error_probabilities: .: (0.055941) test_nalen: .: (0.000913) test_naseq: .: (0.000806) test_quality_scores: .: (0.001250) test_quality_string: .: (0.000720) test_roundtrip: .: (0.056575) test_seq: .: (0.000924) test_sequence_string: .: (0.000898) test_to_biosequence: .: (0.046765) test_to_biosequence_and_output: .: (0.002864) test_to_s: .: (0.000613) test_validate_format: .: (0.000513) test_validate_format_with_array: .: (0.000570) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000465) test_mask_20_with_empty_string: .: (0.000219) test_mask_20_with_longer_string: .: (0.000645) test_mask_20_with_x: .: (0.000311) test_mask_60: .: (0.000272) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.005027) test_error_probabilities_as_sanger: .: (0.002421) test_error_probabilities_as_solexa: .: (0.002374) test_quality_scores_as_illumina: .: (0.000332) test_quality_scores_as_sanger: .: (0.000190) test_quality_scores_as_solexa: .: (0.000605) test_validate_format: .: (0.000431) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.002429) test_error_probabilities_as_sanger: .: (0.001999) test_error_probabilities_as_solexa: .: (0.001739) test_quality_scores_as_illumina: .: (0.000320) test_quality_scores_as_sanger: .: (0.000193) test_quality_scores_as_solexa: .: (0.000520) test_validate_format: .: (0.000605) Bio::TestFeature: test_append: .: (0.000211) test_append_nil: .: (0.000059) test_assoc: .: (0.000119) test_each: .: (0.000050) test_feature: .: (0.000044) test_locations: .: (0.000107) test_new: .: (0.000047) test_position: .: (0.000043) test_qualifiers: .: (0.000042) Bio::TestFeatures: test_append: .: (0.000239) test_arg: .: (0.000052) test_each: .: (0.000047) test_features: .: (0.000049) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000742) test_aaindex2: .: (0.000161) test_blast: .: (0.000129) test_blastxml: .: (0.000984) test_embl: .: (0.002378) test_embl_oldrelease: .: (0.000486) test_fastaformat: .: (0.000618) test_fastanumericformat: .: (0.000299) test_fastq: .: (0.000348) test_genbank: .: (0.000345) test_genpept: .: (0.000359) test_hmmer: .: (0.000370) test_maxml_cluster: .: (0.003126) test_maxml_sequence: .: (0.000284) test_medline: .: (0.000311) test_prosite: .: (0.003618) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003104) test_transfac: .: (0.001524) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000472) test_auto_1arg_filename: .: (0.000783) test_auto_1arg_io: .: (0.000514) test_auto_1arg_io_with_block: .: (0.000794) test_auto_1arg_with_block: .: (0.000711) test_auto_2arg_filename_mode: .: (0.000557) test_auto_2arg_filename_mode_with_block: .: (0.000962) test_auto_3arg: .: (0.000531) test_auto_3arg_with_block: .: (0.000640) test_foreach: .: (0.000646) test_new_2arg_class: .: (0.000316) test_new_2arg_nil: .: (0.000435) test_open_0arg: .: (0.000283) test_open_1arg_class: .: (0.000235) test_open_1arg_filename: .: (0.000534) test_open_1arg_io: .: (0.000630) test_open_1arg_io_with_block: .: (0.000710) test_open_1arg_nil: .: (0.000258) test_open_1arg_with_block: .: (0.000663) test_open_2arg_autodetect: .: (0.000481) test_open_2arg_autodetect_io: .: (0.000473) test_open_2arg_autodetect_io_with_block: .: (0.000653) test_open_2arg_autodetect_with_block: .: (0.000685) test_open_2arg_class: .: (0.000502) test_open_2arg_class_io: .: (0.000314) test_open_2arg_class_io_with_block: .: (0.000551) test_open_2arg_class_with_block: .: (0.000606) test_open_2arg_filename_mode: .: (0.000465) test_open_2arg_filename_mode_with_block: .: (0.005462) test_open_3arg: .: (0.000624) test_open_3arg_with_block: .: (0.001020) test_open_4arg: .: (0.000807) test_to_a: .: (0.000363) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000308) test_close: .: (0.000084) test_dbclass: .: (0.000065) test_dbclass_eq: .: (0.000086) test_dbclass_nil: .: (0.000139) test_each: .: (0.000163) test_each_entry: .: (0.000221) test_ended_pos: .: (0.000144) test_entry_pos_flag: .: (0.000082) test_entry_raw: .: (0.000182) test_eof?: .: (0.000153) test_next_entry: .: (0.000218) test_path: .: (0.000082) test_pos: .: (0.000117) test_raw: .: (0.000187) test_rewind: .: (0.000141) test_start_pos: .: (0.000128) test_start_pos_ended_pos_not_recorded: .: (0.000128) test_to_io: .: (0.000084) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000223) test_simpleformat2: .: (0.000233) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000206) test_eof_false_after_prefetch: .: (0.000124) test_eof_false_first: .: (0.000048) test_eof_true: .: (0.000080) test_getc: .: (0.000061) test_getc_after_prefetch: .: (0.000049) test_gets: .: (0.000047) test_gets_equal_prefetch_gets: .: (0.000053) test_gets_paragraph_mode: .: (0.000084) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000177) test_gets_paragraph_mode_within_buffer: .: (0.000197) test_gets_rs: .: (0.000069) test_gets_rs_equal_prefetch_gets: .: (0.000071) test_gets_rs_within_buffer: .: (0.000144) test_pos: .: (0.000055) test_pos=: .: (0.000059) test_prefetch_buffer: .: (0.000052) test_prefetch_gets: .: (0.000063) test_prefetch_gets_with_arg: .: (0.000071) test_rewind: .: (0.000050) test_skip_spaces: .: (0.000063) test_to_io: .: (0.000066) test_ungetc: .: (0.000055) test_ungetc_after_prefetch: .: (0.000053) test_ungets: .: (0.000064) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000201) test_self_open_file: .: (0.000086) test_self_open_file_with_block: .: (0.041270) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000249) test_parse_file_open_arg_int_perm: .: (0.000045) test_parse_file_open_arg_int_perm_opt: .: (0.000042) test_parse_file_open_arg_integer: .: (0.000038) test_parse_file_open_arg_nil: .: (0.000034) test_parse_file_open_arg_opt: .: (0.000062) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000047) test_parse_file_open_arg_str: .: (0.000041) test_parse_file_open_arg_str_opt: .: (0.000044) test_parse_file_open_arg_str_perm: .: (0.000040) test_parse_file_open_arg_str_perm_opt: .: (0.000042) test_parse_file_open_arg_str_with_enc: .: (0.000045) test_parse_file_open_arg_str_with_ext_enc: .: (0.000041) test_parse_file_open_mode_integer: .: (0.000036) test_parse_file_open_mode_nil: .: (0.000047) test_parse_file_open_mode_str: .: (0.000041) test_parse_file_open_mode_str_with_enc: .: (0.000041) test_parse_file_open_mode_str_with_ext_enc: .: (0.000041) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000149) test_entry: .: (0.000053) test_entry_ended_pos: .: (0.000044) test_entry_pos_flag: .: (0.000051) test_entry_start_pos: .: (0.000041) test_get_entry: .: (0.000080) test_rewind: .: (0.000056) test_skip_leader: .: (0.000710) test_stream: .: (0.000061) test_stream_pos: .: (0.000067) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000166) test_delimiter_overrun: .: (0.000042) test_entry: .: (0.000079) test_entry_ended_pos: .: (0.000051) test_entry_ended_pos_default_nil: .: (0.000060) test_entry_start_pos: .: (0.000057) test_entry_start_pos_default_nil: .: (0.000047) test_get_entry: .: (0.000115) test_get_parsed_entry: .: (0.000116) test_header: .: (0.000039) test_skip_leader: .: (0.000072) test_skip_leader_without_header: .: (0.000066) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000200) test_entry_ended_pos: .: (0.000112) test_entry_start_pos: .: (0.000095) test_flag_to_fetch_header: .: (0.000096) test_get_entry: .: (0.000130) test_get_parsed_entry: .: (0.000148) test_rewind: .: (0.000102) test_skip_leader: .: (0.000059) Bio::TestGCGMsf: test_alignment: .: (0.000715) test_checksum: .: (0.000123) test_compcheck: .: (0.000117) test_date: .: (0.000109) test_description: .: (0.000126) test_entry_id: .: (0.000110) test_gap_length_weight: .: (0.000112) test_gap_weight: .: (0.000106) test_heading: .: (0.000107) test_length: .: (0.000112) test_seq_type: .: (0.000109) test_symbol_comparison_table: .: (0.000113) test_validate_checksum: .: (0.008976) Bio::TestGFF: test_record_class: .: (0.000380) test_records: .: (0.000198) Bio::TestGFF2: test_const_version: .: (0.000359) test_gff_version: .: (0.000220) test_metadata: .: (0.000222) test_metadata_size: .: (0.000204) test_records_size: .: (0.000207) test_to_s: .: (0.000440) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000173) test_attributes_case2: .: (0.000091) test_attributes_incompatible_backslash_semicolon: .: (0.000117) Bio::TestGFF2MetaData: test_data: .: (0.000119) test_directive: .: (0.000036) test_parse: .: (0.000050) Bio::TestGFF2Record: test_attribute: .: (0.000279) test_attribute_nonexistent: .: (0.000139) test_attributes: .: (0.000149) test_attributes_to_hash: .: (0.000156) test_comment_only?: .: (0.000131) test_delete_attribute: .: (0.000146) test_delete_attribute_multiple: .: (0.000154) test_delete_attribute_multiple2: .: (0.000160) test_delete_attribute_multiple_nil: .: (0.000147) test_delete_attribute_nil: .: (0.000140) test_delete_attribute_nonexistent: .: (0.000141) test_delete_attributes: .: (0.000159) test_delete_attributes_multiple: .: (0.000144) test_delete_attributes_nonexistent: .: (0.000147) test_end: .: (0.000130) test_eqeq: .: (0.000433) test_eqeq_false: .: (0.000342) test_feature: .: (0.000132) test_frame: .: (0.000129) test_get_attribute: .: (0.012523) test_get_attribute_nonexistent: .: (0.000196) test_get_attributes: .: (0.000200) test_get_attributes_nonexistent: .: (0.000136) test_replace_attributes: .: (0.000163) test_replace_attributes_multiple_multiple_over: .: (0.000158) test_replace_attributes_multiple_multiple_same: .: (0.000153) test_replace_attributes_multiple_multiple_two: .: (0.000152) test_replace_attributes_multiple_single: .: (0.000144) test_replace_attributes_nonexistent: .: (0.000153) test_replace_attributes_nonexistent_multiple: .: (0.000147) test_replace_attributes_single_multiple: .: (0.000153) test_score: .: (0.000135) test_self_parse: .: (0.000441) test_seqname: .: (0.000143) test_set_attribute: .: (0.000155) test_set_attribute_multiple: .: (0.000157) test_set_attribute_nonexistent: .: (0.000153) test_sort_attributes_by_tag!: .: (0.000209) test_sort_attributes_by_tag_bang_test2: .: (0.000225) test_sort_attributes_by_tag_bang_with_block: .: (0.000182) test_source: .: (0.000132) test_start: .: (0.000134) test_strand: .: (0.000136) test_to_s: .: (0.000255) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000156) test_comment_eq: .: (0.000046) test_comment_only?: .: (0.000043) test_comment_only_false: .: (0.012674) test_to_s: .: (0.000089) test_to_s_not_empty: .: (0.000123) Bio::TestGFF3: test_const_version: .: (0.000643) test_gff_version: .: (0.001113) test_records: .: (0.000466) test_sequence_regions: .: (0.000652) test_sequences: .: (0.000370) test_to_s: .: (0.001022) Bio::TestGFF3MetaData: test_data: .: (0.000159) test_directive: .: (0.000037) test_parse: .: (0.000054) Bio::TestGFF3Record: test_attributes: .: (0.000235) test_end: .: (0.000118) test_feature: .: (0.000109) test_frame: .: (0.012413) test_id: .: (0.000355) test_score: .: (0.000109) test_seqname: .: (0.000111) test_source: .: (0.000106) test_start: .: (0.000102) test_strand: .: (0.000104) test_to_s: .: (0.000406) test_to_s_attr_order_changed: .: (0.000245) Bio::TestGFF3RecordEscape: test_escape: .: (0.000189) test_escape_attribute: .: (0.000075) test_escape_seqid: .: (0.000065) test_unescape: .: (0.000060) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000258) test_eqeq: .: (0.000136) test_new_from_sequences_na: .: (0.000298) test_new_from_sequences_na_aa: .: (0.000199) test_new_from_sequences_na_aa_boundary_gap: .: (0.000244) test_new_from_sequences_na_aa_example: .: (0.000199) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000149) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000138) test_process_sequences_na: .: (0.000137) test_process_sequences_na_aa: .: (0.000144) test_process_sequences_na_aa_reverse_frameshift: .: (0.000096) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000104) test_process_sequences_na_aa_tooshort: .: (0.000195) test_process_sequences_na_tooshort: .: (0.000134) test_to_s: .: (0.000112) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000213) test_attributes_one: .: (0.000063) test_attributes_with_escaping: .: (0.000076) test_id_multiple: .: (0.000339) test_id_multiple2: .: (0.000123) test_id_replace: .: (0.000066) test_id_set: .: (0.000079) test_initialize_9: .: (0.000042) test_phase: .: (0.000074) test_score: .: (0.000059) test_to_s_void: .: (0.000062) Bio::TestGFF3RecordTarget: test_end: .: (0.000159) test_parse: .: (0.000106) test_start: .: (0.000047) test_strand: .: (0.000044) test_target_id: .: (0.000046) test_to_s: .: (0.000094) Bio::TestGFF3SequenceRegion: test_end: .: (0.000598) test_parse: .: (0.000143) test_seqid: .: (0.000053) test_start: .: (0.000045) test_to_s: .: (0.000092) Bio::TestGFFRecord: test_attributes: .: (0.000189) test_comment: .: (0.000060) test_end: .: (0.000053) test_feature: .: (0.000051) test_frame: .: (0.000052) test_score: .: (0.000051) test_seqname: .: (0.000052) test_source: .: (0.000051) test_start: .: (0.000053) test_strand: .: (0.000053) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000112) Bio::TestGeneAssociation: test_aspect: .: (0.000168) test_assigned_by: .: (0.000052) test_date: .: (0.000051) test_db: .: (0.000051) test_db_object_id: .: (0.000053) test_db_object_name: .: (0.000055) test_db_object_symbol: .: (0.000054) test_db_object_synonym: .: (0.000058) test_db_object_type: .: (0.000086) test_db_reference: .: (0.000063) test_evidence: .: (0.000056) test_goid: .: (0.000067) test_parser: .: (0.000373) test_qualifier: .: (0.000062) test_taxon: .: (0.000058) test_to_str: .: (0.000064) test_with: .: (0.000057) Bio::TestGenscanReport: test_date_run: .: (0.000959) test_gccontent: .: (0.000500) test_genscan_version: .: (0.001369) test_isochore: .: (0.000592) test_length: .: (0.000804) test_matrix: .: (0.000529) test_predictions_size: .: (0.000445) test_query_name: .: (0.000433) test_time: .: (0.000449) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000629) test_donor_score: .: (0.000428) test_exon_type: .: (0.000708) test_exon_type_long: .: (0.000476) test_first: .: (0.000446) test_initiation_score: .: (0.000402) test_last: .: (0.000407) test_number: .: (0.000447) test_p_value: .: (0.000458) test_phase: .: (0.006811) test_range: .: (0.000655) test_score: .: (0.000569) test_strand: .: (0.000526) test_t_score: .: (0.001446) test_termination_score: .: (0.000510) Bio::TestGenscanReportGene: test_aaseq: .: (0.000694) test_naseq: .: (0.000558) test_number: .: (0.001186) test_polyA: .: (0.000551) test_promoter: .: (0.000482) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000756) test_reports_ary_contents: .: (0.000550) Bio::TestHMMERReportConstants: test_rs: .: (0.000280) Bio::TestHMMERReportHit: test_accession: .: (0.000874) test_append_hsp: .: (0.000512) test_bit_score: .: (0.000468) test_definition: .: (0.000461) test_description: .: (0.000453) test_each: .: (0.000501) test_each_hsp: .: (0.000470) test_entry_id: .: (0.000933) test_evalue: .: (0.000508) test_hit: .: (0.000491) test_hit_id: .: (0.000473) test_hsps: .: (0.001073) test_num: .: (0.000577) test_score: .: (0.000449) test_target_def: .: (0.000461) test_target_id: .: (0.000462) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000661) test_each: .: (0.000498) test_each_hit: .: (0.000774) test_histogram: .: (0.000490) test_hits: .: (0.000456) test_hsps: .: (0.000440) test_parameter: .: (0.000469) test_program: .: (0.000495) test_query_info: .: (0.000466) test_statistical_detail: .: (0.000653) test_total_seq_searched: .: (0.000464) test_whole_seq_top_hits: .: (0.000420) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000737) test_histogram: .: (0.000513) test_statistical_detail: .: (0.000636) test_total_seq_searched: .: (0.000531) test_whole_seq_top_hit: .: (0.000912) Bio::TestHMMERReportHsp: test_accession: .: (0.000828) test_bit_score: .: (0.000654) test_csline: .: (0.000662) test_domain: .: (0.000684) test_evalue: .: (0.007534) test_flatseq: .: (0.000756) test_hmm_f: .: (0.000725) test_hmm_t: .: (0.000727) test_hmmseq: .: (0.000692) test_hsp: .: (0.000704) test_midline: .: (0.001459) test_query_frame: .: (0.001036) test_query_from: .: (0.000704) test_query_seq: .: (0.000685) test_query_to: .: (0.000681) test_rfline: .: (0.000737) test_score: .: (0.000673) test_seq_f: .: (0.001013) test_seq_ft: .: (0.000762) test_seq_t: .: (0.000632) test_set_alignment: .: (0.000606) test_targat_to: .: (0.000661) test_target_frame: .: (0.000610) test_target_from: .: (0.000839) test_target_seq: .: (0.000679) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000467) test_find_hetatm: .: (0.000264) test_hetatms: .: (0.000304) Bio::TestHeterogen: test_addAtom: .: (0.000367) test_each: .: (0.000468) test_each_hetatm: .: (0.000231) test_get_residue_id_from_atom: .: (0.000231) test_het_atom: .: (0.000191) test_iCode: .: (0.000223) test_inspect: .: (0.000256) test_resSeq: .: (0.000199) test_sort: .: (0.000240) test_square_bracket: .: (0.000228) test_to_s: .: (0.001163) test_update_resudue_id: .: (0.000231) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000327) test_find_heterogen: .: (0.000212) test_heterogens: .: (0.000194) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000340) test_match_description: .: (0.000192) test_match_evalue: .: (0.000192) test_match_ipr_description: .: (0.000201) test_match_ipr_id: .: (0.000196) test_match_match_end: .: (0.000249) test_match_match_start: .: (0.000194) test_match_method: .: (0.001080) test_matches_size: .: (0.000215) test_query_id: .: (0.000199) test_query_length: .: (0.000253) Bio::TestIprscanRawReport: test_entry_id: .: (0.001583) test_match_accession: .: (0.001378) test_match_crc64: .: (0.001366) test_match_date: .: (0.001372) test_match_description: .: (0.001370) test_match_evalue: .: (0.009163) test_match_go_terms: .: (0.002020) test_match_ipr_description: .: (0.001621) test_match_ipr_id: .: (0.001659) test_match_match_end: .: (0.001428) test_match_match_start: .: (0.002266) test_match_method: .: (0.001455) test_match_query_id: .: (0.001456) test_match_query_length: .: (0.006683) test_match_status: .: (0.002280) test_obj: .: (0.001693) test_query_id: .: (0.001815) test_query_length: .: (0.002206) test_self_reports_in_raw: .: (0.002794) Bio::TestIprscanReport: test_output_raw: .: (0.000795) test_to_raw: .: (0.003652) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.011346) test_match_accession: .: (0.000661) test_match_date: .: (0.000565) test_match_description: .: (0.000575) test_match_evalue: .: (0.000553) test_match_go_terms: .: (0.000529) test_match_ipr_description: .: (0.000584) test_match_ipr_id: .: (0.000509) test_match_match_end: .: (0.001106) test_match_match_start: .: (0.000715) test_match_method: .: (0.001836) test_match_status: .: (0.000596) test_matches_size: .: (0.000561) test_query_id: .: (0.000542) test_query_length: .: (0.000480) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000837) test_to_hash_match?: .: (0.000590) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.002686) Bio::TestKeggCompound: test_comment: .: (0.000673) test_dblinks_as_hash: .: (0.000487) test_dblinks_as_strings: .: (0.000368) test_entry_id: .: (0.000393) test_enzymes: .: (0.000559) test_formula: .: (0.000363) test_kcf: .: (0.000310) test_mass: .: (0.000339) test_name: .: (0.000376) test_names: .: (0.000379) test_pathways_as_hash: .: (0.000489) test_pathways_as_strings: .: (0.000394) test_reactions: .: (0.000600) test_remark: .: (0.000349) test_rpairs: .: (0.000351) Bio::TestKeggEnzyme: test_all_reac: .: (0.000728) test_classes: .: (0.000475) test_cofactors: .: (0.000488) test_comment: .: (0.000507) test_dblinks_as_hash: .: (0.000564) test_dblinks_as_strings: .: (0.005272) test_diseases: .: (0.000565) test_entry: .: (0.000619) test_entry_id: .: (0.000635) test_genes: .: (0.055644) test_genes_as_hash: .: (0.014714) test_genes_as_strings: .: (0.003278) test_inhibitors: .: (0.000458) test_iubmb_reactions: .: (0.000332) test_kegg_reactions: .: (0.000312) test_motifs: .: (0.000308) test_name: .: (0.000371) test_names: .: (0.000360) test_obsolete?: .: (0.000574) test_orthologs_as_hash: .: (0.000401) test_orthologs_as_strings: .: (0.000369) test_pathways_as_hash: .: (0.000433) test_pathways_as_strings: .: (0.000384) test_products: .: (0.000397) test_reaction: .: (0.000375) test_structures: .: (0.000553) test_substrates: .: (0.000378) test_sysname: .: (0.000726) Bio::TestKeggGenesDblinks: test_data: .: (0.000353) test_dblinks_0: .: (0.000195) test_dblinks_1: .: (0.000168) test_dblinks_2: .: (0.000163) Bio::TestKeggGenesStructure: test_data: .: (0.000348) test_ids: .: (0.000247) test_ids_in_array: .: (0.000196) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004495) test_graphics__size: .: (0.009482) test_id: .: (0.004906) test_link: .: (0.004155) test_name: .: (0.004186) test_reaction: .: (0.004274) test_type: .: (0.004567) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.004652) test_graphics__size: .: (0.004002) test_id: .: (0.004358) test_link: .: (0.008368) test_name: .: (0.005013) test_reaction: .: (0.004179) test_type: .: (0.004344) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.004894) test_category: .: (0.004473) test_entry_id: .: (0.004159) test_fgcolor=: .: (0.004272) test_height=: .: (0.003969) test_label=: .: (0.009812) test_shape=: .: (0.004950) test_width=: .: (0.004757) test_x=: .: (0.004334) test_y=: .: (0.004314) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.004613) test_graphics__size: .: (0.004645) test_id: .: (0.004061) test_link: .: (0.004234) test_name: .: (0.007569) test_reaction: .: (0.004706) test_type: .: (0.004420) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000182) test_graphics=: .: (0.000053) test_id=: .: (0.000085) test_link=: .: (0.000063) test_name=: .: (0.000067) test_reaction=: .: (0.000050) test_type=: .: (0.000049) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000154) test_category=: .: (0.000179) test_entry_id=: .: (0.000068) test_fgcolor=: .: (0.000069) test_height=: .: (0.000067) test_label=: .: (0.000292) test_pathway=: .: (0.000072) test_shape=: .: (0.000078) test_width=: .: (0.000069) test_x=: .: (0.000069) test_y=: .: (0.000067) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.004528) test_coords: .: (0.004397) test_fgcolor: .: (0.004312) test_height: .: (0.004070) test_name: .: (0.004215) test_type: .: (0.007107) test_width: .: (0.004930) test_x: .: (0.004519) test_y: .: (0.004345) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.004601) test_coords: .: (0.004628) test_fgcolor: .: (0.004291) test_height: .: (0.004096) test_name: .: (0.004219) test_type: .: (0.007291) test_width: .: (0.004670) test_x: .: (0.004506) test_y: .: (0.004546) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000189) test_coords=: .: (0.000294) test_fgcolor=: .: (0.000063) test_height=: .: (0.000052) test_name=: .: (0.000054) test_type=: .: (0.000050) test_width=: .: (0.000049) test_x=: .: (0.000049) test_y=: .: (0.000052) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.004803) test_entries__size: .: (0.004315) test_image: .: (0.004145) test_link: .: (0.004117) test_name: .: (0.007013) test_number: .: (0.004908) test_org: .: (0.004550) test_reactions=: .: (0.004333) test_reactions__size: .: (0.004346) test_relations=: .: (0.004515) test_relations__size: .: (0.004309) test_title: .: (0.004088) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.011649) test_name: .: (0.008765) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000359) test_initialize_0: .: (0.000228) test_initialize_1: .: (0.000190) test_initialize_2: .: (0.000161) test_name=: .: (0.000166) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.004853) test_name: .: (0.004765) test_products: .: (0.004941) test_substrates: .: (0.004287) test_type: .: (0.004325) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000334) test_name=: .: (0.000201) test_products=: .: (0.000180) test_substraces=: .: (0.000166) test_type=: .: (0.000172) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000831) test_entry_id=: .: (0.000474) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.009047) test_entry2: .: (0.006037) test_name: .: (0.005500) test_type: .: (0.004303) test_value: .: (0.005595) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000337) test_node1=: .: (0.000188) test_node2=: .: (0.000400) test_rel=: .: (0.000219) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000376) test_entry2=: .: (0.000178) test_name=: .: (0.000170) test_type=: .: (0.000165) test_value=: .: (0.000161) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.009651) test_name: .: (0.011357) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000373) test_initialize_0: .: (0.000297) test_initialize_1: .: (0.000163) test_initialize_2: .: (0.000157) test_name=: .: (0.000224) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000336) test_initialize_0: .: (0.000147) test_initialize_1: .: (0.000152) test_initialize_2: .: (0.000149) test_name=: .: (0.000163) Bio::TestKeggModule: test_compounds: .: (0.000564) test_compounds_as_hash: .: (0.001067) test_compounds_as_strings: .: (0.000357) test_definition: .: (0.000303) test_entry_id: .: (0.000295) test_keggclass: .: (0.000279) test_name: .: (0.000304) test_new: .: (0.000284) test_orthologs: .: (0.000384) test_orthologs_as_array: .: (0.000351) test_orthologs_as_hash: .: (0.000314) test_orthologs_as_strings: .: (0.000276) test_pathways: .: (0.000275) test_pathways_as_hash: .: (0.000267) test_pathways_as_strings: .: (0.000252) test_reactions: .: (0.000351) test_reactions_as_hash: .: (0.000331) test_reactions_as_strings: .: (0.000314) Bio::TestKeggOrthology: test_dblinks: .: (0.000601) test_dblinks_as_hash: .: (0.000540) test_dblinks_as_strings: .: (0.000428) test_definition: .: (0.000463) test_entry_id: .: (0.000423) test_genes_as_hash: .: (0.011579) test_genes_as_strings: .: (0.005818) test_keggclass: .: (0.000601) test_keggclasses: .: (0.001080) test_modules: .: (0.000743) test_modules_as_hash: .: (0.000452) test_modules_as_strings: .: (0.000434) test_name: .: (0.000451) test_names: .: (0.000467) test_pathways_as_strings: .: (0.000435) test_pathways_in_keggclass: .: (0.000555) test_references: .: (0.000582) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000449) test_compounds_as_strings: .: (0.000275) test_dblinks_as_hash: .: (0.000276) test_dblinks_as_strings: .: (0.000363) test_description: .: (0.001033) test_diseases_as_hash: .: (0.000332) test_diseases_as_strings: .: (0.001503) test_entry_id: .: (0.001356) test_enzymes_as_strings: .: (0.001451) test_genes_as_hash: .: (0.001343) test_genes_as_strings: .: (0.000345) test_keggclass: .: (0.001450) test_ko_pathway: .: (0.000365) test_modules_as_hash: .: (0.001808) test_modules_as_strings: .: (0.000241) test_name: .: (0.001293) test_organism: .: (0.000233) test_orthologs_as_hash: .: (0.001732) test_orthologs_as_strings: .: (0.000214) test_pathways_as_hash: .: (0.000139) test_pathways_as_strings: .: (0.000231) test_reactions_as_hash: .: (0.000117) test_reactions_as_strings: .: (0.001620) test_references: .: (0.002323) test_rel_pathways_as_hash: .: (0.000397) test_rel_pathways_as_strings: .: (0.001360) Bio::TestKeggReaction: test_definition: .: (0.003489) test_entry_id: .: (0.000416) test_enzymes: .: (0.001193) test_equation: .: (0.001398) test_name: .: (0.002489) test_orthologs_as_hash: .: (0.001455) test_orthologs_as_strings: .: (0.001415) test_pathways_as_hash: .: (0.001334) test_pathways_as_strings: .: (0.000339) test_rpairs_as_hash: .: (0.001319) test_rpairs_as_strings: .: (0.001455) test_rpairs_as_tokens: .: (0.006163) Bio::TestLasergene: test_methods: .: (0.032635) Bio::TestLocations: test_complement: .: (0.000409) test_hat: .: (0.000226) test_normal: .: (0.000209) test_replace_single_base: .: (0.000192) test_should_not_modify_argument: .: (0.000177) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.008014) test_locations_to_s: .: (0.001084) Bio::TestMEDLINE: test_authors: .: (0.000849) test_authors_with_last_name_all_caps: .: (0.000227) test_authors_with_suffix: .: (0.000193) Bio::TestMEDLINE_20146148: test_ab: .: (0.000546) test_ad: .: (0.000346) test_au: .: (0.000340) test_authors: .: (0.000537) test_doi: .: (0.000391) test_dp: .: (0.000341) test_ip: .: (0.000343) test_mh: .: (0.000375) test_pages: .: (0.000358) test_pg: .: (0.001348) test_pii: .: (0.000424) test_pmid: .: (0.000340) test_pt: .: (0.000347) test_reference: .: (0.000581) test_self_new: .: (0.000355) test_so: .: (0.000313) test_ta: .: (0.003468) test_ti: .: (0.000450) test_ui: .: (0.000350) test_vi: .: (0.000337) test_year: .: (0.000331) Bio::TestMapSimple: test_attributes: .: (0.000377) Bio::TestMapping: test_add_mapping_as_map: .: (0.000392) test_add_mapping_as_marker: .: (0.000238) test_contains_marker?: .: (0.000439) test_mapped_to?: .: (0.000208) test_mapping_location_comparison: .: (0.000367) test_mappings_as_map_each: .: (0.000191) test_mappings_as_marker_each: .: (0.000230) test_mappings_on: .: (0.000258) test_multiple_mappings_between_same_marker_and_map: .: (0.000328) test_positions_on: .: (0.000237) test_raise_error_kind_of: .: (0.000589) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000458) test_check_options_with_invalid_opts: .: (0.000271) test_check_options_with_valid_opts: .: (0.000232) test_command_to_be_run: .: (0.000224) test_config_defaults: .: (0.000227) test_minimal_config: .: (0.000209) test_more_config: .: (0.000213) test_run: .: (0.000173) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000495) test_report_has_motifs: .: (0.000295) Bio::TestModel: test_addChain: .: (0.000283) test_comp: .: (0.000203) test_each: .: (0.000206) test_each_chain: .: (0.000159) test_inspect: .: (0.000166) test_rehash: .: (0.000150) test_square_brace: .: (0.000181) test_to_s: .: (0.000170) Bio::TestModelFinder: test_find_model: .: (0.000319) Bio::TestMotif: test_creation_and_attributes: .: (0.000283) test_length: .: (0.000152) Bio::TestMyGraph: test_cliquishness: .: (0.000447) Bio::TestNA: test_accessor: .: (0.000245) test_na: .: (0.000166) test_name: .: (0.000149) test_names: .: (0.000140) test_to_re: .: (0.000255) test_weight: .: (0.000157) test_weight_rna: .: (0.000162) Bio::TestNAConstants: test_NAMES: .: (0.000271) test_NAMES_1_to_name: .: (0.000148) test_WEIGHT: .: (0.000150) Bio::TestNATranslate: test_translate: .: (0.000441) test_translate_1: .: (0.000266) test_translate_2: .: (0.000175) test_translate_3: .: (0.000171) test_translate_4: .: (0.000267) test_translate_5: .: (0.000170) test_translate_6: .: (0.000164) Bio::TestNCBIDB: test_fetch: .: (0.000333) test_p_entry2hash: .: (0.000142) test_p_subtag2array: .: (0.000130) test_p_toptag2array: .: (0.000136) Bio::TestNewick: test_reparse: .: (0.001056) test_reparse_before_lazy_parsing: .: (0.000451) test_string_tree: .: (0.000659) Bio::TestNewick2: test_string_tree: .: (0.000707) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000297) test_parse_newick_leaf: .: (0.000248) test_parse_newick_tokenize: .: (0.003938) Bio::TestNexus: test_nexus: .: (0.007904) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000390) test_uncapitalized_letter_Q32725_9POAL: .: (0.000235) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000331) test_load_parameters: .: (0.000204) test_parameters: .: (0.000150) test_set_default_parameters: .: (0.000194) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000628) test_expected_parameters_set_in_control_file: .: (0.000556) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000312) test_new_with_parameters: .: (0.000185) test_new_with_two_argument: .: (0.000195) test_new_without_argument: .: (0.000161) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001068) test_rates_hundred_and_fiftieth_position: .: (0.000933) test_rates_last_position: .: (0.001866) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.000786) test_tree: .: (0.000600) test_tree_length: .: (0.000565) test_tree_log_likelihood: .: (0.000549) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000489) test_parameters_should_be_loaded_from_control: .: (0.000305) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001154) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000421) test_dN_dS: .: (0.000241) test_kappa: .: (0.000233) test_lnL: .: (0.000219) test_m3_classes: .: (0.000299) test_m3_lnL: .: (0.000223) test_m3_to_s: .: (0.000235) test_m3_tree: .: (0.000281) test_omega: .: (0.000235) test_to_s: .: (0.000235) test_tree: .: (0.000283) test_tree_length: .: (0.000224) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000541) test_p: .: (0.000376) test_position: .: (0.000360) test_probability: .: (0.000373) test_w: .: (0.000393) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000534) test_graph_omega: .: (0.000416) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000381) test_footer: .: (0.000220) test_header: .: (0.000237) test_initialize: .: (0.000235) test_models: .: (0.000240) test_nb_sites: .: (0.000521) test_num_codons: .: (0.000252) test_num_sequences: .: (0.000238) test_significant: .: (0.000268) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000388) test_nb_sites: .: (0.000341) test_significant: .: (0.000265) test_sites: .: (0.000728) Bio::TestPDB: test_accession: .: (0.000875) test_addModel: .: (0.000436) test_authors: .: (0.000405) test_bracket: .: (0.000397) test_classification: .: (0.000462) test_dbref: .: (0.000512) test_definition: .: (0.000733) test_each: .: (0.000475) test_each_model: .: (0.000421) test_entry_id: .: (0.000428) test_helix: .: (0.000468) test_inspect: .: (0.000428) test_jrnl: .: (0.000425) test_keywords: .: (0.000419) test_record: .: (0.000790) test_remark: .: (0.000789) test_seqres: .: (0.000826) test_sheet: .: (0.000881) test_ssbond: .: (0.007195) test_to_s: .: (0.000953) test_turn: .: (0.001269) test_version: .: (0.000706) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000373) test_U12: .: (0.000206) test_U13: .: (0.000199) test_U22: .: (0.000191) test_U23: .: (0.000185) test_U33: .: (0.000511) test_altLoc: .: (0.000202) test_chainID: .: (0.000190) test_charge: .: (0.000187) test_element: .: (0.000214) test_iCode: .: (0.000198) test_name: .: (0.000192) test_resName: .: (0.000323) test_resSeq: .: (0.000196) test_segID: .: (0.000191) test_serial: .: (0.000193) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000320) test_anisou: .: (0.000169) test_chainID: .: (0.000161) test_charge: .: (0.000170) test_comparable: .: (0.000193) test_do_parse: .: (0.000165) test_element: .: (0.000163) test_iCode: .: (0.000160) test_name: .: (0.000174) test_occupancy: .: (0.000193) test_original_data: .: (0.000166) test_record_name: .: (0.000158) test_resName: .: (0.000145) test_resSeq: .: (0.000164) test_residue: .: (0.000154) test_segID: .: (0.000159) test_serial: .: (0.000156) test_sigatm: .: (0.000157) test_tempFactor: .: (0.000185) test_ter: .: (0.000165) test_to_a: .: (0.000172) test_to_s: .: (0.000212) test_x: .: (0.000180) test_xyz: .: (0.000207) test_y: .: (0.000174) test_z: .: (0.000180) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000352) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000430) test_idcode: .: (0.000186) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000380) test_chainID2: .: (0.000207) test_icode1: .: (0.000193) test_icode2: .: (0.000191) test_measure: .: (0.000201) test_modNum: .: (0.000223) test_pep1: .: (0.000233) test_pep2: .: (0.000218) test_seqNum1: .: (0.000211) test_seqNum2: .: (0.000188) test_serNum: .: (0.000181) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000326) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000287) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000315) test_alpha: .: (0.000187) test_b: .: (0.000181) test_beta: .: (0.000191) test_c: .: (0.000174) test_gamma: .: (0.000161) test_sGroup: .: (0.000164) test_z: .: (0.000171) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000331) test_database: .: (0.000209) test_dbAccession: .: (0.000237) test_dbIdCode: .: (0.000192) test_dbseqBegin: .: (0.000185) test_dbseqEnd: .: (0.000213) test_idCode: .: (0.000200) test_idbnsBeg: .: (0.000196) test_insertBegin: .: (0.000189) test_insertEnd: .: (0.000179) test_seqBegin: .: (0.000197) test_seqEnd: .: (0.000191) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000290) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000270) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000298) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000418) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000289) test_depDate: .: (0.000195) test_idCode: .: (0.000177) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000328) test_hetID: .: (0.000182) test_iCode: .: (0.000173) test_numHetAtoms: .: (0.000182) test_seqNum: .: (0.000177) test_text: .: (0.000182) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000298) test_anisou: .: (0.000162) test_chainID: .: (0.000159) test_charge: .: (0.000159) test_comparable: .: (0.000188) test_do_parse: .: (0.000159) test_element: .: (0.000160) test_iCode: .: (0.000158) test_name: .: (0.000159) test_occupancy: .: (0.000184) test_original_data: .: (0.000156) test_record_name: .: (0.000248) test_resName: .: (0.000153) test_resSeq: .: (0.000155) test_residue: .: (0.000161) test_segID: .: (0.000350) test_serial: .: (0.000182) test_sigatm: .: (0.000163) test_tempFactor: .: (0.000188) test_ter: .: (0.000168) test_to_a: .: (0.000176) test_to_s: .: (0.000205) test_x: .: (0.000179) test_xyz: .: (0.000194) test_y: .: (0.000176) test_z: .: (0.000205) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000366) test_ChainH: .: (0.000220) test_ICode1: .: (0.000222) test_altLoc1: .: (0.000229) test_altLoc2: .: (0.000203) test_altLocH: .: (0.000212) test_chainID2: .: (0.000228) test_iCode2: .: (0.000201) test_iCodeH: .: (0.000203) test_name1: .: (0.000197) test_name2: .: (0.000194) test_nameH: .: (0.000197) test_resName1: .: (0.000202) test_resName2: .: (0.000200) test_resSeq1: .: (0.000204) test_resSeq2: .: (0.000281) test_resSeqH: .: (0.000403) test_sym1: .: (0.000213) test_sym2: .: (0.000210) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000323) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000340) test_altLoc2: .: (0.000198) test_chainID1: .: (0.000202) test_chainID2: .: (0.000192) test_iCode1: .: (0.000184) test_iCode2: .: (0.000185) test_name1: .: (0.000191) test_name2: .: (0.000186) test_resName1: .: (0.000188) test_resName2: .: (0.000185) test_resSeq1: .: (0.000184) test_resSeq2: .: (0.000198) test_sym1: .: (0.000190) test_sym2: .: (0.000188) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000313) test_numCoord: .: (0.000165) test_numHelix: .: (0.000159) test_numHet: .: (0.000162) test_numRemark: .: (0.000161) test_numSeq: .: (0.000166) test_numSheet: .: (0.000159) test_numSite: .: (0.000389) test_numTer: .: (0.000178) test_numTurn: .: (0.000165) test_numXform: .: (0.000163) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000305) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000349) test_comment: .: (0.000200) test_iCode: .: (0.000186) test_idCode: .: (0.000189) test_resName: .: (0.000174) test_seqNum: .: (0.000203) test_stdRes: .: (0.000178) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000346) test_Mn2: .: (0.000169) test_Mn3: .: (0.000164) test_Vn: .: (0.000161) test_iGiven: .: (0.000169) test_serial: .: (0.000158) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000456) test_Mn2: .: (0.000189) test_Mn3: .: (0.000164) test_Vn: .: (0.000164) test_iGiven: .: (0.000166) test_serial: .: (0.000166) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000320) test_Mn2: .: (0.000179) test_Mn3: .: (0.000168) test_Vn: .: (0.000156) test_iGiven: .: (0.000164) test_serial: .: (0.000172) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000326) test_rIdCode: .: (0.000203) test_repDate: .: (0.000181) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000302) test_On2: .: (0.000164) test_On3: .: (0.000164) test_Tn: .: (0.000168) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000319) test_modId: .: (0.000189) test_modNum: .: (0.000184) test_modType: .: (0.000182) test_record: .: (0.000188) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000304) test_text: .: (0.000160) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000292) test_Sn2: .: (0.000163) test_Sn3: .: (0.000159) test_Un: .: (0.000186) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000296) test_Sn2: .: (0.000410) test_Sn3: .: (0.000167) test_Un: .: (0.000175) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000298) test_Sn2: .: (0.000168) test_Sn3: .: (0.000164) test_Un: .: (0.000166) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000382) test_conflict: .: (0.000199) test_database: .: (0.000186) test_dbIdCode: .: (0.000183) test_dbRes: .: (0.000192) test_dbSeq: .: (0.000182) test_iCode: .: (0.000181) test_idCode: .: (0.000185) test_resName: .: (0.000182) test_seqNum: .: (0.000180) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000329) test_numRes: .: (0.000197) test_resName: .: (0.000216) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000345) test_curChainId: .: (0.000214) test_curICode: .: (0.000206) test_curResName: .: (0.000205) test_curResSeq: .: (0.000211) test_endChainID: .: (0.000205) test_endICode: .: (0.000239) test_endResName: .: (0.000204) test_endSeqNum: .: (0.000208) test_initChainID: .: (0.000226) test_initICode: .: (0.000212) test_initResName: .: (0.000208) test_initSeqNum: .: (0.000214) test_numStrands: .: (0.000206) test_prevAtom: .: (0.000207) test_prevChainId: .: (0.000208) test_prevICode: .: (0.000216) test_prevResName: .: (0.000223) test_prevResSeq: .: (0.000211) test_sense: .: (0.000201) test_sheetID: .: (0.000230) test_strand: .: (0.000206) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000361) test_chainID: .: (0.000202) test_charge: .: (0.000201) test_element: .: (0.000202) test_iCode: .: (0.000206) test_name: .: (0.000232) test_resName: .: (0.000201) test_resSeq: .: (0.000198) test_segID: .: (0.000190) test_serial: .: (0.000192) test_sigOcc: .: (0.000193) test_sigTemp: .: (0.000195) test_sigX: .: (0.000193) test_sigY: .: (0.000189) test_sigZ: .: (0.000183) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000342) test_SigmaU12: .: (0.000190) test_SigmaU13: .: (0.000186) test_SigmaU22: .: (0.000201) test_SigmaU23: .: (0.000191) test_SigmaU33: .: (0.000187) test_altLoc: .: (0.000184) test_chainID: .: (0.000210) test_charge: .: (0.000200) test_element: .: (0.000189) test_iCode: .: (0.000195) test_name: .: (0.000219) test_resName: .: (0.000205) test_resSeq: .: (0.000202) test_segID: .: (0.000200) test_serial: .: (0.000183) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000348) test_chainID2: .: (0.000204) test_chainID3: .: (0.000198) test_chainID4: .: (0.000189) test_iCode1: .: (0.000210) test_iCode2: .: (0.000212) test_iCode3: .: (0.000195) test_iCode4: .: (0.000188) test_numRes: .: (0.000206) test_resName1: .: (0.000186) test_resName2: .: (0.000184) test_resName3: .: (0.000187) test_resName4: .: (0.000195) test_seq1: .: (0.000192) test_seq2: .: (0.000194) test_seq3: .: (0.000186) test_seq4: .: (0.000186) test_seqNum: .: (0.000195) test_siteID: .: (0.000200) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000370) test_altLoc2: .: (0.000197) test_atom1: .: (0.000195) test_atom2: .: (0.000192) test_chainID1: .: (0.000124) test_chainID2: .: (0.000066) test_iCode1: .: (0.000061) test_iCode2: .: (0.000055) test_resName1: .: (0.000053) test_resName2: .: (0.000053) test_resSeq1: .: (0.000053) test_resSeq2: .: (0.000119) test_sym1: .: (0.000060) test_sym2: .: (0.000053) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000195) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000122) test_sIdCode: .: (0.000080) test_sprsdeDate: .: (0.000051) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000129) test_iCode: .: (0.000050) test_resName: .: (0.000043) test_resSeq: .: (0.000047) test_serial: .: (0.000047) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000113) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000118) test_t1: .: (0.000049) test_t2: .: (0.000044) test_t3: .: (0.000069) test_text: .: (0.000049) Bio::TestPROSITE: test_ac: .: (0.000869) test_cc: .: (0.000841) test_de: .: (0.000757) test_division: .: (0.000795) test_dr: .: (0.029905) test_dt: .: (0.001029) test_false_neg: .: (0.001021) test_false_pos: .: (0.001011) test_false_positive_sequences: .: (0.000963) test_list_falsenegative: .: (0.017828) test_list_falsepositive: .: (0.017889) test_list_potentialhit: .: (0.014773) test_list_truepositive: .: (0.018788) test_list_unknown: .: (0.012670) test_list_xref: .: (0.015556) test_ma: .: (0.001006) test_max_repeat: .: (0.001033) test_name: .: (0.000999) test_nr: .: (0.001057) test_pa: .: (0.000925) test_pa2re: .: (0.001178) test_partial: .: (0.001091) test_pdb_xref: .: (0.001059) test_pdoc_xref: .: (0.001235) test_positive: .: (0.001183) test_positive_hits: .: (0.001131) test_positive_sequences: .: (0.001083) test_release: .: (0.001097) test_ru: .: (0.001047) test_self_pa2re: .: (0.001208) test_site: .: (0.001151) test_skip_flag: .: (0.001099) test_swissprot_release_number: .: (0.001370) test_swissprot_release_sequences: .: (0.003690) test_taxon_range: .: (0.001380) test_total: .: (0.001915) test_total_hits: .: (0.001120) test_total_sequences: .: (0.001298) test_unknown: .: (0.001305) test_unknown_hits: .: (0.001076) test_unknown_sequences: .: (0.001196) Bio::TestPROSITEConst: test_delimiter: .: (0.000323) test_tagsize: .: (0.000157) Bio::TestPTS1: test_function_set: .: (0.000322) test_function_set_number_1: .: (0.000176) test_function_set_number_2: .: (0.000155) test_function_set_number_3: .: (0.000162) test_function_show: .: (0.000155) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000263) Bio::TestPTS1New: test_fungi: .: (0.000257) test_general: .: (0.000156) test_metazoa: .: (0.000159) Bio::TestQualifier: test_qualifier: .: (0.000397) test_value: .: (0.000144) Bio::TestREBASE: test_methods: .: (0.000745) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000969) test_bit_score: .: (0.000727) test_evalue: .: (0.000682) test_gaps: .: (0.000600) test_hit_from: .: (0.000861) test_hit_to: .: (0.000612) test_hseq: .: (0.000604) test_identity: .: (0.000569) test_midline: .: (0.000578) test_percent_identity: .: (0.000564) test_positive: .: (0.000585) test_qseq: .: (0.000627) test_query_from: .: (0.000575) test_query_to: .: (0.000577) test_score: .: (0.003469) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.006783) test_hits_size: .: (0.008396) test_iterations_size: .: (0.007246) test_program: .: (0.000736) test_query_def: .: (0.007584) test_query_len: .: (0.004529) test_version: .: (0.000793) test_version_date: .: (0.002001) test_version_number: .: (0.003250) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.002344) test_definition: .: (0.003599) test_evalue: .: (0.003493) test_hsps_size: .: (0.000951) test_identity: .: (0.000786) test_lap_at: .: (0.000732) test_len: .: (0.000683) test_midline: .: (0.000711) test_overlap: .: (0.000704) test_query_end: .: (0.001510) test_query_seq: .: (0.001019) test_query_start: .: (0.000745) test_target_def: .: (0.000694) test_target_end: .: (0.000672) test_target_len: .: (0.000615) test_target_seq: .: (0.000659) test_target_start: .: (0.000671) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001508) test_get_entry: .: (0.000566) test_rewind: .: (0.000224) test_skip_leader: .: (0.000285) Bio::TestReference: test_abstract: .: (0.000307) test_affiliations: .: (0.000156) test_authors: .: (0.000155) test_format_bibitem: .: (0.000216) test_format_bibtex: .: (0.000280) test_format_bibtex_with_arguments: .: (0.000247) test_format_cell: .: (0.000179) test_format_current: .: (0.000205) test_format_endnote: .: (0.000466) test_format_general: .: (0.000210) test_format_genome_biol: .: (0.000191) test_format_genome_res: .: (0.000185) test_format_nar: .: (0.000180) test_format_nature: .: (0.000196) test_format_rd: .: (0.000178) test_format_science: .: (0.000230) test_format_trends: .: (0.000164) test_issue: .: (0.000145) test_journal: .: (0.000175) test_mesh: .: (0.000159) test_pages: .: (0.000147) test_pubmed: .: (0.000142) test_pubmed_url: .: (0.000161) test_url: .: (0.000154) test_volume: .: (0.000147) test_year: .: (0.000142) Bio::TestReference_noURL: test_format_endnote: .: (0.000322) test_url: .: (0.000154) Bio::TestReferences: test_append: .: (0.000389) test_each: .: (0.000182) Bio::TestRelation: test_comparison_operator: .: (0.000310) test_uniq: .: (0.000187) Bio::TestResidue: test_addAtom: .: (0.000394) test_each: .: (0.000271) test_each_atom: .: (0.000235) test_get_residue_id_from_atom: .: (0.000225) test_het_atom: .: (0.000222) test_iCode: .: (0.000360) test_inspect: .: (0.000251) test_resSeq: .: (0.000199) test_sort: .: (0.000281) test_square_bracket: .: (0.000232) test_to_s: .: (0.000284) test_update_resudue_id: .: (0.000212) Bio::TestResidueFinder: test_each_residue: .: (0.000338) test_find_residue: .: (0.000200) test_residues: .: (0.000215) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.093038) test_cut_from_bio_sequence_na: .: (0.017864) test_cut_without_permutations: .: (0.019614) test_view_ranges: .: (0.017238) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001520) test_cuts_after_remove_incomplete_cuts: .: (0.000623) test_strands_for_display: .: (0.002385) test_strands_for_display_current: .: (0.000554) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000662) test_fragments_for_display_1: .: (0.000647) test_fragments_for_display_10: .: (0.000837) test_fragments_for_display_2: .: (0.000596) test_fragments_for_display_3: .: (0.000934) test_fragments_for_display_4: .: (0.000702) test_fragments_for_display_5: .: (0.000686) test_fragments_for_display_6: .: (0.000517) test_fragments_for_display_7: .: (0.000509) test_fragments_for_display_8: .: (0.000498) test_fragments_for_display_9: .: (0.000683) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000417) test_obj_3: .: (0.000270) test_obj_7: .: (0.000248) test_obj_z: .: (0.000255) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000421) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000339) test_bracket_eq: .: (0.000233) test_concat: .: (0.000374) test_delete: .: (0.000229) test_dup: .: (0.000227) test_each: .: (0.000198) test_eqeq: .: (0.000183) test_eqeq_false: .: (0.000163) test_eqeq_other: .: (0.000165) test_eqeq_self: .: (0.000190) test_include?: .: (0.000162) test_internal_data: .: (0.000205) test_internal_data_eq: .: (0.000180) test_length: .: (0.000154) test_ltlt: .: (0.000169) test_ltlt_larger: .: (0.000167) test_ltlt_middle: .: (0.000162) test_plus: .: (0.000187) test_plus_error: .: (0.000214) test_push: .: (0.000186) test_reverse_each: .: (0.000368) test_self_bracket: .: (0.000153) test_self_new: .: (0.000515) test_size: .: (0.000179) test_sort!: .: (0.000191) test_to_a: .: (0.000184) test_uniq!: .: (0.000153) test_unshift: .: (0.000228) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003502) test_complement: .: (0.002995) test_complement_with_cut_symbols: .: (0.002899) test_cut_locations: .: (0.002808) test_cut_locations_in_enzyme_notation: .: (0.002945) test_primary: .: (0.007151) test_primary_with_cut_symbols: .: (0.003708) test_to_re: .: (0.003344) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000977) test_align_with_cuts: .: (0.000758) test_argument_error: .: (0.001030) test_ds: .: (0.000684) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000334) test_complement: .: (0.000106) test_contents: .: (0.000096) test_primary: .: (0.000090) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000250) test_complement: .: (0.000320) test_contents: .: (0.000098) test_primary: .: (0.000084) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000174) test_contents: .: (0.000072) test_primary: .: (0.000378) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000375) test_complement_to_array_index: .: (0.000281) test_complement_to_array_index_class: .: (0.000261) test_contents: .: (0.000219) test_primary: .: (0.000201) test_primary_to_array_index: .: (0.000503) test_primary_to_array_index_class: .: (0.000257) test_to_array_index: .: (0.000430) test_to_array_index_class: .: (0.000404) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000477) test_rebase: .: (0.000209) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001110) test_creation_with_no_cuts: .: (0.000479) test_cut_locations: .: (0.000432) test_cut_locations_in_enzyme_notation: .: (0.000620) test_orientation: .: (0.000400) test_pattern: .: (0.000448) test_pattern_palindromic?: .: (0.000501) test_stripped: .: (0.000426) test_to_re: .: (0.000382) test_with_cut_symbols: .: (0.000415) test_with_spaces: .: (0.000475) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000810) test_creation_with_no_cuts: .: (0.000454) test_cut_locations: .: (0.000426) test_cut_locations_in_enzyme_notation: .: (0.000399) test_orientation: .: (0.000378) test_pattern: .: (0.000405) test_pattern_palindromic?: .: (0.000449) test_stripped: .: (0.000392) test_to_re: .: (0.000358) test_with_cut_symbols: .: (0.000413) test_with_spaces: .: (0.000462) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000515) test_initialize_with_pattern: .: (0.000336) test_max: .: (0.000216) test_min: .: (0.000183) test_to_array_index: .: (0.000218) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000323) test_bracket_eq: .: (0.000215) test_concat: .: (0.000178) test_delete: .: (0.000158) test_dup: .: (0.000205) test_each: .: (0.000193) test_eqeq: .: (0.000179) test_eqeq_false: .: (0.000176) test_eqeq_other: .: (0.000154) test_eqeq_self: .: (0.000146) test_include?: .: (0.000155) test_internal_data_hash: .: (0.000155) test_internal_data_hash_eq: .: (0.000167) test_length: .: (0.000147) test_ltlt: .: (0.000160) test_ltlt_noeffect: .: (0.000156) test_plus: .: (0.000169) test_plus_error: .: (0.000215) test_private_push_element: .: (0.000165) test_private_push_element_intermediate: .: (0.000166) test_private_push_element_last: .: (0.000181) test_private_push_element_noeffect: .: (0.000162) test_private_sorted_keys: .: (0.000164) test_private_unshift_element: .: (0.000182) test_private_unshift_element_first: .: (0.000168) test_private_unshift_element_intermediate: .: (0.000160) test_private_unshift_element_noeffect: .: (0.000211) test_push: .: (0.000180) test_reverse_each: .: (0.000194) test_self_bracket: .: (0.000155) test_self_new: .: (0.000187) test_size: .: (0.000176) test_sort!: .: (0.000156) test_to_a: .: (0.000158) test_uniq!: .: (0.000149) test_unshift: .: (0.000177) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000306) test_left_padding: .: (0.000182) test_right_padding: .: (0.000187) test_strip_padding: .: (0.000198) Bio::TestSOFT: test_dataset: .: (0.011137) test_series: .: (0.005371) Bio::TestSOSUIReport: test_entry_id: .: (0.000512) test_prediction: .: (0.000482) test_tmh: .: (0.000230) test_tmhs: .: (0.000252) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000310) test_rs: .: (0.000169) Bio::TestSOSUITMH: test_grade: .: (0.000384) test_range: .: (0.000234) test_sequence: .: (0.000222) Bio::TestSampleGraph: test_bellman_ford: .: (0.000484) test_bfs_shortest_path: .: (0.000235) test_breadth_first_search: .: (0.000421) test_depth_first_search: .: (0.000313) test_dijkstra: .: (0.000293) test_dump_list: .: (0.000266) test_dump_matrix: .: (0.000386) test_extract_subgraph_by_label: .: (0.000254) test_extract_subgraph_by_list: .: (0.000253) test_extract_subgraph_retains_disconnected_nodes: .: (0.000207) test_small_world_aka_node_degree_histogram: .: (0.000204) test_to_matrix: .: (0.000368) test_to_matrix_fixed_index: .: (0.000313) test_undirected_cliquishness: .: (0.000355) Bio::TestScf_version_2: test_complement: .: (0.004787) test_seq: .: (0.004521) test_to_biosequence: .: (0.004550) Bio::TestScf_version_3: test_complement: .: (0.012627) test_seq: .: (0.012296) test_to_biosequence: .: (0.013400) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000364) test_AA_new_sequence_all_legal_symbols: .: (0.000180) test_AA_new_sequence_removes_whitespace: .: (0.000169) test_AA_new_sequence_upcases_symbols: .: (0.000183) test_DNA_new_blank_sequence: .: (0.000169) test_DNA_new_sequence_downcases_symbols: .: (0.000159) test_DNA_new_sequence_removes_whitespace: .: (0.000165) test_NA_randomize_with_counts: .: (0.007692) test_NA_randomize_with_counts_and_block: .: (0.001636) test_RNA_new_sequence: .: (0.000210) test_ambiguous_dna_sequence_complement: .: (0.000197) test_ambiguous_rna_sequence_complement: .: (0.000170) test_amino_acid_codes: .: (0.000240) test_amino_acid_molecular_weight: .: (0.000278) test_amino_acid_names: .: (0.000223) test_amino_acid_randomize_can_be_chained: .: (0.001363) test_amino_acid_randomize_has_same_composition: .: (0.000930) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000554) test_dna_composition: .: (0.000211) test_dna_gc_percent: .: (0.000206) test_dna_molecular_weight: .: (0.000739) test_dna_pikachu: .: (0.000196) test_dna_sequence_complement: .: (0.000254) test_dna_sequence_translate: .: (0.000409) test_dna_to_re: .: (0.000248) test_element_reference_operator_with_one_argument: .: (0.000174) test_element_reference_operator_with_two_arguments: .: (0.000169) test_invalid_nucleic_acid_illegal_bases: .: (0.000216) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000216) test_nucleic_acid_names: .: (0.000204) test_randomize_dna_can_be_chained: .: (0.000386) test_randomize_dna_retains_composition: .: (0.000356) test_randomize_dna_with_block: .: (0.000330) test_rna_composition: .: (0.000243) test_rna_gc_percent: .: (0.000200) test_rna_molecular_weight: .: (0.000222) test_rna_pikachu: .: (0.000176) test_rna_sequence_complement: .: (0.000165) test_rna_sequence_translate: .: (0.000385) test_rna_to_re: .: (0.000255) test_total: .: (0.000180) test_two_consecutive_dna_randomizations_not_equal: .: (0.000450) test_valid_dna_sequence_illegal_bases: .: (0.000178) Bio::TestSequenceAA: test_codes: .: (0.000330) test_molecular_weight: .: (0.000200) test_names: .: (0.000188) test_to_re: .: (0.000230) test_to_s: .: (0.000152) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000356) Bio::TestSequenceAANew: test_new: .: (0.000256) test_new_n: .: (0.000165) test_new_r: .: (0.000155) test_new_t: .: (0.000156) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000587) test_concat: .: (0.000183) test_push: .: (0.000156) test_seq: .: (0.000143) test_splicing: .: (0.000278) test_sum: .: (0.000156) test_to_s: .: (0.000160) test_to_str: .: (0.000154) test_total: .: (0.000165) test_window_search: .: (0.000288) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000289) test_normalize_A: .: (0.000162) test_normalize_a: .: (0.000154) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000991) test_randomize_with_block: .: (0.022519) test_randomize_with_hash: .: (0.010639) test_randomize_with_hash_block: .: (0.021334) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.001314) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.001093) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000376) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000200) test_subseq_returns_subsequence: .: (0.000220) test_to_s_returns_self_as_string: .: (0.000223) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000291) test_window_search_with_width_3_step_two_with_residual: .: (0.000172) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000314) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000257) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000321) test_na_self_randomize: .: (0.000232) Bio::TestSequenceDBLink: test_database: .: (0.000475) test_id: .: (0.000152) test_secondary_ids: .: (0.000145) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000300) test_parse_uniprot_DR_line: .: (0.000175) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000822) test_output_width_35: .: (0.000328) test_output_width_nil: .: (0.000560) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000482) test_output_after_adding_sequence: .: (0.000340) test_output_after_truncating_sequence: .: (0.000245) test_output_from_error_probabilities: .: (0.002973) test_output_width45: .: (0.000362) test_output_with_converting_score_phred2solexa: .: (0.000529) test_output_with_converting_score_solexa2phred: .: (0.000371) test_output_with_default_score: .: (0.000289) Bio::TestSequenceMasker: test_mask: .: (0.000366) test_mask_with_enumerator: .: (0.000231) test_mask_with_enumerator_empty_mask_char: .: (0.000205) test_mask_with_enumerator_excess: .: (0.000387) test_mask_with_enumerator_longer_mask_char: .: (0.000200) test_mask_with_enumerator_shorter: .: (0.000529) test_mask_with_error_probability: .: (0.000205) test_mask_with_quality_score: .: (0.000176) Bio::TestSequenceNA: test_at_content: .: (0.000480) test_at_skew: .: (0.000253) test_codon_usage: .: (0.000199) test_complement: .: (0.000176) test_dna: .: (0.000172) test_dna!: .: (0.000165) test_forward_complement: .: (0.000197) test_gc_content: .: (0.000299) test_gc_percent: .: (0.000224) test_gc_skew: .: (0.000339) test_iliegal_bases: .: (0.000168) test_molecular_weight: .: (0.000409) test_names: .: (0.000225) test_reverse_complement: .: (0.000190) test_rna: .: (0.000154) test_rna!: .: (0.000158) test_splicing: .: (0.000236) test_to_re: .: (0.000225) test_to_s: .: (0.000161) Bio::TestSequenceNACommon: test_composition: .: (0.000312) test_concat: .: (0.000161) test_push: .: (0.000148) test_seq: .: (0.000150) test_splicing: .: (0.000237) test_sum: .: (0.000159) test_to_s: .: (0.000140) test_to_str: .: (0.000157) test_total: .: (0.000153) test_window_search: .: (0.000342) Bio::TestSequenceNANew: test_new: .: (0.000276) test_new_n: .: (0.000161) test_new_r: .: (0.000151) test_new_t: .: (0.000150) Bio::TestSequenceNATranslation: test_translate: .: (0.000475) test_translate_0: .: (0.000703) test_translate_1: .: (0.000338) test_translate_2: .: (0.000295) test_translate_3: .: (0.000301) test_translate_4: .: (0.000308) test_translate_5: .: (0.000291) test_translate_6: .: (0.000282) test_translate_7: .: (0.000571) test_translate_given_codon_table: .: (0.029753) test_translate_n1: .: (0.000616) test_translate_n2: .: (0.000484) test_translate_n3: .: (0.000490) test_translate_unknown_o: .: (0.000319) test_translate_unknown_x: .: (0.000316) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000486) test_convert_scores_from_phred_to_solexa: .: (0.000356) test_convert_scores_from_solexa_to_phred: .: (0.000191) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000258) test_convert_scores_from_phred: .: (0.000166) test_convert_scores_from_phred_to_solexa: .: (0.000330) test_convert_scores_from_solexa: .: (0.000201) test_convert_scores_from_solexa_to_phred: .: (0.000203) test_convert_scores_to_phred: .: (0.000138) test_convert_scores_to_solexa: .: (0.000349) test_p2q: .: (0.000191) test_phred_p2q: .: (0.000179) test_phred_q2p: .: (0.001829) test_q2p: .: (0.008209) test_quality_score_type: .: (0.000238) test_self_convert_scores_to_solexa: .: (0.000394) test_self_p2q: .: (0.000205) test_self_q2p: .: (0.001448) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000549) test_convert_scores_from_phred: .: (0.000376) test_convert_scores_from_phred_to_solexa: .: (0.000337) test_convert_scores_from_solexa: .: (0.000220) test_convert_scores_from_solexa_to_phred: .: (0.000208) test_convert_scores_to_phred: .: (0.000198) test_convert_scores_to_solexa: .: (0.000148) test_p2q: .: (0.000255) test_q2p: .: (0.004897) test_quality_score_type: .: (0.000228) test_self_convert_scores_to_phred: .: (0.000247) test_self_p2q: .: (0.000242) test_self_q2p: .: (0.006489) test_solexa_p2q: .: (0.000318) test_solexa_q2p: .: (0.001500) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000443) test_center: .: (0.000208) test_chomp: .: (0.000216) test_chop: .: (0.000191) test_delete: .: (0.000174) test_delete_prefix: .: (0.000172) test_delete_suffix: .: (0.000179) test_downcase: .: (0.000165) test_each_char: .: (0.000217) test_each_char_enum: .: (0.000206) test_each_grapheme_cluster: .: (0.001427) test_each_grapheme_cluster_enum: .: (0.000289) test_each_line: .: (0.000376) test_each_line_enum: .: (0.000214) test_gsub: .: (0.000209) test_gsub_with_block: .: (0.000498) test_ljust: .: (0.000095) test_lstrip: .: (0.000057) test_multiply: .: (0.000055) test_next: .: (0.000060) test_reverse: .: (0.000068) test_rjust: .: (0.000067) test_rstrip: .: (0.000055) test_slice: .: (0.000059) test_slice2: .: (0.000059) test_split: .: (0.000085) test_squeeze: .: (0.000055) test_strip: .: (0.000060) test_sub: .: (0.000073) test_sub_with_block: .: (0.008172) test_succ: .: (0.000321) test_swapcase: .: (0.000188) test_tr: .: (0.000190) test_tr_s: .: (0.000395) test_upcase: .: (0.000202) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000359) test_partition_nomatch: .: (0.000201) test_partition_sep_TSeq: .: (0.000210) test_partition_sep_regexp: .: (0.000217) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000344) test_rpartition_nomatch: .: (0.000193) test_rpartition_sep_TSeq: .: (0.000221) test_rpartition_sep_regexp: .: (0.000200) Bio::TestShRNA: test_blocK_it: .: (0.038188) test_blocK_it_: .: (0.047737) test_blocK_it_BLOCK_IT: .: (0.037708) test_blocK_it_BLOCK_iT: .: (0.023554) test_blocK_it_piGene: .: (0.019767) test_bottom_strand: .: (0.020020) test_bottom_strand_class: .: (0.019510) test_bottom_strand_nil: .: (0.019522) test_design: .: (0.018441) test_design_BLOCK_IT: .: (0.020512) test_report: .: (0.019902) test_report_before_design: .: (0.019892) test_top_strand: .: (0.019979) test_top_strand_class: .: (0.020206) test_top_strand_nil: .: (0.019416) Bio::TestShRNANew: test_new: .: (0.000501) Bio::TestSiRNA: test_antisense_size: .: (0.000937) test_design: .: (0.019481) test_design_reynolds: .: (0.023498) test_design_uitei: .: (0.019484) test_max_gc_percent: .: (0.000216) test_min_gc_percent: .: (0.000177) test_reynolds: .: (0.023552) test_reynolds?: .: (0.000244) test_uitei: .: (0.019991) test_uitei?: .: (0.000240) Bio::TestSiRNANew: test_new: .: (0.000507) Bio::TestSiRNAPair: test_antisense: .: (0.020002) test_gc_percent: .: (0.020013) test_report: .: (0.020043) test_rule: .: (0.019341) test_sense: .: (0.019924) test_start: .: (0.020231) test_stop: .: (0.019937) test_target: .: (0.020730) Bio::TestSiRNAPairNew: test_new: .: (0.000539) Bio::TestSim4Report: test_all_hits: .: (0.000561) test_each: .: (0.000273) test_each_hit: .: (0.000153) test_hits: .: (0.000155) test_num_hits: .: (0.000109) test_query_def: .: (0.000113) test_query_id: .: (0.000127) test_query_len: .: (0.000115) test_seq1: .: (0.000158) Bio::TestSim4Report2: test_all_hits: .: (0.000524) test_each: .: (0.000138) test_each_hit: .: (0.000108) test_hits: .: (0.000111) test_num_hits: .: (0.000096) test_query_def: .: (0.000085) test_query_id: .: (0.000088) test_query_len: .: (0.000086) test_seq1: .: (0.000123) Bio::TestSim4Report4: test_all_hits: .: (0.000251) test_each: .: (0.000129) test_each_hit: .: (0.000153) test_hits: .: (0.000122) test_num_hits: .: (0.000098) test_query_def: .: (0.000097) test_query_id: .: (0.000093) test_query_len: .: (0.000092) test_seq1: .: (0.000176) Bio::TestSim4ReportHit: test_align: .: (0.000306) test_complement?: .: (0.000112) test_definition: .: (0.000094) test_each: .: (0.000252) test_exons: .: (0.000445) test_hit_id: .: (0.000257) test_hsps: .: (0.000380) test_introns: .: (0.000358) test_len: .: (0.000247) test_query_def: .: (0.000256) test_query_id: .: (0.000250) test_query_len: .: (0.000249) test_segmentpairs: .: (0.000419) test_seq1: .: (0.000313) test_seq2: .: (0.000373) test_target_def: .: (0.000247) test_target_id: .: (0.000179) test_target_len: .: (0.000116) Bio::TestSim4ReportHit2: test_align: .: (0.000298) test_complement?: .: (0.000107) test_definition: .: (0.000097) test_each: .: (0.000248) test_exons: .: (0.000196) test_hit_id: .: (0.000103) test_hsps: .: (0.000177) test_introns: .: (0.000232) test_len: .: (0.000125) test_query_def: .: (0.000087) test_query_id: .: (0.000082) test_query_len: .: (0.000079) test_segmentpairs: .: (0.000180) test_seq1: .: (0.000114) test_seq2: .: (0.000107) test_target_def: .: (0.000080) test_target_id: .: (0.000079) test_target_len: .: (0.000078) Bio::TestSim4ReportHit4: test_align: .: (0.000318) test_complement?: .: (0.000107) test_definition: .: (0.000095) test_each: .: (0.000319) test_exons: .: (0.000251) test_hit_id: .: (0.000105) test_hsps: .: (0.000223) test_introns: .: (0.000252) test_len: .: (0.000162) test_query_def: .: (0.000102) test_query_id: .: (0.000095) test_query_len: .: (0.000093) test_segmentpairs: .: (0.000608) test_seq1: .: (0.000304) test_seq2: .: (0.000296) test_target_def: .: (0.000262) test_target_id: .: (0.000259) test_target_len: .: (0.000253) Bio::TestSim4ReportSegment: test_from: .: (0.000285) test_self_new: .: (0.000194) test_seq: .: (0.000161) test_to: .: (0.000156) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000519) test_direction: .: (0.000356) test_hit_from: .: (0.000355) test_hit_to: .: (0.000373) test_hseq: .: (0.000384) test_midline: .: (0.000342) test_percent_identity: .: (0.000337) test_qseq: .: (0.000372) test_query_from: .: (0.000372) test_query_to: .: (0.000353) test_seq1: .: (0.000369) test_seq2: .: (0.000374) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000473) test_direction: .: (0.000309) test_hit_from: .: (0.000342) test_hit_to: .: (0.000320) test_hseq: .: (0.000277) test_midline: .: (0.000268) test_percent_identity: .: (0.000274) test_qseq: .: (0.000311) test_query_from: .: (0.000274) test_query_to: .: (0.000272) test_seq1: .: (0.000417) test_seq2: .: (0.000344) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000497) test_direction: .: (0.000342) test_hit_from: .: (0.000359) test_hit_to: .: (0.000445) test_hseq: .: (0.000340) test_midline: .: (0.000354) test_percent_identity: .: (0.000318) test_qseq: .: (0.000322) test_query_from: .: (0.000333) test_query_to: .: (0.000275) test_seq1: .: (0.000272) test_seq2: .: (0.000253) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000423) test_direction: .: (0.000236) test_hit_from: .: (0.000203) test_hit_to: .: (0.000205) test_hseq: .: (0.000246) test_midline: .: (0.000202) test_percent_identity: .: (0.000185) test_qseq: .: (0.002890) test_query_from: .: (0.000780) test_query_to: .: (0.000313) test_seq1: .: (0.000269) test_seq2: .: (0.000275) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000362) test_direction: .: (0.000231) test_hit_from: .: (0.001013) test_hit_to: .: (0.000521) test_hseq: .: (0.000217) test_midline: .: (0.000397) test_percent_identity: .: (0.000282) test_qseq: .: (0.000229) test_query_from: .: (0.000222) test_query_to: .: (0.000202) test_seq1: .: (0.000246) test_seq2: .: (0.000749) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000328) test_direction: .: (0.000220) test_hit_from: .: (0.000163) test_hit_to: .: (0.000149) test_hseq: .: (0.000158) test_midline: .: (0.000163) test_percent_identity: .: (0.000158) test_qseq: .: (0.000443) test_query_from: .: (0.000272) test_query_to: .: (0.000178) test_seq1: .: (0.000209) test_seq2: .: (0.000184) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000294) test_direction: .: (0.000157) test_hit_from: .: (0.000151) test_hit_to: .: (0.000150) test_hseq: .: (0.000142) test_midline: .: (0.000219) test_percent_identity: .: (0.000151) test_qseq: .: (0.000151) test_query_from: .: (0.000161) test_query_to: .: (0.000152) test_seq1: .: (0.000269) test_seq2: .: (0.000202) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000189) test_entry_id: .: (0.000054) test_filename: .: (0.000048) test_len: .: (0.000053) test_self_new: .: (0.000060) test_self_parse: .: (0.000062) Bio::TestTMHMMReport: test_entry_id: .: (0.000321) test_exp_aas_in_tmhs: .: (0.000191) test_exp_first_60aa: .: (0.000184) test_helix: .: (0.000213) test_predicted_tmhs: .: (0.000183) test_query_len: .: (0.000184) test_tmhs: .: (0.001492) test_to_s: .: (0.000300) test_total_prob_of_N_in: .: (0.000201) Bio::TestTMHMMReport_reports: test_reports: .: (0.000201) Bio::TestTMHMMTMH: test_entry_id: .: (0.000272) test_pos: .: (0.000184) test_range: .: (0.000178) test_status: .: (0.000176) test_version: .: (0.000186) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000272) test_cutoff: .: (0.000155) test_entry_id: .: (0.000120) test_length: .: (0.000116) test_loc: .: (0.000116) test_name: .: (0.000106) test_networks: .: (0.000107) test_prediction: .: (0.000121) test_query_len: .: (0.000109) test_query_sequences: .: (0.000369) test_rc: .: (0.000127) test_version: .: (0.000111) Bio::TestTargetPReportConst: test_delimiter: .: (0.000141) test_rs: .: (0.000040) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000105) test_togows_access_wait: .: (2.003126) Bio::TestTogoWSREST: test_debug: .: (0.000440) test_debug_default: .: (0.000109) test_internal_http: .: (0.000102) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000118) test_entry: .: (0.000040) test_entry_database_list: .: (0.000037) test_new: .: (0.000106) test_new_with_uri_object: .: (0.000115) test_new_with_uri_string: .: (0.000100) test_retrieve: .: (0.000039) test_search: .: (0.000036) test_search_database_list: .: (0.000035) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000205) test_prepare_return_value: .: (0.000133) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000251) Bio::TestTree: test_get_edge_distance: .: (0.000151) test_get_edge_distance_string: .: (0.000101) test_get_node_name: .: (0.000050) test_initialize: .: (0.000062) test_options: .: (0.000051) test_root: .: (0.000036) test_root=: .: (0.000045) Bio::TestTree2: test_add_edge: .: (0.000247) test_add_node: .: (0.000126) test_adjacency_matrix: .: (0.000140) test_adjacency_matrix_with_block: .: (0.000145) test_adjacent_nodes: .: (0.000130) test_adjacent_nodes_nonexistent: .: (0.000076) test_ancestors: .: (0.000101) test_children: .: (0.000087) test_clear: .: (0.000093) test_clear_node: .: (0.000116) test_clear_node_nonexistent: .: (0.000125) test_collect_edge!: .: (0.000150) test_collect_node!: .: (0.016118) test_concat: .: (0.000196) test_descendents: .: (0.000113) test_distance_matrix: .: (0.000525) test_each_edge: .: (0.000144) test_each_node: .: (0.000116) test_each_out_edge: .: (0.000103) test_each_out_edge_chimpanzee: .: (0.000096) test_each_out_edge_human: .: (0.000096) test_each_out_edge_mammals: .: (0.000150) test_each_out_edge_nonexistent: .: (0.000176) test_each_out_edge_primates: .: (0.000156) test_each_out_edge_rat: .: (0.000100) test_each_out_edge_rodents: .: (0.000125) test_edges: .: (0.000098) test_get_edge: .: (0.000208) test_get_edge_indirect: .: (0.000078) test_get_edge_merged: .: (0.000094) test_get_edge_nonexistent: .: (0.000071) test_get_node_bootstrap: .: (0.000085) test_get_node_bootstrap_string=: .: (0.000086) test_get_node_by_name: .: (0.000129) test_get_node_by_name_noexistent: .: (0.000104) test_include?: .: (0.000102) test_include_nonexistent: .: (0.000076) test_insert_node: .: (0.000149) test_leaves: .: (0.000118) test_leaves_noargs: .: (0.000079) test_lowest_common_ancestor: .: (0.000090) test_nodes: .: (0.000082) test_number_of_edges: .: (0.000072) test_number_of_nodes: .: (0.000071) test_out_degree: .: (0.000141) test_out_degree_nonexistent: .: (0.000483) test_out_edges: .: (0.000447) test_out_edges_mammals: .: (0.000288) test_out_edges_nonexistent: .: (0.000100) test_out_edges_primates: .: (0.000128) test_out_edges_rodents: .: (0.000157) test_parent: .: (0.000119) test_path: .: (0.000093) test_remove_edge: .: (0.000115) test_remove_edge_if: .: (0.000114) test_remove_edge_if_nothing_removed: .: (0.000126) test_remove_edge_nonexistent: .: (0.000168) test_remove_node: .: (0.000364) test_remove_node_if: .: (0.000093) test_remove_node_if_false: .: (0.000101) test_remove_node_nonexistent: .: (0.000135) test_remove_nonsense_nodes: .: (0.000114) test_subtree: .: (0.000138) test_subtree_with_all_paths: .: (0.000186) test_total_distance: .: (0.000090) Bio::TestTreeEdge: test_distance: .: (0.000156) test_distance=: .: (0.000069) test_distance_string: .: (0.000040) test_distance_string=: .: (0.000064) test_initialize: .: (0.000230) test_inspect: .: (0.000039) test_to_s: .: (0.000037) Bio::TestTreeNode: test_bootstrap: .: (0.000117) test_bootstrap=: .: (0.000062) test_bootstrap_string: .: (0.000036) test_bootstrap_string=: .: (0.000067) test_initialize: .: (0.000055) test_inspect: .: (0.000057) test_name: .: (0.000042) test_to_s: .: (0.000037) Bio::TestUniProt: test_gene_name: .: (0.003430) Bio::TestUniProtKB: test_ac: .: (0.011724) test_accession: .: (0.023447) test_cc: .: (0.019977) test_cc_alternative_products: .: (0.005140) test_cc_database: .: (0.003760) test_cc_mass_spectrometry: .: (0.003693) test_de: .: (0.002179) test_dr: .: (0.007636) test_dr_with_key: .: (0.004289) test_dr_with_key_empty: .: (0.003812) test_dt: .: (0.005848) test_dt_annotation: .: (0.003133) test_dt_created: .: (0.002017) test_dt_sequence: .: (0.002136) test_entry: .: (0.002441) test_ft: .: (0.009127) test_gene_name: .: (0.002993) test_gene_names: .: (0.002598) test_gn: .: (0.002321) test_gn_old_parser: .: (0.002385) test_gn_uniprot_parser: .: (0.002136) test_id_line: .: (0.002179) test_id_line_data_class: .: (0.005799) test_id_line_entry_name: .: (0.002830) test_id_line_molecule_type: .: (0.002418) test_id_line_sequence_length: .: (0.002428) test_kw: .: (0.018499) test_molecule: .: (0.022374) test_oc: .: (0.014195) test_og_1: .: (0.003419) test_og_2: .: (0.002343) test_og_3: .: (0.002299) test_og_4: .: (0.002383) test_og_5: .: (0.001982) test_og_6: .: (0.002239) test_os: .: (0.004278) test_os_access: .: (0.004012) test_os_access2: .: (0.002743) test_ox: .: (0.002131) test_protein_name: .: (0.002634) test_ref: .: (0.007974) test_seq: .: (0.003953) test_sequence_length: .: (0.002569) test_sq: .: (0.002445) test_sq_crc64: .: (0.002368) test_sq_len: .: (0.002303) test_sq_mw: .: (0.002105) test_synonyms: .: (0.004165) Bio::TestUniProtKB_CC: test_allergen: .: (0.000455) test_alternative_products_access_as_hash: .: (0.000313) test_alternative_products_ai: .: (0.000359) test_alternative_products_apu: .: (0.000506) test_alternative_products_as: .: (0.000367) test_alternative_products_rf: .: (0.000177) test_biophysicochemical_properties: .: (0.001305) test_biotechnology: .: (0.000343) test_catalytic_activity: .: (0.000264) test_caution: .: (0.000279) test_cofactor: .: (0.000246) test_developmental_stage: .: (0.000273) test_disease: .: (0.000318) test_domain: .: (0.000338) test_enzyme_regulation: .: (0.000260) test_function: .: (0.000252) test_induction: .: (0.000208) test_interaction: .: (0.000320) test_mass_spectrometry: .: (0.000343) test_miscellaneous: .: (0.000217) test_pathway: .: (0.001028) test_pharmaceutical: .: (0.000644) test_polymorphism: .: (0.000380) test_ptm: .: (0.000279) test_rna_editing: .: (0.000326) test_similarity: .: (0.000227) test_subcellular_location: .: (0.000325) test_subunit: .: (0.000222) test_tissue_specificity: .: (0.000299) test_toxic_dose: .: (0.000226) test_web_resource: .: (0.000311) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000759) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000546) test_protein_name: .: (0.000333) test_synonyms: .: (0.000370) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000309) test_entry: .: (0.000164) test_entry_id: .: (0.000153) test_entry_name: .: (0.000141) test_id_line: .: (0.000155) test_molecule: .: (0.000222) test_sequence_length: .: (0.000192) Bio::TestUniProtKB_P03589: test_ac: .: (0.000808) test_accession: .: (0.000514) test_cc: .: (0.000667) test_cc_alternative_products: .: (0.000597) test_cc_database: .: (0.000742) test_cc_mass_spectrometry: .: (0.000588) test_de: .: (0.000465) test_dr: .: (0.000606) test_dr_with_key: .: (0.000600) test_dr_with_key_empty: .: (0.000571) test_dt: .: (0.000396) test_dt_annotation: .: (0.000382) test_dt_created: .: (0.000422) test_dt_sequence: .: (0.000508) test_entry: .: (0.000409) test_ft: .: (0.000566) test_gene_name: .: (0.000445) test_gene_names: .: (0.000446) test_gn: .: (0.000603) test_gn_old_parser: .: (0.000476) test_gn_uniprot_parser: .: (0.000372) test_id_line: .: (0.000383) test_id_line_data_class: .: (0.000330) test_id_line_entry_name: .: (0.000223) test_id_line_sequence_length: .: (0.000205) test_kw: .: (0.000257) test_oc: .: (0.000234) test_oh: .: (0.000416) test_os: .: (0.000248) test_os_access: .: (0.000278) test_os_access2: .: (0.000258) test_ox: .: (0.000251) test_protein_name: .: (0.000605) test_protein_name_after_calling_de: .: (0.000389) test_ref: .: (0.000355) test_seq: .: (0.000517) test_sequence_length: .: (0.000322) test_sq: .: (0.000257) test_sq_crc64: .: (0.000228) test_sq_len: .: (0.000266) test_sq_mw: .: (0.000277) test_synonyms: .: (0.000288) Bio::TestUniProtKB_P28907: test_ac: .: (0.000876) test_accession: .: (0.000767) test_cc: .: (0.004134) test_cc_alternative_products: .: (0.002265) test_cc_database: .: (0.001489) test_cc_mass_spectrometry: .: (0.001983) test_de: .: (0.001399) test_dr: .: (0.003132) test_dr_with_key: .: (0.002501) test_dr_with_key_empty: .: (0.006425) test_dt: .: (0.001088) test_dt_annotation: .: (0.001768) test_dt_created: .: (0.001303) test_dt_sequence: .: (0.001124) test_entry: .: (0.001116) test_ft: .: (0.002138) test_gene_name: .: (0.001106) test_gene_names: .: (0.001038) test_gn: .: (0.000926) test_gn_old_parser: .: (0.000903) test_gn_uniprot_parser: .: (0.000960) test_id_line: .: (0.001139) test_id_line_data_class: .: (0.000870) test_id_line_entry_name: .: (0.001374) test_id_line_sequence_length: .: (0.001681) test_kw: .: (0.001453) test_oc: .: (0.001177) test_os: .: (0.001193) test_os_access: .: (0.001043) test_os_access2: .: (0.000991) test_ox: .: (0.001051) test_protein_name: .: (0.001092) test_protein_name_after_calling_de: .: (0.001015) test_ref: .: (0.001473) test_seq: .: (0.001137) test_sequence_length: .: (0.000803) test_sq: .: (0.000745) test_sq_crc64: .: (0.000759) test_sq_len: .: (0.000843) test_sq_mw: .: (0.001149) test_synonyms: .: (0.003910) test_synonyms_after_calling_de: .: (0.001764) Bio::TestUniProtKB_P49144: test_ac: .: (0.000649) test_accession: .: (0.001343) test_cc: .: (0.000825) test_cc_alternative_products: .: (0.000710) test_cc_database: .: (0.000771) test_cc_mass_spectrometry: .: (0.000948) test_de: .: (0.000618) test_dr: .: (0.000714) test_dr_with_key: .: (0.000796) test_dr_with_key_empty: .: (0.000737) test_dt: .: (0.000515) test_dt_annotation: .: (0.000605) test_dt_created: .: (0.000805) test_dt_sequence: .: (0.000332) test_entry: .: (0.000354) test_ft: .: (0.001029) test_gene_name: .: (0.000447) test_gene_names: .: (0.000654) test_gn: .: (0.000439) test_gn_old_parser: .: (0.000423) test_gn_uniprot_parser: .: (0.000411) test_id_line: .: (0.000368) test_id_line_data_class: .: (0.000369) test_id_line_entry_name: .: (0.000355) test_id_line_sequence_length: .: (0.000403) test_kw: .: (0.000468) test_oc: .: (0.000658) test_os: .: (0.002802) test_os_access: .: (0.000606) test_os_access2: .: (0.001340) test_ox: .: (0.000604) test_protein_name: .: (0.000468) test_protein_name_after_calling_de: .: (0.001056) test_ref: .: (0.001015) test_seq: .: (0.000550) test_sequence_length: .: (0.000689) test_sq: .: (0.000421) test_sq_crc64: .: (0.000531) test_sq_len: .: (0.000429) test_sq_mw: .: (0.000422) test_synonyms: .: (0.000810) test_synonyms_after_calling_de: .: (0.000458) Bio::TestUniProtKB_Ref: test_RA: .: (0.000311) test_RC: .: (0.000162) test_RG: .: (0.000156) test_RL: .: (0.000140) test_RN: .: (0.000133) test_RP: .: (0.000140) test_RT: .: (0.000131) test_RX: .: (0.000133) test_ref: .: (0.000141) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000348) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000339) test_alternative_products_with_ft: .: (0.000740) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000266) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000186) test_RL_lines: .: (0.000266) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000332) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000130) test_RG_line: .: (0.000076) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000321) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000182) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000123) test_RL_line: .: (0.000104) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000559) test_RP_line: .: (0.000138) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000084) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000434) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000123) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000095) test_CC_interaction_isoform: .: (0.000090) test_CC_interaction_no_gene_name: .: (0.000085) test_CC_interaction_self_association: .: (0.000116) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000156) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000156) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000198) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000184) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000166) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000135) test_DT_line: .: (0.000090) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.002573) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000668) test_CC_web_resource: .: (0.000148) test_FT_VER_SEQ: .: (0.000278) test_OH_line_exception: .: (0.000302) test_OH_lines: .: (0.000344) Bio::TestUtils: test_centreOfGravity: .: (0.000507) test_dihedral_angle: .: (0.000467) test_distance: .: (0.000477) test_geometricCentre: .: (0.000298) test_rad2deg: .: (0.000241) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000357) test_dijkstra_on_weighted_graph: .: (0.000222) Finished in 11.879778946 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 331.74 tests/s, 1818.30 assertions/s /usr/bin/ruby3.1 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.1 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.1.0:/var/lib/gems/3.1.0:/usr/local/lib/ruby/gems/3.1.0:/usr/lib/ruby/gems/3.1.0:/usr/lib/aarch64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000426) test_dbs: .: (0.000126) test_go_ids: .: (0.000355) test_go_terms: .: (0.000161) test_parser: .: (0.000288) test_set_date: .: (0.000116) test_set_desc: .: (0.000175) test_to_str: .: (0.000122) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000518) test_mktmpdir_without_block: .: (0.000343) test_remove_entry_secure: .: (0.000255) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.003053) test_call_command_fork: .: (0.000140) test_call_command_open3: .: (0.010167) test_call_command_popen: .: (0.015990) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.023648) test_call_command_fork: .: (0.000133) test_call_command_open3: .: (0.027657) test_call_command_popen: .: (0.020023) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.019873) test_call_command_fork: .: (0.000138) test_call_command_open3: .: (0.031692) test_call_command_popen: .: (0.020003) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.011956) test_call_command_fork_chdir: .: (0.000264) test_call_command_popen_chdir: .: (0.011560) test_query_command_chdir: .: (0.001562) test_query_command_fork_chdir: .: (0.000257) test_query_command_popen_chdir: .: (0.001489) Bio::FuncTestCommandQuery: test_query_command: .: (0.028620) test_query_command_fork: .: (0.009041) test_query_command_open3: .: (0.050596) test_query_command_popen: .: (0.039937) Bio::FuncTestCommandTmpdir: test_close!: .: (0.018824) test_initialize: .: (0.000445) test_path: .: (0.000274) test_path_after_close: .: (0.000384) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.018250) test_output_fasta: .: (0.014058) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000583) test_accession: .: (0.000114) test_accessions: .: (0.000088) test_comment: .: (0.000071) test_common_name: .: (0.000111) test_definition: .: (0.000094) test_features: .: (0.000228) test_gi: .: (0.000137) test_keywords: .: (0.000107) test_locus: .: (0.000058) test_nid: .: (0.000090) test_organism: .: (0.000240) test_origin: .: (0.000075) test_references: .: (0.008828) test_segment: .: (0.019495) test_source: .: (0.000361) test_taxonomy: .: (0.027686) test_version: .: (0.000256) test_versions: .: (0.013490) Bio::TestAA: test_13: .: (0.000239) test_1n: .: (0.000175) test_name2one: .: (0.000107) test_name2three: .: (0.008363) test_one2name: .: (0.000075) test_one2three: .: (0.000049) test_three2name: .: (0.000045) test_three2one: .: (0.000069) test_to_1_1: .: (0.000055) test_to_1_3: .: (0.000076) test_to_1_name: .: (0.000067) test_to_3_1: .: (0.000052) test_to_3_3: .: (0.000047) test_to_3_name: .: (0.000061) test_to_re: .: (0.000103) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000182) Bio::TestAAindex: test_api: .: (0.000144) test_auto_aax1: .: (0.000885) test_auto_aax2: .: (0.000178) Bio::TestAAindex1: test_author: .: (0.000278) test_comment: .: (0.000153) test_correlation_coefficient: .: (0.000263) test_dblinks: .: (0.000125) test_definition: .: (0.000117) test_entry_id: .: (0.000112) test_index: .: (0.000711) test_journal: .: (0.000305) test_title: .: (0.000135) Bio::TestAAindex2: test_access_A_R: .: (0.000762) test_access_R_A: .: (0.000823) test_author: .: (0.000274) test_cols: .: (0.000138) test_comment: .: (0.000111) test_dblinks: .: (0.000115) test_definition: .: (0.000119) test_entry_id: .: (0.000110) test_journal: .: (0.000128) test_matrix: .: (0.000807) test_matrix_1_2: .: (0.000494) test_matrix_2_2: .: (0.000535) test_matrix_A_R: .: (0.000682) test_matrix_R_A: .: (0.000438) test_matrix_determinant: .: (0.002703) test_matrix_rank: .: (0.002365) test_matrix_transpose: .: (0.000548) test_rows: .: (0.000361) test_title: .: (0.000137) Bio::TestAAindexConstant: test_delimiter: .: (0.000176) test_tagsize: .: (0.000044) Bio::TestAbif: test_complement: .: (0.006570) test_seq: .: (0.005911) test_to_biosequence: .: (0.007060) Bio::TestActsLikeMap: test_mixin: .: (0.000238) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000191) Bio::TestActsLikeMarker: test_mixin: .: (0.000126) Bio::TestAlignment: test_add_seq_no_key: .: (0.000206) test_add_seq_using_seq_with_aaseq_method: .: (0.000085) test_add_seq_using_seq_with_definition_method: .: (0.000059) test_add_seq_using_seq_with_entry_id_method: .: (0.000064) test_add_seq_using_seq_with_naseq_method: .: (0.000099) test_add_seq_using_seq_with_seq_method: .: (0.000058) test_consensus_iupac_gap_modes: .: (0.000290) test_consensus_iupac_missing_char: .: (0.000097) test_consensus_iupac_missing_char_option: .: (0.000100) test_consensus_iupac_no_gaps: .: (0.000145) test_consensus_iupac_of_ambiguous_bases: .: (0.000295) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002927) test_consensus_opt_gap_mode: .: (0.000561) test_consensus_opt_missing_char: .: (0.000232) test_consensus_string_no_gaps: .: (0.000219) test_consensus_threshold_four_sequences: .: (0.000221) test_consensus_threshold_two_sequences: .: (0.000207) test_convert_match: .: (0.000166) test_convert_unmatch: .: (0.000124) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000086) test_convert_unmatch_different_match_char: .: (0.000097) test_convert_unmatch_multiple_sequences: .: (0.000124) test_default_gap_char: .: (0.000044) test_default_gap_regexp_matches_default_gap_char: .: (0.000059) test_default_missing_char: .: (0.000049) test_each_site_equal_length: .: (0.000094) test_each_site_unequal_length: .: (0.000106) test_equals: .: (0.000118) test_match_line_protein: .: (0.000360) test_normalizebang_extends_sequences_with_gaps: .: (0.000090) test_seq_length_is_max_seq_length: .: (0.000075) test_seq_length_when_one_sequence: .: (0.000044) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000046) test_seqclass_when_seqclass_set: .: (0.000068) test_seqclass_when_sequence_used: .: (0.000046) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000044) test_set_and_get_gap_char: .: (0.000044) test_store_cannot_override_key: .: (0.000052) test_store_with_default_keys_and_user_defined_keys: .: (0.000050) test_store_with_nil_key_uses_next_number_for_key: .: (0.000062) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000187) test_alignment_concat: .: (0.000114) test_alignment_length: .: (0.000045) test_alignment_lstrip!: .: (0.000160) test_alignment_lstrip_nil: .: (0.000068) test_alignment_normalize!: .: (0.000049) test_alignment_rstrip!: .: (0.000118) test_alignment_rstrip_nil: .: (0.000052) test_alignment_site: .: (0.000051) test_alignment_slice: .: (0.000049) test_alignment_strip!: .: (0.000093) test_alignment_strip_nil: .: (0.000076) test_alignment_subseq: .: (0.000073) test_alignment_window: .: (0.000065) test_collect_each_site: .: (0.000116) test_consensus_each_site_default: .: (0.000122) test_consensus_each_site_gap_mode_1: .: (0.000089) test_consensus_each_site_gap_mode_minus1: .: (0.000106) test_consensus_iupac: .: (0.000227) test_consensus_string_default: .: (0.000084) test_consensus_string_half: .: (0.000086) test_convert_match: .: (0.000068) test_convert_unmatch: .: (0.000053) test_each_seq: .: (0.000071) test_each_site: .: (0.000091) test_each_site_step: .: (0.000084) test_each_window: .: (0.000084) test_match_line: .: (0.000509) test_match_line_amino: .: (0.000859) test_match_line_nuc: .: (0.000141) test_private_alignment_site: .: (0.000060) test_remove_all_gaps!: .: (0.000103) test_seqclass: .: (0.000056) test_seqclass=: .: (0.000068) test_seqclass_default: .: (0.000058) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002675) test_determine_seq_method: .: (0.001313) test_entries: .: (0.000428) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000261) test_avoid_same_name_numbering: .: (0.000104) test_clustal_have_same_name_true: .: (0.000054) test_have_same_name_false: .: (0.000076) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000133) test_gap_char_default: .: (0.000083) test_gap_char_never_nil: .: (0.000043) test_gap_regexp: .: (0.000048) test_gap_regexp=: .: (0.000054) test_gap_regexp_never_nil: .: (0.000043) test_get_all_property_default: .: (0.000087) test_get_all_property_nodefault: .: (0.000064) test_is_gap_default_false: .: (0.000053) test_is_gap_default_true: .: (0.000073) test_is_gap_nodefault_false: .: (0.000047) test_is_gap_nodefault_true: .: (0.000076) test_missing_char=: .: (0.000052) test_missing_char_default: .: (0.000042) test_missing_char_never_nil: .: (0.000061) test_seqclass=: .: (0.000052) test_seqclass_default: .: (0.000045) test_seqclass_never_nil: .: (0.000060) test_set_all_property: .: (0.000058) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000465) test_consensus_string_50percent: .: (0.000096) test_consensus_string_50percent_nil: .: (0.000055) test_consensus_string_default: .: (0.000042) test_consensus_string_default_nil: .: (0.000064) test_has_gap_false: .: (0.000052) test_has_gap_true: .: (0.000043) test_match_line_amino_100percent: .: (0.000096) test_match_line_amino_missing: .: (0.000207) test_match_line_amino_strong: .: (0.000121) test_match_line_amino_weak: .: (0.000085) test_match_line_nuc_100percent: .: (0.000091) test_match_line_nuc_missing: .: (0.000059) test_remove_gaps!: .: (0.000049) test_remove_gaps_bang_not_removed: .: (0.000061) Bio::TestAtomFinder: test_atoms: .: (0.013409) test_each_atom: .: (0.000277) test_find_atom: .: (0.000188) Bio::TestBioFastaDefline: test_acc_version: .: (0.000469) test_accession: .: (0.000414) test_accessions: .: (0.000259) test_description: .: (0.000188) test_descriptions: .: (0.000181) test_entry_id: .: (0.000169) test_get: .: (0.000204) test_get_all_by_type: .: (0.000164) test_get_by_type: .: (0.000201) test_gi: .: (0.000159) test_id_strings: .: (0.000395) test_locus: .: (0.000155) test_method_missing: .: (0.000213) test_to_s: .: (0.000217) test_words: .: (0.000486) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000869) test_goid2term: .: (0.000330) test_parse_goids: .: (0.000257) Bio::TestBioGenBank: test_basecount: .: (0.000351) test_circular: .: (0.000187) test_classification: .: (0.000239) test_date: .: (0.000166) test_date_modified: .: (0.000768) test_division: .: (0.000229) test_each_cds_feature: .: (0.000639) test_each_cds_qualifiers: .: (0.000997) test_each_gene: .: (0.000845) test_entry_id: .: (0.000239) test_length: .: (0.000177) test_locus_circular: .: (0.000305) test_locus_class: .: (0.000195) test_locus_date: .: (0.000198) test_locus_division: .: (0.000189) test_locus_entry_id: .: (0.000193) test_locus_length: .: (0.000194) test_locus_natype: .: (0.000241) test_locus_strand: .: (0.000462) test_natype: .: (0.000230) test_seq: .: (0.000386) test_seq_len: .: (0.000243) test_strand: .: (0.000178) test_strandedness: .: (0.000173) test_to_biosequence: .: (0.002021) Bio::TestBioGenPept: test_circular: .: (0.000354) test_date: .: (0.000126) test_dbsource: .: (0.000505) test_division: .: (0.000224) test_entry_id: .: (0.000116) test_length: .: (0.000109) test_locus: .: (0.000121) test_seq: .: (0.000143) test_seq_len: .: (0.000120) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000311) test_aaseq: .: (0.000187) test_chromosome: .: (0.000397) test_codon_usage: .: (0.000241) test_cu_list: .: (0.000115) test_dblinks_as_hash: .: (0.000171) test_dblinks_as_strings: .: (0.000181) test_definition: .: (0.000176) test_division: .: (0.000129) test_eclinks: .: (0.000153) test_entry: .: (0.000228) test_entry_id: .: (0.000116) test_gbposition: .: (0.000168) test_gene: .: (0.000139) test_genes: .: (0.000120) test_keggclass: .: (0.000142) test_keggclasses: .: (0.000142) test_locations: .: (0.000240) test_motifs_as_hash: .: (0.000291) test_motifs_as_strings: .: (0.000131) test_name: .: (0.000118) test_names_as_array: .: (0.000124) test_new: .: (0.000134) test_ntlen: .: (0.000184) test_ntseq: .: (0.000214) test_organism: .: (0.000120) test_orthologs_as_hash: .: (0.000146) test_orthologs_as_strings: .: (0.000446) test_pathway: .: (0.000155) test_pathway_after_pathways_as_strings: .: (0.000175) test_pathway_before_pathways_as_strings: .: (0.000168) test_pathways_as_hash: .: (0.000283) test_pathways_as_strings: .: (0.000163) test_position: .: (0.000140) test_structure: .: (0.000129) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000842) test_comment: .: (0.000372) test_data_source: .: (0.000232) test_definition: .: (0.000238) test_disease: .: (0.000215) test_entry_id: .: (0.000267) test_lineage: .: (0.000331) test_nalen: .: (0.000227) test_name: .: (0.000370) test_new: .: (0.000255) test_num_gene: .: (0.000213) test_num_rna: .: (0.000202) test_original_databases: .: (0.000303) test_original_db: .: (0.000238) test_plasmids: .: (0.000226) test_references: .: (0.001817) test_statistics: .: (0.000300) test_taxid: .: (0.000442) test_taxonomy: .: (0.000276) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000473) test_comment: .: (0.000191) test_data_source: .: (0.000133) test_definition: .: (0.000121) test_disease: .: (0.000123) test_entry_id: .: (0.000126) test_lineage: .: (0.000150) test_nalen: .: (0.000127) test_name: .: (0.000123) test_new: .: (0.000213) test_num_gene: .: (0.000170) test_num_rna: .: (0.000151) test_original_databases: .: (0.000137) test_original_db: .: (0.000127) test_plasmids: .: (0.000227) test_references: .: (0.000350) test_statistics: .: (0.000234) test_taxid: .: (0.000170) test_taxonomy: .: (0.000149) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000315) test_compounds_as_strings: .: (0.000122) test_dblinks_as_hash: .: (0.000100) test_dblinks_as_strings: .: (0.000090) test_description: .: (0.000118) test_diseases_as_hash: .: (0.000097) test_diseases_as_strings: .: (0.000089) test_entry_id: .: (0.000122) test_enzymes_as_strings: .: (0.000108) test_genes_as_hash: .: (0.000095) test_genes_as_strings: .: (0.000139) test_keggclass: .: (0.000108) test_ko_pathway: .: (0.000101) test_modules_as_hash: .: (0.000108) test_modules_as_strings: .: (0.000129) test_name: .: (0.000132) test_new: .: (0.000136) test_organism: .: (0.000112) test_orthologs_as_hash: .: (0.000227) test_orthologs_as_strings: .: (0.000108) test_pathways_as_hash: .: (0.000106) test_pathways_as_strings: .: (0.000140) test_reactions_as_hash: .: (0.000106) test_reactions_as_strings: .: (0.000094) test_references: .: (0.000107) test_rel_pathways_as_hash: .: (0.000126) test_rel_pathways_as_strings: .: (0.000099) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000551) test_compounds_as_strings: .: (0.000217) test_dblinks_as_hash: .: (0.000124) test_dblinks_as_strings: .: (0.000102) test_description: .: (0.000124) test_diseases_as_hash: .: (0.000120) test_diseases_as_strings: .: (0.000114) test_entry_id: .: (0.000128) test_enzymes_as_strings: .: (0.000326) test_genes_as_hash: .: (0.000204) test_genes_as_strings: .: (0.000140) test_keggclass: .: (0.000131) test_ko_pathway: .: (0.000108) test_modules_as_hash: .: (0.000128) test_modules_as_strings: .: (0.000124) test_name: .: (0.000190) test_new: .: (0.000148) test_organism: .: (0.000206) test_orthologs_as_hash: .: (0.000118) test_orthologs_as_strings: .: (0.000104) test_pathways_as_hash: .: (0.000142) test_pathways_as_strings: .: (0.000120) test_reactions_as_hash: .: (0.000109) test_reactions_as_strings: .: (0.000108) test_references: .: (0.000109) test_rel_pathways_as_hash: .: (0.000129) test_rel_pathways_as_strings: .: (0.000190) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000274) test_compounds_as_strings: .: (0.000101) test_dblinks_as_hash: .: (0.000086) test_dblinks_as_strings: .: (0.000094) test_description: .: (0.000111) test_diseases_as_hash: .: (0.000089) test_diseases_as_strings: .: (0.000107) test_entry_id: .: (0.000134) test_enzymes_as_strings: .: (0.000103) test_genes_as_hash: .: (0.000093) test_genes_as_strings: .: (0.000198) test_keggclass: .: (0.000127) test_ko_pathway: .: (0.000100) test_modules_as_hash: .: (0.000088) test_modules_as_strings: .: (0.000120) test_name: .: (0.000112) test_new: .: (0.000117) test_organism: .: (0.000104) test_orthologs_as_hash: .: (0.000136) test_orthologs_as_strings: .: (0.000106) test_pathways_as_hash: .: (0.000098) test_pathways_as_strings: .: (0.000312) test_reactions_as_hash: .: (0.000156) test_reactions_as_strings: .: (0.000092) test_references: .: (0.000089) test_rel_pathways_as_hash: .: (0.000098) test_rel_pathways_as_strings: .: (0.000104) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000256) test_compounds_as_strings: .: (0.000123) test_dblinks_as_hash: .: (0.000139) test_dblinks_as_strings: .: (0.000115) test_description: .: (0.000451) test_diseases_as_hash: .: (0.000153) test_diseases_as_strings: .: (0.000111) test_entry_id: .: (0.000126) test_enzymes_as_strings: .: (0.000112) test_genes_as_hash: .: (0.000104) test_genes_as_strings: .: (0.000096) test_keggclass: .: (0.000186) test_ko_pathway: .: (0.000125) test_modules_as_hash: .: (0.000478) test_modules_as_strings: .: (0.000144) test_name: .: (0.000142) test_new: .: (0.000136) test_organism: .: (0.000138) test_orthologs_as_hash: .: (0.000120) test_orthologs_as_strings: .: (0.000123) test_pathways_as_hash: .: (0.000151) test_pathways_as_strings: .: (0.000259) test_reactions_as_hash: .: (0.000143) test_reactions_as_strings: .: (0.000106) test_references: .: (0.000539) test_rel_pathways_as_hash: .: (0.000202) test_rel_pathways_as_strings: .: (0.000228) Bio::TestBioKeggDRUG: test_activity: .: (0.000431) test_comment: .: (0.000171) test_dblinks_as_hash: .: (0.000197) test_dblinks_as_strings: .: (0.000148) test_entry_id: .: (0.000137) test_formula: .: (0.000147) test_kcf: .: (0.000120) test_mass: .: (0.000207) test_name: .: (0.000165) test_names: .: (0.000151) test_pathways_as_hash: .: (0.000151) test_pathways_as_strings: .: (0.000133) test_products: .: (0.000144) test_remark: .: (0.000142) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000281) test_composition: .: (0.000309) test_compounds: .: (0.000157) test_dblinks_as_hash: .: (0.000250) test_dblinks_as_strings: .: (0.000161) test_entry_id: .: (0.000300) test_enzymes: .: (0.000167) test_kcf: .: (0.000115) test_keggclass: .: (0.000225) test_mass: .: (0.000138) test_name: .: (0.000113) test_orthologs_as_hash: .: (0.000175) test_orthologs_as_strings: .: (0.000133) test_pathways_as_hash: .: (0.000126) test_pathways_as_strings: .: (0.004132) test_reactions: .: (0.000339) test_references: .: (0.000207) test_remark: .: (0.000157) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000276) test_composition: .: (0.000175) test_compounds: .: (0.000131) test_dblinks_as_hash: .: (0.000180) test_dblinks_as_strings: .: (0.000451) test_entry_id: .: (0.000215) test_enzymes: .: (0.000126) test_kcf: .: (0.000108) test_keggclass: .: (0.000116) test_mass: .: (0.000121) test_name: .: (0.000118) test_orthologs_as_hash: .: (0.000116) test_orthologs_as_strings: .: (0.000103) test_pathways_as_hash: .: (0.000104) test_pathways_as_strings: .: (0.000414) test_reactions: .: (0.000162) test_references: .: (0.000097) test_remark: .: (0.000102) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000429) test_compounds_as_strings: .: (0.000253) test_dblinks_as_hash: .: (0.000182) test_dblinks_as_strings: .: (0.000448) test_description: .: (0.000403) test_diseases_as_hash: .: (0.000204) test_diseases_as_strings: .: (0.000154) test_entry_id: .: (0.000168) test_enzymes_as_strings: .: (0.000127) test_genes_as_hash: .: (0.000127) test_genes_as_strings: .: (0.000117) test_keggclass: .: (0.000139) test_ko_pathway: .: (0.000529) test_modules_as_hash: .: (0.000216) test_modules_as_strings: .: (0.000156) test_name: .: (0.000152) test_new: .: (0.000159) test_organism: .: (0.000146) test_orthologs_as_hash: .: (0.000166) test_orthologs_as_strings: .: (0.000149) test_pathways_as_hash: .: (0.000406) test_pathways_as_strings: .: (0.000181) test_reactions_as_hash: .: (0.000582) test_reactions_as_strings: .: (0.000272) test_references: .: (0.000562) test_rel_pathways_as_hash: .: (0.000270) test_rel_pathways_as_strings: .: (0.000183) Bio::TestBioLITDB: test_author: .: (0.000273) test_entry_id: .: (0.000114) test_field: .: (0.000103) test_journal: .: (0.000102) test_keyword: .: (0.000438) test_reference: .: (0.000247) test_title: .: (0.000133) test_volume: .: (0.000102) Bio::TestBioNBRF: test_aalen: .: (0.000367) test_aaseq: .: (0.000122) test_entry: .: (0.000090) test_length: .: (0.000085) test_nalen: .: (0.000144) test_naseq: .: (0.000311) test_seq: .: (0.000148) test_seq_class: .: (0.000076) test_to_nbrf: .: (0.000092) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000241) test_to_newick_format_leaf: .: (0.000170) test_to_newick_format_leaf_NHX: .: (0.000118) Bio::TestBl2seqReport: test_db_len: .: (0.000513) test_db_num: .: (0.000570) test_new: .: (0.000250) test_undefed_methods: .: (0.000841) test_undefed_methods_for_iteration: .: (0.000708) Bio::TestBl2seqReportConstants: test_rs: .: (0.000178) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000275) test_hits: .: (0.000393) Bio::TestBlast: test_blast_reports_format0: .: (0.004879) test_blast_reports_format0_with_block: .: (0.000661) test_blast_reports_format7: .: (0.009895) test_blast_reports_format7_with_block: .: (0.009960) test_blast_reports_format7_with_parser: .: (0.060421) test_blast_reports_format7_with_parser_with_block: .: (0.010872) test_blast_reports_format8: .: (0.001349) test_blast_reports_format8_with_block: .: (0.000487) test_blast_reports_format8_with_parser: .: (0.000217) test_blast_reports_format8_with_parser_with_block: .: (0.000164) test_blast_reports_xml: .: (0.009781) test_blast_reports_xml_with_block: .: (0.009522) test_blastll: .: (0.000167) test_db: .: (0.000079) test_exec_genomenet: .: (0.000085) test_exec_local: .: (0.000068) test_exec_ncbi: .: (0.000061) test_filter: .: (0.000264) test_format: .: (0.000086) test_make_command_line: .: (0.000455) test_make_command_line_2: .: (0.000215) test_matrix: .: (0.000076) test_new: .: (0.000175) test_new_opt_string: .: (0.000352) test_option: .: (0.000101) test_option_set: .: (0.000146) test_option_set_m0: .: (0.000117) test_options: .: (0.000073) test_output: .: (0.000137) test_parse_result: .: (0.009185) test_parser: .: (0.000177) test_program: .: (0.000092) test_query: .: (0.000067) test_self_local: .: (0.000226) test_self_remote: .: (0.002010) test_server: .: (0.000245) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000315) test_delete: .: (0.000211) test_equal_equal: .: (0.001699) test_get: .: (0.000261) test_make_command_line_options: .: (0.000218) test_normalize!: .: (0.000145) test_parse: .: (0.000551) test_set: .: (0.000335) Bio::TestBlastReport: test_db: .: (0.010033) test_db_len: .: (0.009721) test_db_num: .: (0.008988) test_each_hit: .: (0.009328) test_each_iteration: .: (0.011244) test_eff_space: .: (0.009746) test_entrez_query: .: (0.009259) test_entropy: .: (0.009021) test_expect: .: (0.008749) test_filter: .: (0.010208) test_gap_extend: .: (0.010090) test_gap_open: .: (0.009520) test_hits: .: (0.009078) test_hsp_len: .: (0.009346) test_inclusion: .: (0.011159) test_iterations: .: (0.009805) test_kappa: .: (0.009542) test_lambda: .: (0.010141) test_matrix: .: (0.010608) test_message: .: (0.010576) test_parameters: .: (0.009436) test_pattern: .: (0.009305) test_program: .: (0.009011) test_query_def: .: (0.010207) test_query_id: .: (0.010718) test_query_len: .: (0.009241) test_reference: .: (0.009033) test_sc_match: .: (0.010038) test_sc_mismatch: .: (0.009056) test_statistics: .: (0.010917) test_version: .: (0.009290) Bio::TestBlastReportDefault: test_db: .: (0.000651) test_db_len: .: (0.000349) test_db_num: .: (0.000318) test_each_hit: .: (0.000583) test_each_iteration: .: (0.000426) test_eff_space: .: (0.000539) test_entropy: .: (0.000530) test_expect: .: (0.000520) test_gap_extend: .: (0.000524) test_gap_open: .: (0.000621) test_gapped_entropy: .: (0.000498) test_gapped_kappa: .: (0.000447) test_gapped_lambda: .: (0.000459) test_hits: .: (0.000410) test_iterations: .: (0.000416) test_kappa: .: (0.000416) test_lambda: .: (0.000414) test_matrix: .: (0.000547) test_message: .: (0.000387) test_pattern: .: (0.000405) test_program: .: (0.000439) test_query_def: .: (0.000466) test_query_len: .: (0.000400) test_reference: .: (0.000421) test_sc_match: .: (0.000477) test_sc_mismatch: .: (0.000581) test_version: .: (0.000419) Bio::TestBlastReportHit: test_Hit_accession: .: (0.008952) test_Hit_bit_score: .: (0.009161) test_Hit_definition: .: (0.011114) test_Hit_evalue: .: (0.009518) test_Hit_hit_id: .: (0.009670) test_Hit_hsps: .: (0.011339) test_Hit_identity: .: (0.017446) test_Hit_lap_at: .: (0.010707) test_Hit_len: .: (0.009529) test_Hit_midline: .: (0.009285) test_Hit_num: .: (0.009104) test_Hit_overlap: .: (0.009146) test_Hit_query_def: .: (0.010695) test_Hit_query_end: .: (0.009207) test_Hit_query_id: .: (0.009076) test_Hit_query_len: .: (0.009416) test_Hit_query_seq: .: (0.010693) test_Hit_query_start: .: (0.009697) test_Hit_taeget_def: .: (0.009408) test_Hit_target_end: .: (0.009083) test_Hit_target_id: .: (0.009124) test_Hit_target_len: .: (0.010643) test_Hit_target_seq: .: (0.009528) test_Hit_target_start: .: (0.009050) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000749) test_Hit_definition: .: (0.000370) test_Hit_evalue: .: (0.000495) test_Hit_hsps: .: (0.000319) test_Hit_identity: .: (0.000301) test_Hit_lap_at: .: (0.000408) test_Hit_len: .: (0.000279) test_Hit_midline: .: (0.000468) test_Hit_overlap: .: (0.000282) test_Hit_query_end: .: (0.000345) test_Hit_query_seq: .: (0.000399) test_Hit_query_start: .: (0.000377) test_Hit_taeget_def: .: (0.000273) test_Hit_target_end: .: (0.000550) test_Hit_target_id: .: (0.000401) test_Hit_target_len: .: (0.000357) test_Hit_target_seq: .: (0.000448) test_Hit_target_start: .: (0.000438) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.027030) test_Hit_bit_score: .: (0.024787) test_Hit_definition: .: (0.026202) test_Hit_evalue: .: (0.026696) test_Hit_hit_id: .: (0.025427) test_Hit_hsps: .: (0.025007) test_Hit_identity: .: (0.026678) test_Hit_lap_at: .: (0.025910) test_Hit_len: .: (0.024871) test_Hit_midline: .: (0.027202) test_Hit_num: .: (0.026423) test_Hit_overlap: .: (0.024761) test_Hit_query_def: .: (0.026948) test_Hit_query_end: .: (0.026701) test_Hit_query_id: .: (0.024787) test_Hit_query_len: .: (0.026772) test_Hit_query_seq: .: (0.026701) test_Hit_query_start: .: (0.024258) test_Hit_taeget_def: .: (0.026744) test_Hit_target_end: .: (0.027284) test_Hit_target_id: .: (0.024709) test_Hit_target_len: .: (0.026639) test_Hit_target_seq: .: (0.026991) test_Hit_target_start: .: (0.024579) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.026644) test_Hit_bit_score: .: (0.027617) test_Hit_definition: .: (0.025959) test_Hit_evalue: .: (0.025311) test_Hit_hit_id: .: (0.027391) test_Hit_hsps: .: (0.026357) test_Hit_identity: .: (0.024992) test_Hit_lap_at: .: (0.027053) test_Hit_len: .: (0.026846) test_Hit_midline: .: (0.024299) test_Hit_num: .: (0.026381) test_Hit_overlap: .: (0.027155) test_Hit_query_def: .: (0.024994) test_Hit_query_end: .: (0.026820) test_Hit_query_id: .: (0.027767) test_Hit_query_len: .: (0.025050) test_Hit_query_seq: .: (0.026603) test_Hit_query_start: .: (0.027194) test_Hit_taeget_def: .: (0.026869) test_Hit_target_end: .: (0.026487) test_Hit_target_id: .: (0.027502) test_Hit_target_len: .: (0.026818) test_Hit_target_seq: .: (0.024706) test_Hit_target_start: .: (0.026942) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.009253) test_Hit_bit_score: .: (0.009305) test_Hit_definition: .: (0.010717) test_Hit_evalue: .: (0.008689) test_Hit_hit_id: .: (0.017247) test_Hit_hsps: .: (0.021842) test_Hit_identity: .: (0.027467) test_Hit_lap_at: .: (0.017640) test_Hit_len: .: (0.017394) test_Hit_midline: .: (0.014440) test_Hit_num: .: (0.009253) test_Hit_overlap: .: (0.010438) test_Hit_query_def: .: (0.009690) test_Hit_query_end: .: (0.008789) test_Hit_query_id: .: (0.009103) test_Hit_query_len: .: (0.010351) test_Hit_query_seq: .: (0.009550) test_Hit_query_start: .: (0.009515) test_Hit_taeget_def: .: (0.008959) test_Hit_target_end: .: (0.009165) test_Hit_target_id: .: (0.010627) test_Hit_target_len: .: (0.009655) test_Hit_target_seq: .: (0.009323) test_Hit_target_start: .: (0.009123) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000404) test_Hit_bit_score: .: (0.000098) test_Hit_definition: .: (0.000081) test_Hit_evalue: .: (0.000078) test_Hit_hit_id: .: (0.000081) test_Hit_hsps: .: (0.000073) test_Hit_identity: .: (0.000074) test_Hit_lap_at: .: (0.000089) test_Hit_len: .: (0.000078) test_Hit_midline: .: (0.000246) test_Hit_num: .: (0.000159) test_Hit_overlap: .: (0.000085) test_Hit_query_def: .: (0.000083) test_Hit_query_end: .: (0.000073) test_Hit_query_id: .: (0.000073) test_Hit_query_len: .: (0.000071) test_Hit_query_seq: .: (0.000068) test_Hit_query_start: .: (0.000069) test_Hit_taeget_def: .: (0.000069) test_Hit_target_end: .: (0.000290) test_Hit_target_id: .: (0.000113) test_Hit_target_len: .: (0.000080) test_Hit_target_seq: .: (0.000253) test_Hit_target_start: .: (0.000129) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.010816) test_Hsp_bit_score: .: (0.009563) test_Hsp_density: .: (0.009294) test_Hsp_evalue: .: (0.008974) test_Hsp_gaps: .: (0.009353) test_Hsp_hit_frame: .: (0.010772) test_Hsp_hit_from: .: (0.009403) test_Hsp_hit_to: .: (0.009108) test_Hsp_hseq: .: (0.009416) test_Hsp_identity: .: (0.010838) test_Hsp_midline: .: (0.010866) test_Hsp_mismatch_count: .: (0.009682) test_Hsp_num: .: (0.009154) test_Hsp_pattern_from: .: (0.009245) test_Hsp_pattern_to: .: (0.010555) test_Hsp_percent_identity: .: (0.009238) test_Hsp_positive: .: (0.009269) test_Hsp_qseq: .: (0.009131) test_Hsp_query_frame: .: (0.010741) test_Hsp_query_from: .: (0.009552) test_Hsp_query_to: .: (0.009473) test_Hsp_score: .: (0.009354) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000734) test_Hsp_bit_score: .: (0.000340) test_Hsp_evalue: .: (0.000331) test_Hsp_gaps: .: (0.000297) test_Hsp_hit_frame: .: (0.000292) test_Hsp_hit_from: .: (0.000525) test_Hsp_hit_to: .: (0.000459) test_Hsp_hseq: .: (0.000414) test_Hsp_identity: .: (0.000597) test_Hsp_midline: .: (0.000431) test_Hsp_percent_identity: .: (0.000292) test_Hsp_positive: .: (0.000309) test_Hsp_qseq: .: (0.000371) test_Hsp_query_frame: .: (0.000263) test_Hsp_query_from: .: (0.000336) test_Hsp_query_to: .: (0.000360) test_Hsp_score: .: (0.000375) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.027238) test_Hsp_bit_score: .: (0.074438) test_Hsp_density: .: (0.026281) test_Hsp_evalue: .: (0.029203) test_Hsp_gaps: .: (0.027539) test_Hsp_hit_frame: .: (0.025674) test_Hsp_hit_from: .: (0.027751) test_Hsp_hit_to: .: (0.024950) test_Hsp_hseq: .: (0.026377) test_Hsp_identity: .: (0.027444) test_Hsp_midline: .: (0.024605) test_Hsp_mismatch_count: .: (0.026477) test_Hsp_num: .: (0.026791) test_Hsp_pattern_from: .: (0.024471) test_Hsp_pattern_to: .: (0.026578) test_Hsp_percent_identity: .: (0.025557) test_Hsp_positive: .: (0.025360) test_Hsp_qseq: .: (0.060847) test_Hsp_query_frame: .: (0.043971) test_Hsp_query_from: .: (0.035649) test_Hsp_query_to: .: (0.040634) test_Hsp_score: .: (0.035325) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.029652) test_Hsp_bit_score: .: (0.028740) test_Hsp_density: .: (0.025501) test_Hsp_evalue: .: (0.027285) test_Hsp_gaps: .: (0.025171) test_Hsp_hit_frame: .: (0.026580) test_Hsp_hit_from: .: (0.030178) test_Hsp_hit_to: .: (0.027814) test_Hsp_hseq: .: (0.027928) test_Hsp_identity: .: (0.031040) test_Hsp_midline: .: (0.038694) test_Hsp_mismatch_count: .: (0.082830) test_Hsp_num: .: (0.075867) test_Hsp_pattern_from: .: (0.094513) test_Hsp_pattern_to: .: (0.109276) test_Hsp_percent_identity: .: (0.063867) test_Hsp_positive: .: (0.059564) test_Hsp_qseq: .: (0.069111) test_Hsp_query_frame: .: (0.057874) test_Hsp_query_from: .: (0.064367) test_Hsp_query_to: .: (0.064241) test_Hsp_score: .: (0.058905) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.022194) test_Hsp_bit_score: .: (0.039050) test_Hsp_density: .: (0.021948) test_Hsp_evalue: .: (0.026107) test_Hsp_gaps: .: (0.039624) test_Hsp_hit_frame: .: (0.017257) test_Hsp_hit_from: .: (0.018559) test_Hsp_hit_to: .: (0.021558) test_Hsp_hseq: .: (0.026325) test_Hsp_identity: .: (0.016828) test_Hsp_midline: .: (0.021210) test_Hsp_mismatch_count: .: (0.022509) test_Hsp_num: .: (0.017652) test_Hsp_pattern_from: .: (0.017076) test_Hsp_pattern_to: .: (0.012999) test_Hsp_percent_identity: .: (0.009864) test_Hsp_positive: .: (0.010126) test_Hsp_qseq: .: (0.010517) test_Hsp_query_frame: .: (0.009909) test_Hsp_query_from: .: (0.009026) test_Hsp_query_to: .: (0.009203) test_Hsp_score: .: (0.012364) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000361) test_Hsp_bit_score: .: (0.000095) test_Hsp_density: .: (0.000084) test_Hsp_evalue: .: (0.000147) test_Hsp_gaps: .: (0.000106) test_Hsp_hit_frame: .: (0.000081) test_Hsp_hit_from: .: (0.000074) test_Hsp_hit_to: .: (0.000077) test_Hsp_hseq: .: (0.000075) test_Hsp_identity: .: (0.000077) test_Hsp_midline: .: (0.000073) test_Hsp_mismatch_count: .: (0.000216) test_Hsp_num: .: (0.000090) test_Hsp_pattern_from: .: (0.000087) test_Hsp_pattern_to: .: (0.000081) test_Hsp_percent_identity: .: (0.000074) test_Hsp_positive: .: (0.000114) test_Hsp_qseq: .: (0.000090) test_Hsp_query_frame: .: (0.000080) test_Hsp_query_from: .: (0.000074) test_Hsp_query_to: .: (0.000070) test_Hsp_score: .: (0.000073) Bio::TestBlastReportIteration: test_hits: .: (0.009966) test_message: .: (0.009217) test_num: .: (0.009186) test_statistics: .: (0.009377) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000724) test_message: .: (0.001745) test_num: .: (0.000414) Bio::TestBlastReportIterationMulti: test_each: .: (0.026153) test_hits: .: (0.027133) test_message: .: (0.024729) test_num: .: (0.026734) test_query_def: .: (0.027618) test_query_id: .: (0.025150) test_query_len: .: (0.026650) test_statistics: .: (0.027053) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.025451) test_hits: .: (0.026407) test_message: .: (0.026380) test_num: .: (0.024968) test_query_def: .: (0.027204) test_query_id: .: (0.026087) test_query_len: .: (0.025590) test_statistics: .: (0.027941) Bio::TestBlastReportIterationREXML: test_hits: .: (0.010106) test_message: .: (0.009363) test_num: .: (0.009467) test_statistics: .: (0.011095) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000671) test_message: .: (0.000142) test_num: .: (0.000091) test_statistics: .: (0.000085) Bio::TestBlastReportMulti: test_db: .: (0.025652) test_db_len: .: (0.027695) test_db_num: .: (0.027355) test_each_hit: .: (0.024928) test_each_iteration: .: (0.027449) test_eff_space: .: (0.027585) test_entropy: .: (0.025418) test_expect: .: (0.029135) test_filter: .: (0.028894) test_gap_extend: .: (0.027431) test_gap_open: .: (0.030134) test_hits: .: (0.028553) test_hsp_len: .: (0.025684) test_iterations: .: (0.028039) test_kappa: .: (0.026881) test_lambda: .: (0.026012) test_matrix: .: (0.028280) test_message: .: (0.026865) test_parameters: .: (0.026437) test_pattern: .: (0.028592) test_program: .: (0.028205) test_query_def: .: (0.026528) test_query_id: .: (0.027591) test_query_len: .: (0.026932) test_reference: .: (0.025352) test_reports: .: (0.027394) test_statistics: .: (0.028373) test_version: .: (0.025769) Bio::TestBlastReportMultiREXML: test_db: .: (0.028001) test_db_len: .: (0.027592) test_db_num: .: (0.024948) test_each_hit: .: (0.027052) test_each_iteration: .: (0.027845) test_eff_space: .: (0.024595) test_entropy: .: (0.026821) test_expect: .: (0.027767) test_filter: .: (0.026320) test_gap_extend: .: (0.026185) test_gap_open: .: (0.028334) test_hits: .: (0.027141) test_hsp_len: .: (0.025460) test_iterations: .: (0.027555) test_kappa: .: (0.028106) test_lambda: .: (0.025540) test_matrix: .: (0.027497) test_message: .: (0.027458) test_parameters: .: (0.025998) test_pattern: .: (0.026173) test_program: .: (0.027719) test_query_def: .: (0.039135) test_query_id: .: (0.049931) test_query_len: .: (0.052983) test_reference: .: (0.054810) test_reports: .: (0.049373) test_statistics: .: (0.056449) test_version: .: (0.057952) Bio::TestBlastReportREXML: test_db: .: (0.008946) test_db_len: .: (0.021316) test_db_num: .: (0.027076) test_each_hit: .: (0.026231) test_each_iteration: .: (0.021273) test_eff_space: .: (0.021591) test_entrez_query: .: (0.030140) test_entropy: .: (0.027317) test_expect: .: (0.017464) test_filter: .: (0.021099) test_gap_extend: .: (0.017358) test_gap_open: .: (0.023061) test_hits: .: (0.017940) test_hsp_len: .: (0.017449) test_inclusion: .: (0.020642) test_iterations: .: (0.018622) test_kappa: .: (0.021913) test_lambda: .: (0.009644) test_matrix: .: (0.009047) test_message: .: (0.009607) test_parameters: .: (0.011157) test_pattern: .: (0.010058) test_program: .: (0.009237) test_query_def: .: (0.009322) test_query_id: .: (0.011155) test_query_len: .: (0.009486) test_reference: .: (0.009224) test_sc_match: .: (0.009583) test_sc_mismatch: .: (0.009536) test_statistics: .: (0.011670) test_version: .: (0.009717) Bio::TestBlastReportTabular: test_db: .: (0.000403) test_db_len: .: (0.000096) test_db_num: .: (0.000079) test_each_hit: .: (0.000085) test_each_iteration: .: (0.000076) test_eff_space: .: (0.000171) test_entrez_query: .: (0.000116) test_entropy: .: (0.000159) test_expect: .: (0.000079) test_filter: .: (0.000076) test_gap_extend: .: (0.000072) test_gap_open: .: (0.000071) test_hits: .: (0.000080) test_hsp_len: .: (0.000074) test_inclusion: .: (0.000074) test_iterations: .: (0.000071) test_kappa: .: (0.000068) test_lambda: .: (0.000067) test_matrix: .: (0.000196) test_message: .: (0.000118) test_parameters: .: (0.000094) test_pattern: .: (0.000081) test_program: .: (0.000069) test_query_def: .: (0.000080) test_query_id: .: (0.000069) test_query_len: .: (0.000066) test_reference: .: (0.000070) test_sc_match: .: (0.000078) test_sc_mismatch: .: (0.000071) test_statistics: .: (0.000071) test_version: .: (0.000081) Bio::TestChain: test_aaseq: .: (0.000849) test_addLigand: .: (0.000079) test_addResidue: .: (0.000051) test_atom_seq: .: (0.000061) test_comp: .: (0.000086) test_each: .: (0.000060) test_each_heterogen: .: (0.000055) test_each_residue: .: (0.000052) test_get_heterogen_by_id: .: (0.000055) test_get_residue_by_id: .: (0.000049) test_inspect: .: (0.000080) test_rehash: .: (0.000057) test_rehash_heterogens: .: (0.000046) test_rehash_residues: .: (0.000234) test_square_brace: .: (0.000059) test_to_s: .: (0.000070) Bio::TestChainFinder: test_chains: .: (0.000209) test_each_chain: .: (0.000066) test_find_chain: .: (0.000056) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005884) test_header: .: (0.000510) test_match_line: .: (0.000462) test_sequence0: .: (0.000621) test_sequence1: .: (0.000399) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.006075) test_header: .: (0.000679) test_match_line: .: (0.000549) test_sequence0: .: (0.000749) test_sequence1: .: (0.000544) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.009895) test_header: .: (0.000665) test_match_line: .: (0.000487) test_sequence0: .: (0.000668) test_sequence1: .: (0.001993) Bio::TestCodonTable: test_Tables: .: (0.000220) test_accessor: .: (0.000077) test_definition: .: (0.000046) test_each: .: (0.000068) test_revtrans: .: (0.000115) test_self_accessor: .: (0.000234) test_self_copy: .: (0.000624) test_set_accessor: .: (0.107029) test_start: .: (0.000097) test_start_codon?: .: (0.000061) test_stop: .: (0.000045) test_stop_codon?: .: (0.000049) test_table: .: (0.000044) Bio::TestCodonTableConstants: test_Definitions: .: (0.000172) test_Starts: .: (0.000054) test_Tables: .: (0.000041) test_stops: .: (0.000045) Bio::TestColorScheme: test_buried: .: (0.001243) Bio::TestCommand: test_command_constants: .: (0.000173) test_escape_shell: .: (0.000090) test_escape_shell_unix: .: (0.000060) test_escape_shell_windows: .: (0.000065) test_make_cgi_params_by_array_of_array: .: (0.000217) test_make_cgi_params_by_array_of_hash: .: (0.000170) test_make_cgi_params_by_array_of_string: .: (0.000186) test_make_cgi_params_by_hash_in_string: .: (0.000259) test_make_cgi_params_by_hash_in_symbol: .: (0.000243) test_make_cgi_params_by_string: .: (0.000114) test_make_command_line: .: (0.000073) test_make_command_line_unix: .: (0.000057) test_make_command_line_windows: .: (0.000064) test_safe_command_line_array: .: (0.000099) test_safe_command_line_array_passthrough: .: (0.000175) Bio::TestContingencyTable: test_lite_example: .: (0.110062) Bio::TestDB: test_entry_id: .: (0.000250) test_exists: .: (0.000056) test_fetch: .: (0.000102) test_get: .: (0.000048) test_open: .: (0.000043) test_tags: .: (0.000048) Bio::TestDataType: test_const_like_method: .: (0.000440) test_pdb_achar: .: (0.000183) test_pdb_atom: .: (0.000130) test_pdb_character: .: (0.000112) test_pdb_date: .: (0.000104) test_pdb_idcode: .: (0.000104) test_pdb_integer: .: (0.000048) test_pdb_list: .: (0.000059) test_pdb_lstring: .: (0.000107) test_pdb_real: .: (0.000083) test_pdb_resudue_name: .: (0.001038) test_pdb_slist: .: (0.000078) test_pdb_string: .: (0.000247) test_pdb_stringrj: .: (0.000061) test_pdb_symop: .: (0.000139) test_specification_list: .: (0.000084) Bio::TestEMBL: test_ac: .: (0.000497) test_accession: .: (0.000250) test_cc: .: (0.000200) test_de: .: (0.000398) test_division: .: (0.000281) test_dr: .: (0.000211) test_dt: .: (0.000554) test_dt_created: .: (0.000257) test_dt_iterator: .: (0.000283) test_dt_updated: .: (0.000197) test_each_cds: .: (0.000368) test_each_gene: .: (0.000401) test_entry: .: (0.000290) test_fh: .: (0.000233) test_ft: .: (0.000344) test_ft_accessor: .: (0.000400) test_ft_iterator: .: (0.000317) test_id_line: .: (0.000535) test_id_line_data_class: .: (0.000284) test_id_line_division: .: (0.000336) test_id_line_entry_name: .: (0.000212) test_id_line_iterator: .: (0.000207) test_id_line_molecule_type: .: (0.000193) test_id_line_sequence_length: .: (0.000191) test_kw: .: (0.000251) test_molecule: .: (0.000216) test_oc: .: (0.000232) test_og: .: (0.000222) test_os: .: (0.000359) test_ref: .: (0.000297) test_references: .: (0.000706) test_seq: .: (0.000548) test_sequence_length: .: (0.000234) test_sq: .: (0.000216) test_sq_get: .: (0.000196) test_sv: .: (0.000297) test_version: .: (0.000202) Bio::TestEMBL89: test_ac: .: (0.000353) test_accession: .: (0.000236) test_cc: .: (0.000296) test_de: .: (0.000202) test_division: .: (0.000210) test_dr: .: (0.000446) test_dt: .: (0.000270) test_dt_created: .: (0.000293) test_dt_iterator: .: (0.000181) test_dt_updated: .: (0.000170) test_each_cds: .: (0.000308) test_each_gene: .: (0.000384) test_entry: .: (0.000249) test_fh: .: (0.000192) test_ft: .: (0.000290) test_ft_accessor: .: (0.000417) test_ft_iterator: .: (0.000302) test_id_line: .: (0.000227) test_id_line_data_class: .: (0.000567) test_id_line_division: .: (0.000367) test_id_line_entry_name: .: (0.000208) test_id_line_iterator: .: (0.000201) test_id_line_molecule_type: .: (0.000255) test_id_line_sequence_length: .: (0.000240) test_id_line_sequence_version: .: (0.003004) test_kw: .: (0.000289) test_molecule: .: (0.000331) test_oc: .: (0.000310) test_og: .: (0.000326) test_os: .: (0.000234) test_ref: .: (0.000276) test_references: .: (0.000580) test_seq: .: (0.000416) test_sequence_length: .: (0.000585) test_sq: .: (0.000288) test_sq_get: .: (0.000321) test_sv: .: (0.000295) test_version: .: (0.000299) Bio::TestEMBLAPI: test_ac: .: (0.000249) test_accessions: .: (0.000086) Bio::TestEMBLCommon: test_ac: .: (0.000219) test_accession: .: (0.000046) test_accessions: .: (0.000041) test_de: .: (0.000044) test_definition: .: (0.000042) test_description: .: (0.000041) test_dr: .: (0.000042) test_keywords: .: (0.000046) test_kw: .: (0.000040) test_oc: .: (0.000040) test_og: .: (0.000046) test_os: .: (0.000045) test_ref: .: (0.000041) test_references: .: (0.000042) Bio::TestEMBLDB: test_fetch: .: (0.000281) test_p_entry2hash: .: (0.000045) Bio::TestEMBLToBioSequence: test_classification: .: (0.002772) test_date_created: .: (0.000492) test_date_modified: .: (0.000345) test_definition: .: (0.000279) test_division: .: (0.000733) test_entry_id: .: (0.000305) test_entry_version: .: (0.000261) test_features: .: (0.000501) test_keywords: .: (0.000268) test_molecule_type: .: (0.000248) test_primary_accession: .: (0.000225) test_references: .: (0.000505) test_release_created: .: (0.000247) test_release_modified: .: (0.000213) test_secondary_accessions: .: (0.000572) test_sequence_version: .: (0.000348) test_species: .: (0.000244) test_topology: .: (0.000246) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002461) test_date_created: .: (0.002551) test_date_modified: .: (0.002699) test_definition: .: (0.002415) test_division: .: (0.003010) test_entry_id: .: (0.002946) test_entry_version: .: (0.002673) test_features: .: (0.002746) test_keywords: .: (0.002921) test_molecule_type: .: (0.002683) test_primary_accession: .: (0.002520) test_references: .: (0.002874) test_release_created: .: (0.002707) test_release_modified: .: (0.006332) test_secondary_accessions: .: (0.002932) test_sequence_version: .: (0.003021) test_species: .: (0.002785) test_topology: .: (0.002475) Bio::TestFasta: test_db: .: (0.000182) test_format: .: (0.000047) test_format_arg_integer: .: (0.000062) test_format_arg_str: .: (0.000046) test_ktup: .: (0.000051) test_matrix: .: (0.000042) test_option: .: (0.000091) test_options: .: (0.000059) test_output: .: (0.000040) test_program: .: (0.000047) test_server: .: (0.000488) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000190) test_accession: .: (0.000062) test_accessions: .: (0.000065) test_description: .: (0.000054) test_descriptions: .: (0.000059) test_entry_id: .: (0.000052) test_get_all_by_type: .: (0.000051) test_gi: .: (0.000055) test_id_strings: .: (0.000120) test_list_ids: .: (0.000061) test_locus: .: (0.000058) test_words: .: (0.000225) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000177) test_accession: .: (0.000065) test_accessions: .: (0.000066) test_description: .: (0.000060) test_descriptions: .: (0.000057) test_emb: .: (0.000066) test_entry_id: .: (0.000051) test_get_all_by_type: .: (0.000056) test_get_emb: .: (0.000063) test_gi: .: (0.000058) test_id_strings: .: (0.000117) test_list_ids: .: (0.000214) test_locus: .: (0.000068) test_words: .: (0.000084) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000153) test_accession: .: (0.000113) test_accessions: .: (0.000067) test_description: .: (0.000335) test_descriptions: .: (0.000075) test_entry_id: .: (0.000055) test_get_all_by_type: .: (0.000057) test_gi: .: (0.000055) test_id_strings: .: (0.000100) test_list_ids: .: (0.000057) test_locus: .: (0.000168) test_sp: .: (0.000065) test_words: .: (0.000077) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000180) test_accession: .: (0.000097) test_accessions: .: (0.000090) test_description: .: (0.000071) test_descriptions: .: (0.000070) test_entry_id: .: (0.000098) test_get_all_by_type: .: (0.000077) test_gi: .: (0.000211) test_id_strings: .: (0.000162) test_list_ids: .: (0.000075) test_locus: .: (0.000073) test_words: .: (0.000139) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000186) test_accession: .: (0.000072) test_accessions: .: (0.000063) test_description: .: (0.000064) test_descriptions: .: (0.000222) test_entry_id: .: (0.000064) test_get_all_by_type: .: (0.000060) test_gi: .: (0.000058) test_id_strings: .: (0.000209) test_list_ids: .: (0.000082) test_locus: .: (0.000077) test_words: .: (0.000120) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000147) test_accession: .: (0.000056) test_accessions: .: (0.000044) test_description: .: (0.000287) test_descriptions: .: (0.000068) test_entry_id: .: (0.000043) test_get_all_by_type: .: (0.000044) test_gi: .: (0.000045) test_id_strings: .: (0.000067) test_list_ids: .: (0.000044) test_locus: .: (0.000043) test_words: .: (0.000055) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000155) test_accession: .: (0.000061) test_accessions: .: (0.000050) test_description: .: (0.000048) test_descriptions: .: (0.000047) test_entry_id: .: (0.000276) test_get: .: (0.000071) test_get_all_by_type: .: (0.000050) test_id_strings: .: (0.000093) test_list_ids: .: (0.000051) test_locus: .: (0.000049) test_sp: .: (0.000058) test_words: .: (0.000090) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000155) test_accession: .: (0.000057) test_accessions: .: (0.000355) test_description: .: (0.000081) test_descriptions: .: (0.000055) test_entry_id: .: (0.000310) test_get: .: (0.000065) test_get_all_by_type: .: (0.000052) test_id_strings: .: (0.000114) test_list_ids: .: (0.000049) test_locus: .: (0.000050) test_tr: .: (0.000058) test_words: .: (0.000111) Bio::TestFastaFirstName: test_first_name1: .: (0.000178) test_first_name_multi_identifier: .: (0.000050) test_first_name_single_worded_defintion: .: (0.000046) test_no_definition: .: (0.000043) test_space_before_first_name: .: (0.000296) test_tabbed_defintion: .: (0.000054) Bio::TestFastaFormat: test_aalen: .: (0.000231) test_aaseq: .: (0.000075) test_acc_version: .: (0.000117) test_accession: .: (0.000087) test_accessions: .: (0.000084) test_data: .: (0.000053) test_definition: .: (0.000051) test_entry: .: (0.000057) test_entry_id: .: (0.000071) test_entry_overrun: .: (0.000050) test_first_name: .: (0.000056) test_gi: .: (0.000081) test_identifiers: .: (0.000656) test_length: .: (0.000189) test_query: .: (0.000086) test_seq: .: (0.000062) Bio::TestFastaFormatConst: test_delimiter: .: (0.000163) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000184) test_data: .: (0.000084) test_definition: .: (0.000057) test_entry: .: (0.000059) test_entry_id: .: (0.000098) test_first_name: .: (0.000063) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000160) test_naseq: .: (0.000275) test_naseq_class: .: (0.000056) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000160) Bio::TestFastaInitialize: test_new_1: .: (0.000371) test_option: .: (0.000058) test_option_backward_compatibility: .: (0.000078) Bio::TestFastaNumericFormat: test_arg: .: (0.000193) test_data: .: (0.000086) test_definition: .: (0.000051) test_each: .: (0.000586) test_entry: .: (0.000075) test_entry_id: .: (0.000069) test_length: .: (0.000070) test_to_biosequence: .: (0.000849) Bio::TestFastaQuery: test_query: .: (0.000135) test_self_local: .: (0.000034) test_self_parser: .: (0.000030) test_self_remote: .: (0.000030) Bio::TestFastacmd: test_database: .: (0.000140) test_fastacmd: .: (0.000052) test_methods: .: (0.000064) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000792) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000359) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000623) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000584) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000474) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000366) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000294) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000508) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000392) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000291) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000580) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000363) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000348) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000902) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000778) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000741) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000322) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000269) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.002072) test_error_probabilities_as_sanger: .: (0.006777) test_error_probabilities_as_solexa: .: (0.002745) test_quality_scores_as_illumina: .: (0.000433) test_quality_scores_as_sanger: .: (0.000306) test_quality_scores_as_solexa: .: (0.000254) test_validate_format: .: (0.000611) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000731) test_entry_id: .: (0.001171) test_error_probabilities: .: (0.121290) test_nalen: .: (0.001506) test_naseq: .: (0.000993) test_quality_scores: .: (0.001272) test_quality_string: .: (0.000796) test_roundtrip: .: (0.073024) test_seq: .: (0.000846) test_sequence_string: .: (0.000528) test_to_biosequence: .: (0.047763) test_to_biosequence_and_output: .: (0.004127) test_to_s: .: (0.000859) test_validate_format: .: (0.000664) test_validate_format_with_array: .: (0.001090) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000538) test_mask_20_with_empty_string: .: (0.000299) test_mask_20_with_longer_string: .: (0.000265) test_mask_20_with_x: .: (0.000377) test_mask_60: .: (0.000324) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.002862) test_error_probabilities_as_sanger: .: (0.002692) test_error_probabilities_as_solexa: .: (0.002641) test_quality_scores_as_illumina: .: (0.000355) test_quality_scores_as_sanger: .: (0.000205) test_quality_scores_as_solexa: .: (0.000557) test_validate_format: .: (0.000474) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.001952) test_error_probabilities_as_sanger: .: (0.002143) test_error_probabilities_as_solexa: .: (0.001935) test_quality_scores_as_illumina: .: (0.000387) test_quality_scores_as_sanger: .: (0.000388) test_quality_scores_as_solexa: .: (0.000549) test_validate_format: .: (0.000420) Bio::TestFeature: test_append: .: (0.000197) test_append_nil: .: (0.000053) test_assoc: .: (0.000062) test_each: .: (0.000063) test_feature: .: (0.000043) test_locations: .: (0.000107) test_new: .: (0.000046) test_position: .: (0.000039) test_qualifiers: .: (0.000144) Bio::TestFeatures: test_append: .: (0.000198) test_arg: .: (0.000052) test_each: .: (0.000048) test_features: .: (0.000049) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000714) test_aaindex2: .: (0.000184) test_blast: .: (0.000134) test_blastxml: .: (0.000977) test_embl: .: (0.000273) test_embl_oldrelease: .: (0.000162) test_fastaformat: .: (0.000331) test_fastanumericformat: .: (0.000097) test_fastq: .: (0.000145) test_genbank: .: (0.000158) test_genpept: .: (0.000168) test_hmmer: .: (0.000151) test_maxml_cluster: .: (0.002902) test_maxml_sequence: .: (0.000296) test_medline: .: (0.000322) test_prosite: .: (0.003625) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.003262) test_transfac: .: (0.003958) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000477) test_auto_1arg_filename: .: (0.000644) test_auto_1arg_io: .: (0.000553) test_auto_1arg_io_with_block: .: (0.000885) test_auto_1arg_with_block: .: (0.001005) test_auto_2arg_filename_mode: .: (0.000578) test_auto_2arg_filename_mode_with_block: .: (0.000747) test_auto_3arg: .: (0.000557) test_auto_3arg_with_block: .: (0.001033) test_foreach: .: (0.000829) test_new_2arg_class: .: (0.000378) test_new_2arg_nil: .: (0.000522) test_open_0arg: .: (0.000288) test_open_1arg_class: .: (0.000269) test_open_1arg_filename: .: (0.000634) test_open_1arg_io: .: (0.000649) test_open_1arg_io_with_block: .: (0.000750) test_open_1arg_nil: .: (0.000273) test_open_1arg_with_block: .: (0.000845) test_open_2arg_autodetect: .: (0.000521) test_open_2arg_autodetect_io: .: (0.000547) test_open_2arg_autodetect_io_with_block: .: (0.000731) test_open_2arg_autodetect_with_block: .: (0.000687) test_open_2arg_class: .: (0.000414) test_open_2arg_class_io: .: (0.000368) test_open_2arg_class_io_with_block: .: (0.000783) test_open_2arg_class_with_block: .: (0.000580) test_open_2arg_filename_mode: .: (0.000524) test_open_2arg_filename_mode_with_block: .: (0.000836) test_open_3arg: .: (0.000964) test_open_3arg_with_block: .: (0.001518) test_open_4arg: .: (0.001414) test_to_a: .: (0.000726) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000868) test_close: .: (0.000424) test_dbclass: .: (0.000322) test_dbclass_eq: .: (0.000348) test_dbclass_nil: .: (0.000406) test_each: .: (0.000435) test_each_entry: .: (0.000583) test_ended_pos: .: (0.000405) test_entry_pos_flag: .: (0.000327) test_entry_raw: .: (0.000697) test_eof?: .: (0.000491) test_next_entry: .: (0.000509) test_path: .: (0.000329) test_pos: .: (0.000457) test_raw: .: (0.000517) test_rewind: .: (0.000454) test_start_pos: .: (0.000389) test_start_pos_ended_pos_not_recorded: .: (0.000436) test_to_io: .: (0.000640) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000488) test_simpleformat2: .: (0.000393) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000447) test_eof_false_after_prefetch: .: (0.000344) test_eof_false_first: .: (0.000233) test_eof_true: .: (0.000357) test_getc: .: (0.000256) test_getc_after_prefetch: .: (0.000251) test_gets: .: (0.000249) test_gets_equal_prefetch_gets: .: (0.000320) test_gets_paragraph_mode: .: (0.000713) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000603) test_gets_paragraph_mode_within_buffer: .: (0.000504) test_gets_rs: .: (0.000285) test_gets_rs_equal_prefetch_gets: .: (0.000327) test_gets_rs_within_buffer: .: (0.000462) test_pos: .: (0.000295) test_pos=: .: (0.000263) test_prefetch_buffer: .: (0.000248) test_prefetch_gets: .: (0.000299) test_prefetch_gets_with_arg: .: (0.000288) test_rewind: .: (0.000247) test_skip_spaces: .: (0.000269) test_to_io: .: (0.000293) test_ungetc: .: (0.000401) test_ungetc_after_prefetch: .: (0.000318) test_ungets: .: (0.000334) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000417) test_self_open_file: .: (0.000310) test_self_open_file_with_block: .: (0.000358) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000488) test_parse_file_open_arg_int_perm: .: (0.000240) test_parse_file_open_arg_int_perm_opt: .: (0.000239) test_parse_file_open_arg_integer: .: (0.000221) test_parse_file_open_arg_nil: .: (0.000236) test_parse_file_open_arg_opt: .: (0.000297) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000290) test_parse_file_open_arg_str: .: (0.000359) test_parse_file_open_arg_str_opt: .: (0.000275) test_parse_file_open_arg_str_perm: .: (0.000283) test_parse_file_open_arg_str_perm_opt: .: (0.000272) test_parse_file_open_arg_str_with_enc: .: (0.000273) test_parse_file_open_arg_str_with_ext_enc: .: (0.000276) test_parse_file_open_mode_integer: .: (0.000253) test_parse_file_open_mode_nil: .: (0.000255) test_parse_file_open_mode_str: .: (0.000232) test_parse_file_open_mode_str_with_enc: .: (0.000151) test_parse_file_open_mode_str_with_ext_enc: .: (0.000069) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000224) test_entry: .: (0.000086) test_entry_ended_pos: .: (0.000114) test_entry_pos_flag: .: (0.000097) test_entry_start_pos: .: (0.000066) test_get_entry: .: (0.000123) test_rewind: .: (0.000106) test_skip_leader: .: (0.000090) test_stream: .: (0.000053) test_stream_pos: .: (0.000070) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000205) test_delimiter_overrun: .: (0.000073) test_entry: .: (0.000104) test_entry_ended_pos: .: (0.000070) test_entry_ended_pos_default_nil: .: (0.000061) test_entry_start_pos: .: (0.000062) test_entry_start_pos_default_nil: .: (0.000082) test_get_entry: .: (0.000255) test_get_parsed_entry: .: (0.000127) test_header: .: (0.000046) test_skip_leader: .: (0.000350) test_skip_leader_without_header: .: (0.000138) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000294) test_entry_ended_pos: .: (0.000167) test_entry_start_pos: .: (0.000140) test_flag_to_fetch_header: .: (0.000275) test_get_entry: .: (0.000206) test_get_parsed_entry: .: (0.000184) test_rewind: .: (0.000135) test_skip_leader: .: (0.000088) Bio::TestGCGMsf: test_alignment: .: (0.000979) test_checksum: .: (0.000172) test_compcheck: .: (0.000146) test_date: .: (0.000123) test_description: .: (0.000436) test_entry_id: .: (0.000301) test_gap_length_weight: .: (0.000131) test_gap_weight: .: (0.000154) test_heading: .: (0.000144) test_length: .: (0.000142) test_seq_type: .: (0.000117) test_symbol_comparison_table: .: (0.000138) test_validate_checksum: .: (0.001312) Bio::TestGFF: test_record_class: .: (0.000437) test_records: .: (0.000216) Bio::TestGFF2: test_const_version: .: (0.000994) test_gff_version: .: (0.000278) test_metadata: .: (0.000244) test_metadata_size: .: (0.000410) test_records_size: .: (0.000253) test_to_s: .: (0.000471) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000417) test_attributes_case2: .: (0.000097) test_attributes_incompatible_backslash_semicolon: .: (0.000144) Bio::TestGFF2MetaData: test_data: .: (0.000148) test_directive: .: (0.000042) test_parse: .: (0.000056) Bio::TestGFF2Record: test_attribute: .: (0.000427) test_attribute_nonexistent: .: (0.000144) test_attributes: .: (0.000178) test_attributes_to_hash: .: (0.000185) test_comment_only?: .: (0.000137) test_delete_attribute: .: (0.000177) test_delete_attribute_multiple: .: (0.000185) test_delete_attribute_multiple2: .: (0.000321) test_delete_attribute_multiple_nil: .: (0.000188) test_delete_attribute_nil: .: (0.000173) test_delete_attribute_nonexistent: .: (0.000169) test_delete_attributes: .: (0.000180) test_delete_attributes_multiple: .: (0.000170) test_delete_attributes_nonexistent: .: (0.000154) test_end: .: (0.000539) test_eqeq: .: (0.000505) test_eqeq_false: .: (0.000380) test_feature: .: (0.000305) test_frame: .: (0.000152) test_get_attribute: .: (0.000185) test_get_attribute_nonexistent: .: (0.000124) test_get_attributes: .: (0.000181) test_get_attributes_nonexistent: .: (0.000235) test_replace_attributes: .: (0.000161) test_replace_attributes_multiple_multiple_over: .: (0.000170) test_replace_attributes_multiple_multiple_same: .: (0.000145) test_replace_attributes_multiple_multiple_two: .: (0.000139) test_replace_attributes_multiple_single: .: (0.000139) test_replace_attributes_nonexistent: .: (0.000161) test_replace_attributes_nonexistent_multiple: .: (0.000417) test_replace_attributes_single_multiple: .: (0.000209) test_score: .: (0.000138) test_self_parse: .: (0.000528) test_seqname: .: (0.000130) test_set_attribute: .: (0.000207) test_set_attribute_multiple: .: (0.000156) test_set_attribute_nonexistent: .: (0.000145) test_sort_attributes_by_tag!: .: (0.000380) test_sort_attributes_by_tag_bang_test2: .: (0.000193) test_sort_attributes_by_tag_bang_with_block: .: (0.000170) test_source: .: (0.000119) test_start: .: (0.000138) test_strand: .: (0.000120) test_to_s: .: (0.000456) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000497) test_comment_eq: .: (0.000057) test_comment_only?: .: (0.000058) test_comment_only_false: .: (0.000051) test_to_s: .: (0.000058) test_to_s_not_empty: .: (0.000127) Bio::TestGFF3: test_const_version: .: (0.000957) test_gff_version: .: (0.000371) test_records: .: (0.005905) test_sequence_regions: .: (0.000473) test_sequences: .: (0.000798) test_to_s: .: (0.000719) Bio::TestGFF3MetaData: test_data: .: (0.000415) test_directive: .: (0.000070) test_parse: .: (0.000065) Bio::TestGFF3Record: test_attributes: .: (0.000270) test_end: .: (0.000160) test_feature: .: (0.000141) test_frame: .: (0.000445) test_id: .: (0.000155) test_score: .: (0.000129) test_seqname: .: (0.000113) test_source: .: (0.000116) test_start: .: (0.000119) test_strand: .: (0.000369) test_to_s: .: (0.000258) test_to_s_attr_order_changed: .: (0.000269) Bio::TestGFF3RecordEscape: test_escape: .: (0.000209) test_escape_attribute: .: (0.000081) test_escape_seqid: .: (0.000105) test_unescape: .: (0.000074) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000253) test_eqeq: .: (0.000147) test_new_from_sequences_na: .: (0.000143) test_new_from_sequences_na_aa: .: (0.000587) test_new_from_sequences_na_aa_boundary_gap: .: (0.000488) test_new_from_sequences_na_aa_example: .: (0.000192) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000162) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000173) test_process_sequences_na: .: (0.000190) test_process_sequences_na_aa: .: (0.000129) test_process_sequences_na_aa_reverse_frameshift: .: (0.000371) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000115) test_process_sequences_na_aa_tooshort: .: (0.000212) test_process_sequences_na_tooshort: .: (0.000175) test_to_s: .: (0.000126) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000205) test_attributes_one: .: (0.000071) test_attributes_with_escaping: .: (0.000102) test_id_multiple: .: (0.000490) test_id_multiple2: .: (0.000175) test_id_replace: .: (0.000085) test_id_set: .: (0.000102) test_initialize_9: .: (0.000049) test_phase: .: (0.000082) test_score: .: (0.000070) test_to_s_void: .: (0.000066) Bio::TestGFF3RecordTarget: test_end: .: (0.000246) test_parse: .: (0.000121) test_start: .: (0.000055) test_strand: .: (0.000047) test_target_id: .: (0.000051) test_to_s: .: (0.000109) Bio::TestGFF3SequenceRegion: test_end: .: (0.000136) test_parse: .: (0.000108) test_seqid: .: (0.000058) test_start: .: (0.000050) test_to_s: .: (0.000110) Bio::TestGFFRecord: test_attributes: .: (0.000189) test_comment: .: (0.000067) test_end: .: (0.000062) test_feature: .: (0.000058) test_frame: .: (0.000058) test_score: .: (0.000057) test_seqname: .: (0.000310) test_source: .: (0.000115) test_start: .: (0.000073) test_strand: .: (0.000063) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000383) Bio::TestGeneAssociation: test_aspect: .: (0.000149) test_assigned_by: .: (0.000059) test_date: .: (0.000062) test_db: .: (0.000077) test_db_object_id: .: (0.000063) test_db_object_name: .: (0.000064) test_db_object_symbol: .: (0.000057) test_db_object_synonym: .: (0.000066) test_db_object_type: .: (0.000061) test_db_reference: .: (0.000059) test_evidence: .: (0.000063) test_goid: .: (0.000255) test_parser: .: (0.000366) test_qualifier: .: (0.000073) test_taxon: .: (0.000061) test_to_str: .: (0.000068) test_with: .: (0.000065) Bio::TestGenscanReport: test_date_run: .: (0.001196) test_gccontent: .: (0.000601) test_genscan_version: .: (0.000645) test_isochore: .: (0.000533) test_length: .: (0.000448) test_matrix: .: (0.000746) test_predictions_size: .: (0.000755) test_query_name: .: (0.000488) test_time: .: (0.000560) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000619) test_donor_score: .: (0.000674) test_exon_type: .: (0.000448) test_exon_type_long: .: (0.000881) test_first: .: (0.000485) test_initiation_score: .: (0.000436) test_last: .: (0.000630) test_number: .: (0.000427) test_p_value: .: (0.000541) test_phase: .: (0.000423) test_range: .: (0.000842) test_score: .: (0.000480) test_strand: .: (0.000422) test_t_score: .: (0.000591) test_termination_score: .: (0.000433) Bio::TestGenscanReportGene: test_aaseq: .: (0.000780) test_naseq: .: (0.000463) test_number: .: (0.000773) test_polyA: .: (0.000480) test_promoter: .: (0.000411) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000893) test_reports_ary_contents: .: (0.000515) Bio::TestHMMERReportConstants: test_rs: .: (0.000144) Bio::TestHMMERReportHit: test_accession: .: (0.000827) test_append_hsp: .: (0.000725) test_bit_score: .: (0.000570) test_definition: .: (0.000484) test_description: .: (0.000427) test_each: .: (0.004563) test_each_hsp: .: (0.005722) test_entry_id: .: (0.006567) test_evalue: .: (0.003933) test_hit: .: (0.004251) test_hit_id: .: (0.005845) test_hsps: .: (0.004888) test_num: .: (0.005004) test_score: .: (0.005136) test_target_def: .: (0.004210) test_target_id: .: (0.003708) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.001055) test_each: .: (0.000851) test_each_hit: .: (0.000709) test_histogram: .: (0.000736) test_hits: .: (0.000642) test_hsps: .: (0.000632) test_parameter: .: (0.000894) test_program: .: (0.000673) test_query_info: .: (0.000521) test_statistical_detail: .: (0.000489) test_total_seq_searched: .: (0.000800) test_whole_seq_top_hits: .: (0.000445) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000809) test_histogram: .: (0.001104) test_statistical_detail: .: (0.000656) test_total_seq_searched: .: (0.000593) test_whole_seq_top_hit: .: (0.000853) Bio::TestHMMERReportHsp: test_accession: .: (0.000689) test_bit_score: .: (0.000755) test_csline: .: (0.000696) test_domain: .: (0.000485) test_evalue: .: (0.000423) test_flatseq: .: (0.000431) test_hmm_f: .: (0.000628) test_hmm_t: .: (0.000505) test_hmmseq: .: (0.000768) test_hsp: .: (0.000565) test_midline: .: (0.000513) test_query_frame: .: (0.000544) test_query_from: .: (0.000475) test_query_seq: .: (0.000778) test_query_to: .: (0.000896) test_rfline: .: (0.000491) test_score: .: (0.000416) test_seq_f: .: (0.000661) test_seq_ft: .: (0.000480) test_seq_t: .: (0.000479) test_set_alignment: .: (0.000416) test_targat_to: .: (0.001050) test_target_frame: .: (0.000519) test_target_from: .: (0.000446) test_target_seq: .: (0.000433) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000450) test_find_hetatm: .: (0.000151) test_hetatms: .: (0.000184) Bio::TestHeterogen: test_addAtom: .: (0.000588) test_each: .: (0.000475) test_each_hetatm: .: (0.000110) test_get_residue_id_from_atom: .: (0.000095) test_het_atom: .: (0.000077) test_iCode: .: (0.000075) test_inspect: .: (0.000267) test_resSeq: .: (0.000090) test_sort: .: (0.000106) test_square_bracket: .: (0.000293) test_to_s: .: (0.000232) test_update_resudue_id: .: (0.000086) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000225) test_find_heterogen: .: (0.000077) test_heterogens: .: (0.000081) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000242) test_match_description: .: (0.000093) test_match_evalue: .: (0.000135) test_match_ipr_description: .: (0.000565) test_match_ipr_id: .: (0.000091) test_match_match_end: .: (0.000079) test_match_match_start: .: (0.000070) test_match_method: .: (0.000071) test_matches_size: .: (0.000072) test_query_id: .: (0.000070) test_query_length: .: (0.000075) Bio::TestIprscanRawReport: test_entry_id: .: (0.002301) test_match_accession: .: (0.002097) test_match_crc64: .: (0.001720) test_match_date: .: (0.001940) test_match_description: .: (0.001887) test_match_evalue: .: (0.002008) test_match_go_terms: .: (0.001953) test_match_ipr_description: .: (0.005064) test_match_ipr_id: .: (0.002082) test_match_match_end: .: (0.002215) test_match_match_start: .: (0.002084) test_match_method: .: (0.002168) test_match_query_id: .: (0.001840) test_match_query_length: .: (0.001832) test_match_status: .: (0.001580) test_obj: .: (0.002066) test_query_id: .: (0.001639) test_query_length: .: (0.001828) test_self_reports_in_raw: .: (0.005415) Bio::TestIprscanReport: test_output_raw: .: (0.000646) test_to_raw: .: (0.000384) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000469) test_match_accession: .: (0.000869) test_match_date: .: (0.000384) test_match_description: .: (0.000322) test_match_evalue: .: (0.000321) test_match_go_terms: .: (0.000624) test_match_ipr_description: .: (0.000365) test_match_ipr_id: .: (0.000341) test_match_match_end: .: (0.000420) test_match_match_start: .: (0.000870) test_match_method: .: (0.000415) test_match_status: .: (0.000301) test_matches_size: .: (0.000304) test_query_id: .: (0.000565) test_query_length: .: (0.000386) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000583) test_to_hash_match?: .: (0.000665) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.000951) Bio::TestKeggCompound: test_comment: .: (0.000582) test_dblinks_as_hash: .: (0.000358) test_dblinks_as_strings: .: (0.000229) test_entry_id: .: (0.000199) test_enzymes: .: (0.000455) test_formula: .: (0.000184) test_kcf: .: (0.000191) test_mass: .: (0.000538) test_name: .: (0.000243) test_names: .: (0.000200) test_pathways_as_hash: .: (0.000328) test_pathways_as_strings: .: (0.000498) test_reactions: .: (0.000583) test_remark: .: (0.000222) test_rpairs: .: (0.000169) Bio::TestKeggEnzyme: test_all_reac: .: (0.000545) test_classes: .: (0.000746) test_cofactors: .: (0.000379) test_comment: .: (0.000406) test_dblinks_as_hash: .: (0.000395) test_dblinks_as_strings: .: (0.000333) test_diseases: .: (0.000351) test_entry: .: (0.000605) test_entry_id: .: (0.000359) test_genes: .: (0.010277) test_genes_as_hash: .: (0.018515) test_genes_as_strings: .: (0.007717) test_inhibitors: .: (0.000837) test_iubmb_reactions: .: (0.000613) test_kegg_reactions: .: (0.000467) test_motifs: .: (0.000344) test_name: .: (0.000471) test_names: .: (0.000396) test_obsolete?: .: (0.000988) test_orthologs_as_hash: .: (0.000410) test_orthologs_as_strings: .: (0.000384) test_pathways_as_hash: .: (0.000445) test_pathways_as_strings: .: (0.000358) test_products: .: (0.000354) test_reaction: .: (0.000635) test_structures: .: (0.000557) test_substrates: .: (0.000559) test_sysname: .: (0.000374) Bio::TestKeggGenesDblinks: test_data: .: (0.000250) test_dblinks_0: .: (0.000092) test_dblinks_1: .: (0.000070) test_dblinks_2: .: (0.000312) Bio::TestKeggGenesStructure: test_data: .: (0.000200) test_ids: .: (0.000106) test_ids_in_array: .: (0.000084) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.006364) test_graphics__size: .: (0.012556) test_id: .: (0.007746) test_link: .: (0.008012) test_name: .: (0.006481) test_reaction: .: (0.005985) test_type: .: (0.060638) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.009734) test_graphics__size: .: (0.006886) test_id: .: (0.007059) test_link: .: (0.007529) test_name: .: (0.006046) test_reaction: .: (0.007905) test_type: .: (0.007153) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.007722) test_category: .: (0.018665) test_entry_id: .: (0.014189) test_fgcolor=: .: (0.012606) test_height=: .: (0.040854) test_label=: .: (0.015387) test_shape=: .: (0.017509) test_width=: .: (0.007777) test_x=: .: (0.007213) test_y=: .: (0.006524) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.005796) test_graphics__size: .: (0.006030) test_id: .: (0.011266) test_link: .: (0.009891) test_name: .: (0.012487) test_reaction: .: (0.006640) test_type: .: (0.007285) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000482) test_graphics=: .: (0.000464) test_id=: .: (0.000277) test_link=: .: (0.000263) test_name=: .: (0.000242) test_reaction=: .: (0.000246) test_type=: .: (0.000231) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000415) test_category=: .: (0.000272) test_entry_id=: .: (0.000252) test_fgcolor=: .: (0.000481) test_height=: .: (0.000493) test_label=: .: (0.000258) test_pathway=: .: (0.000300) test_shape=: .: (0.000279) test_width=: .: (0.000303) test_x=: .: (0.000297) test_y=: .: (0.000251) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.005522) test_coords: .: (0.012222) test_fgcolor: .: (0.015203) test_height: .: (0.008137) test_name: .: (0.009736) test_type: .: (0.005864) test_width: .: (0.007699) test_x: .: (0.015592) test_y: .: (0.005781) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.006068) test_coords: .: (0.008011) test_fgcolor: .: (0.007558) test_height: .: (0.005985) test_name: .: (0.008105) test_type: .: (0.011065) test_width: .: (0.010787) test_x: .: (0.005778) test_y: .: (0.005652) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000219) test_coords=: .: (0.000060) test_fgcolor=: .: (0.000163) test_height=: .: (0.000054) test_name=: .: (0.000052) test_type=: .: (0.000051) test_width=: .: (0.000049) test_x=: .: (0.000050) test_y=: .: (0.000052) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.007913) test_entries__size: .: (0.008404) test_image: .: (0.005713) test_link: .: (0.007483) test_name: .: (0.005811) test_number: .: (0.006088) test_org: .: (0.006051) test_reactions=: .: (0.006518) test_reactions__size: .: (0.009339) test_relations=: .: (0.006290) test_relations__size: .: (0.005848) test_title: .: (0.005911) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.012557) test_name: .: (0.015501) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000375) test_initialize_0: .: (0.000049) test_initialize_1: .: (0.000055) test_initialize_2: .: (0.000049) test_name=: .: (0.001583) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.006347) test_name: .: (0.010915) test_products: .: (0.006191) test_substrates: .: (0.006478) test_type: .: (0.005624) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000226) test_name=: .: (0.000066) test_products=: .: (0.000236) test_substraces=: .: (0.000062) test_type=: .: (0.000055) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000160) test_entry_id=: .: (0.004305) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.014096) test_entry2: .: (0.015645) test_name: .: (0.018544) test_type: .: (0.015320) test_value: .: (0.013200) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000212) test_node1=: .: (0.000082) test_node2=: .: (0.000069) test_rel=: .: (0.000075) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000282) test_entry2=: .: (0.000058) test_name=: .: (0.000059) test_type=: .: (0.000054) test_value=: .: (0.000055) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.030912) test_name: .: (0.011867) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000376) test_initialize_0: .: (0.000049) test_initialize_1: .: (0.000043) test_initialize_2: .: (0.000046) test_name=: .: (0.000057) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000142) test_initialize_0: .: (0.000042) test_initialize_1: .: (0.000045) test_initialize_2: .: (0.000044) test_name=: .: (0.000059) Bio::TestKeggModule: test_compounds: .: (0.000542) test_compounds_as_hash: .: (0.000441) test_compounds_as_strings: .: (0.000225) test_definition: .: (0.000175) test_entry_id: .: (0.000128) test_keggclass: .: (0.000124) test_name: .: (0.000123) test_new: .: (0.000133) test_orthologs: .: (0.000200) test_orthologs_as_array: .: (0.000237) test_orthologs_as_hash: .: (0.000170) test_orthologs_as_strings: .: (0.000135) test_pathways: .: (0.000120) test_pathways_as_hash: .: (0.000110) test_pathways_as_strings: .: (0.000101) test_reactions: .: (0.000166) test_reactions_as_hash: .: (0.000314) test_reactions_as_strings: .: (0.000186) Bio::TestKeggOrthology: test_dblinks: .: (0.000456) test_dblinks_as_hash: .: (0.000566) test_dblinks_as_strings: .: (0.000266) test_definition: .: (0.000274) test_entry_id: .: (0.000279) test_genes_as_hash: .: (0.010069) test_genes_as_strings: .: (0.002906) test_keggclass: .: (0.000474) test_keggclasses: .: (0.000380) test_modules: .: (0.000272) test_modules_as_hash: .: (0.000537) test_modules_as_strings: .: (0.000609) test_name: .: (0.000593) test_names: .: (0.000484) test_pathways_as_strings: .: (0.000505) test_pathways_in_keggclass: .: (0.000566) test_references: .: (0.000628) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000477) test_compounds_as_strings: .: (0.000301) test_dblinks_as_hash: .: (0.000436) test_dblinks_as_strings: .: (0.000303) test_description: .: (0.000323) test_diseases_as_hash: .: (0.000316) test_diseases_as_strings: .: (0.000323) test_entry_id: .: (0.000313) test_enzymes_as_strings: .: (0.000289) test_genes_as_hash: .: (0.000279) test_genes_as_strings: .: (0.000273) test_keggclass: .: (0.000461) test_ko_pathway: .: (0.000334) test_modules_as_hash: .: (0.000350) test_modules_as_strings: .: (0.000319) test_name: .: (0.000319) test_organism: .: (0.000300) test_orthologs_as_hash: .: (0.000289) test_orthologs_as_strings: .: (0.000293) test_pathways_as_hash: .: (0.000319) test_pathways_as_strings: .: (0.000479) test_reactions_as_hash: .: (0.000373) test_reactions_as_strings: .: (0.000298) test_references: .: (0.000289) test_rel_pathways_as_hash: .: (0.000343) test_rel_pathways_as_strings: .: (0.000297) Bio::TestKeggReaction: test_definition: .: (0.000533) test_entry_id: .: (0.000310) test_enzymes: .: (0.000602) test_equation: .: (0.000403) test_name: .: (0.000327) test_orthologs_as_hash: .: (0.000374) test_orthologs_as_strings: .: (0.000311) test_pathways_as_hash: .: (0.000354) test_pathways_as_strings: .: (0.000309) test_rpairs_as_hash: .: (0.000390) test_rpairs_as_strings: .: (0.000316) test_rpairs_as_tokens: .: (0.000523) Bio::TestLasergene: test_methods: .: (0.004909) Bio::TestLocations: test_complement: .: (0.003623) test_hat: .: (0.000255) test_normal: .: (0.000102) test_replace_single_base: .: (0.000082) test_should_not_modify_argument: .: (0.000076) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002839) test_locations_to_s: .: (0.001160) Bio::TestMEDLINE: test_authors: .: (0.001347) test_authors_with_last_name_all_caps: .: (0.000097) test_authors_with_suffix: .: (0.000061) Bio::TestMEDLINE_20146148: test_ab: .: (0.000462) test_ad: .: (0.000258) test_au: .: (0.000487) test_authors: .: (0.000354) test_doi: .: (0.000258) test_dp: .: (0.000230) test_ip: .: (0.001074) test_mh: .: (0.000376) test_pages: .: (0.000228) test_pg: .: (0.000201) test_pii: .: (0.000204) test_pmid: .: (0.000575) test_pt: .: (0.000406) test_reference: .: (0.000503) test_self_new: .: (0.000695) test_so: .: (0.000396) test_ta: .: (0.000243) test_ti: .: (0.000224) test_ui: .: (0.000406) test_vi: .: (0.000273) test_year: .: (0.000206) Bio::TestMapSimple: test_attributes: .: (0.000223) Bio::TestMapping: test_add_mapping_as_map: .: (0.000218) test_add_mapping_as_marker: .: (0.000340) test_contains_marker?: .: (0.000088) test_mapped_to?: .: (0.000057) test_mapping_location_comparison: .: (0.000259) test_mappings_as_map_each: .: (0.000073) test_mappings_as_marker_each: .: (0.000095) test_mappings_on: .: (0.000094) test_multiple_mappings_between_same_marker_and_map: .: (0.000513) test_positions_on: .: (0.000133) test_raise_error_kind_of: .: (0.000444) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000276) test_check_options_with_invalid_opts: .: (0.000120) test_check_options_with_valid_opts: .: (0.000099) test_command_to_be_run: .: (0.000097) test_config_defaults: .: (0.000072) test_minimal_config: .: (0.000077) test_more_config: .: (0.000070) test_run: .: (0.000048) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000545) test_report_has_motifs: .: (0.000187) Bio::TestModel: test_addChain: .: (0.000154) test_comp: .: (0.000078) test_each: .: (0.000071) test_each_chain: .: (0.000054) test_inspect: .: (0.000057) test_rehash: .: (0.000048) test_square_brace: .: (0.000055) test_to_s: .: (0.000053) Bio::TestModelFinder: test_find_model: .: (0.000557) Bio::TestMotif: test_creation_and_attributes: .: (0.000171) test_length: .: (0.000047) Bio::TestMyGraph: test_cliquishness: .: (0.000280) Bio::TestNA: test_accessor: .: (0.000115) test_na: .: (0.000048) test_name: .: (0.000044) test_names: .: (0.000039) test_to_re: .: (0.000141) test_weight: .: (0.000051) test_weight_rna: .: (0.000207) Bio::TestNAConstants: test_NAMES: .: (0.000108) test_NAMES_1_to_name: .: (0.000040) test_WEIGHT: .: (0.000044) Bio::TestNATranslate: test_translate: .: (0.000246) test_translate_1: .: (0.000087) test_translate_2: .: (0.000051) test_translate_3: .: (0.000047) test_translate_4: .: (0.000100) test_translate_5: .: (0.000055) test_translate_6: .: (0.000049) Bio::TestNCBIDB: test_fetch: .: (0.000357) test_p_entry2hash: .: (0.000046) test_p_subtag2array: .: (0.000033) test_p_toptag2array: .: (0.000033) Bio::TestNewick: test_reparse: .: (0.001099) test_reparse_before_lazy_parsing: .: (0.000252) test_string_tree: .: (0.000892) Bio::TestNewick2: test_string_tree: .: (0.000451) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000152) test_parse_newick_leaf: .: (0.000116) test_parse_newick_tokenize: .: (0.000217) Bio::TestNexus: test_nexus: .: (0.008258) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000519) test_uncapitalized_letter_Q32725_9POAL: .: (0.000107) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000175) test_load_parameters: .: (0.000071) test_parameters: .: (0.000043) test_set_default_parameters: .: (0.000058) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000826) test_expected_parameters_set_in_control_file: .: (0.000398) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000169) test_new_with_parameters: .: (0.000062) test_new_with_two_argument: .: (0.000061) test_new_without_argument: .: (0.000052) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.002467) test_rates_hundred_and_fiftieth_position: .: (0.001070) test_rates_last_position: .: (0.001035) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.005775) test_tree: .: (0.011016) test_tree_length: .: (0.006301) test_tree_log_likelihood: .: (0.005780) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000526) test_parameters_should_be_loaded_from_control: .: (0.004596) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001202) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000284) test_dN_dS: .: (0.000350) test_kappa: .: (0.000167) test_lnL: .: (0.000102) test_m3_classes: .: (0.000200) test_m3_lnL: .: (0.000110) test_m3_to_s: .: (0.000095) test_m3_tree: .: (0.000460) test_omega: .: (0.000100) test_to_s: .: (0.000087) test_tree: .: (0.000340) test_tree_length: .: (0.000091) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000467) test_p: .: (0.000267) test_position: .: (0.000284) test_probability: .: (0.000457) test_w: .: (0.000279) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000680) test_graph_omega: .: (0.000310) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000207) test_footer: .: (0.000096) test_header: .: (0.000337) test_initialize: .: (0.000177) test_models: .: (0.000100) test_nb_sites: .: (0.000388) test_num_codons: .: (0.000111) test_num_sequences: .: (0.000119) test_significant: .: (0.000114) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000782) test_nb_sites: .: (0.000204) test_significant: .: (0.000132) test_sites: .: (0.001078) Bio::TestPDB: test_accession: .: (0.000951) test_addModel: .: (0.000883) test_authors: .: (0.000583) test_bracket: .: (0.000743) test_classification: .: (0.000507) test_dbref: .: (0.000796) test_definition: .: (0.000498) test_each: .: (0.001104) test_each_model: .: (0.000714) test_entry_id: .: (0.000827) test_helix: .: (0.000807) test_inspect: .: (0.000742) test_jrnl: .: (0.000507) test_keywords: .: (0.000516) test_record: .: (0.000729) test_remark: .: (0.000655) test_seqres: .: (0.000933) test_sheet: .: (0.001444) test_ssbond: .: (0.000547) test_to_s: .: (0.000981) test_turn: .: (0.000541) test_version: .: (0.000480) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000476) test_U12: .: (0.000080) test_U13: .: (0.000067) test_U22: .: (0.000064) test_U23: .: (0.000062) test_U33: .: (0.000063) test_altLoc: .: (0.000065) test_chainID: .: (0.000065) test_charge: .: (0.000064) test_element: .: (0.000063) test_iCode: .: (0.000069) test_name: .: (0.000067) test_resName: .: (0.000071) test_resSeq: .: (0.000280) test_segID: .: (0.000072) test_serial: .: (0.000059) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000174) test_anisou: .: (0.000049) test_chainID: .: (0.000045) test_charge: .: (0.000045) test_comparable: .: (0.000063) test_do_parse: .: (0.000048) test_element: .: (0.000080) test_iCode: .: (0.000050) test_name: .: (0.000049) test_occupancy: .: (0.000078) test_original_data: .: (0.000055) test_record_name: .: (0.000311) test_resName: .: (0.000048) test_resSeq: .: (0.000044) test_residue: .: (0.000044) test_segID: .: (0.000042) test_serial: .: (0.000044) test_sigatm: .: (0.000283) test_tempFactor: .: (0.000098) test_ter: .: (0.000062) test_to_a: .: (0.000061) test_to_s: .: (0.000092) test_x: .: (0.000061) test_xyz: .: (0.000105) test_y: .: (0.000152) test_z: .: (0.000060) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000245) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000131) test_idcode: .: (0.000051) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000158) test_chainID2: .: (0.000065) test_icode1: .: (0.000070) test_icode2: .: (0.000067) test_measure: .: (0.000064) test_modNum: .: (0.000064) test_pep1: .: (0.000061) test_pep2: .: (0.000061) test_seqNum1: .: (0.000267) test_seqNum2: .: (0.000082) test_serNum: .: (0.000057) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000166) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000131) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000139) test_alpha: .: (0.000283) test_b: .: (0.000098) test_beta: .: (0.000057) test_c: .: (0.000053) test_gamma: .: (0.000050) test_sGroup: .: (0.000056) test_z: .: (0.000053) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000238) test_database: .: (0.000080) test_dbAccession: .: (0.000071) test_dbIdCode: .: (0.000070) test_dbseqBegin: .: (0.000072) test_dbseqEnd: .: (0.000075) test_idCode: .: (0.000072) test_idbnsBeg: .: (0.000069) test_insertBegin: .: (0.004913) test_insertEnd: .: (0.000149) test_seqBegin: .: (0.007805) test_seqEnd: .: (0.000216) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000193) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000311) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000143) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000311) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000151) test_depDate: .: (0.000186) test_idCode: .: (0.000059) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.006978) test_hetID: .: (0.000177) test_iCode: .: (0.000070) test_numHetAtoms: .: (0.004685) test_seqNum: .: (0.000152) test_text: .: (0.000074) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.005785) test_anisou: .: (0.000071) test_chainID: .: (0.006557) test_charge: .: (0.000072) test_comparable: .: (0.000082) test_do_parse: .: (0.000056) test_element: .: (0.000051) test_iCode: .: (0.000054) test_name: .: (0.000052) test_occupancy: .: (0.000088) test_original_data: .: (0.000061) test_record_name: .: (0.000059) test_resName: .: (0.000055) test_resSeq: .: (0.000088) test_residue: .: (0.000069) test_segID: .: (0.000061) test_serial: .: (0.000279) test_sigatm: .: (0.000058) test_tempFactor: .: (0.000066) test_ter: .: (0.000047) test_to_a: .: (0.000058) test_to_s: .: (0.000087) test_x: .: (0.000057) test_xyz: .: (0.000333) test_y: .: (0.000087) test_z: .: (0.000068) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000258) test_ChainH: .: (0.000096) test_ICode1: .: (0.000300) test_altLoc1: .: (0.000093) test_altLoc2: .: (0.000076) test_altLocH: .: (0.000076) test_chainID2: .: (0.000077) test_iCode2: .: (0.000082) test_iCodeH: .: (0.000080) test_name1: .: (0.000085) test_name2: .: (0.000081) test_nameH: .: (0.000080) test_resName1: .: (0.000280) test_resName2: .: (0.000083) test_resSeq1: .: (0.000072) test_resSeq2: .: (0.000103) test_resSeqH: .: (0.000112) test_sym1: .: (0.000086) test_sym2: .: (0.000077) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000180) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000154) test_altLoc2: .: (0.000472) test_chainID1: .: (0.000129) test_chainID2: .: (0.000073) test_iCode1: .: (0.000077) test_iCode2: .: (0.000070) test_name1: .: (0.000070) test_name2: .: (0.000068) test_resName1: .: (0.000069) test_resName2: .: (0.000070) test_resSeq1: .: (0.000067) test_resSeq2: .: (0.000067) test_sym1: .: (0.000071) test_sym2: .: (0.000272) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000184) test_numCoord: .: (0.000054) test_numHelix: .: (0.000050) test_numHet: .: (0.000048) test_numRemark: .: (0.000050) test_numSeq: .: (0.000049) test_numSheet: .: (0.000051) test_numSite: .: (0.000051) test_numTer: .: (0.000050) test_numTurn: .: (0.000052) test_numXform: .: (0.000052) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000125) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000459) test_comment: .: (0.000069) test_iCode: .: (0.000055) test_idCode: .: (0.000055) test_resName: .: (0.000058) test_seqNum: .: (0.000057) test_stdRes: .: (0.000056) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000407) test_Mn2: .: (0.000066) test_Mn3: .: (0.000051) test_Vn: .: (0.000049) test_iGiven: .: (0.000054) test_serial: .: (0.000052) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000378) test_Mn2: .: (0.000049) test_Mn3: .: (0.000051) test_Vn: .: (0.000044) test_iGiven: .: (0.000045) test_serial: .: (0.000043) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000120) test_Mn2: .: (0.000049) test_Mn3: .: (0.000046) test_Vn: .: (0.000048) test_iGiven: .: (0.000048) test_serial: .: (0.000044) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000136) test_rIdCode: .: (0.000058) test_repDate: .: (0.000251) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000134) test_On2: .: (0.000044) test_On3: .: (0.000074) test_Tn: .: (0.000053) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000139) test_modId: .: (0.000058) test_modNum: .: (0.000053) test_modType: .: (0.000051) test_record: .: (0.000056) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000119) test_text: .: (0.000048) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000304) test_Sn2: .: (0.000081) test_Sn3: .: (0.000060) test_Un: .: (0.000046) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000131) test_Sn2: .: (0.000047) test_Sn3: .: (0.000043) test_Un: .: (0.000042) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000111) test_Sn2: .: (0.000048) test_Sn3: .: (0.000046) test_Un: .: (0.000046) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000146) test_conflict: .: (0.000066) test_database: .: (0.000064) test_dbIdCode: .: (0.000071) test_dbRes: .: (0.000057) test_dbSeq: .: (0.000057) test_iCode: .: (0.000057) test_idCode: .: (0.000057) test_resName: .: (0.000059) test_seqNum: .: (0.000058) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000151) test_numRes: .: (0.000066) test_resName: .: (0.000093) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000395) test_curChainId: .: (0.000096) test_curICode: .: (0.000095) test_curResName: .: (0.000095) test_curResSeq: .: (0.000093) test_endChainID: .: (0.000303) test_endICode: .: (0.000117) test_endResName: .: (0.000094) test_endSeqNum: .: (0.000087) test_initChainID: .: (0.000296) test_initICode: .: (0.000089) test_initResName: .: (0.000076) test_initSeqNum: .: (0.000073) test_numStrands: .: (0.000075) test_prevAtom: .: (0.000083) test_prevChainId: .: (0.000084) test_prevICode: .: (0.000082) test_prevResName: .: (0.000082) test_prevResSeq: .: (0.000085) test_sense: .: (0.000080) test_sheetID: .: (0.000287) test_strand: .: (0.000079) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000210) test_chainID: .: (0.000075) test_charge: .: (0.000068) test_element: .: (0.000064) test_iCode: .: (0.000082) test_name: .: (0.000069) test_resName: .: (0.000078) test_resSeq: .: (0.000076) test_segID: .: (0.000067) test_serial: .: (0.000064) test_sigOcc: .: (0.000247) test_sigTemp: .: (0.000072) test_sigX: .: (0.000060) test_sigY: .: (0.000325) test_sigZ: .: (0.000084) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000204) test_SigmaU12: .: (0.000073) test_SigmaU13: .: (0.000067) test_SigmaU22: .: (0.000065) test_SigmaU23: .: (0.000061) test_SigmaU33: .: (0.000064) test_altLoc: .: (0.000065) test_chainID: .: (0.000062) test_charge: .: (0.000281) test_element: .: (0.000075) test_iCode: .: (0.000060) test_name: .: (0.000061) test_resName: .: (0.000060) test_resSeq: .: (0.000093) test_segID: .: (0.000061) test_serial: .: (0.000059) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000186) test_chainID2: .: (0.000073) test_chainID3: .: (0.000069) test_chainID4: .: (0.000069) test_iCode1: .: (0.000261) test_iCode2: .: (0.000088) test_iCode3: .: (0.000071) test_iCode4: .: (0.000067) test_numRes: .: (0.000067) test_resName1: .: (0.000070) test_resName2: .: (0.000070) test_resName3: .: (0.000071) test_resName4: .: (0.000072) test_seq1: .: (0.000068) test_seq2: .: (0.000065) test_seq3: .: (0.000372) test_seq4: .: (0.000296) test_seqNum: .: (0.000072) test_siteID: .: (0.000074) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000183) test_altLoc2: .: (0.000061) test_atom1: .: (0.000055) test_atom2: .: (0.000058) test_chainID1: .: (0.000056) test_chainID2: .: (0.000055) test_iCode1: .: (0.000055) test_iCode2: .: (0.000057) test_resName1: .: (0.000055) test_resName2: .: (0.000055) test_resSeq1: .: (0.000070) test_resSeq2: .: (0.000064) test_sym1: .: (0.000055) test_sym2: .: (0.000053) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000162) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000121) test_sIdCode: .: (0.000053) test_sprsdeDate: .: (0.000052) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000152) test_iCode: .: (0.000057) test_resName: .: (0.000051) test_resSeq: .: (0.000157) test_serial: .: (0.000053) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000130) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000120) test_t1: .: (0.000053) test_t2: .: (0.000249) test_t3: .: (0.000089) test_text: .: (0.000061) Bio::TestPROSITE: test_ac: .: (0.001168) test_cc: .: (0.001101) test_de: .: (0.001160) test_division: .: (0.001380) test_dr: .: (0.015549) test_dt: .: (0.001480) test_false_neg: .: (0.001422) test_false_pos: .: (0.001401) test_false_positive_sequences: .: (0.001406) test_list_falsenegative: .: (0.011462) test_list_falsepositive: .: (0.012652) test_list_potentialhit: .: (0.015339) test_list_truepositive: .: (0.014163) test_list_unknown: .: (0.017995) test_list_xref: .: (0.013884) test_ma: .: (0.001498) test_max_repeat: .: (0.001717) test_name: .: (0.001762) test_nr: .: (0.001988) test_pa: .: (0.001193) test_pa2re: .: (0.031916) test_partial: .: (0.029190) test_pdb_xref: .: (0.001745) test_pdoc_xref: .: (0.001546) test_positive: .: (0.001650) test_positive_hits: .: (0.001453) test_positive_sequences: .: (0.001974) test_release: .: (0.001416) test_ru: .: (0.001477) test_self_pa2re: .: (0.006939) test_site: .: (0.039806) test_skip_flag: .: (0.001897) test_swissprot_release_number: .: (0.001631) test_swissprot_release_sequences: .: (0.001504) test_taxon_range: .: (0.001422) test_total: .: (0.001582) test_total_hits: .: (0.001440) test_total_sequences: .: (0.001518) test_unknown: .: (0.001332) test_unknown_hits: .: (0.001284) test_unknown_sequences: .: (0.001387) Bio::TestPROSITEConst: test_delimiter: .: (0.000434) test_tagsize: .: (0.000170) Bio::TestPTS1: test_function_set: .: (0.000389) test_function_set_number_1: .: (0.000200) test_function_set_number_2: .: (0.000159) test_function_set_number_3: .: (0.000156) test_function_show: .: (0.000162) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000282) Bio::TestPTS1New: test_fungi: .: (0.000290) test_general: .: (0.000173) test_metazoa: .: (0.000178) Bio::TestQualifier: test_qualifier: .: (0.000279) test_value: .: (0.000223) Bio::TestREBASE: test_methods: .: (0.000931) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001052) test_bit_score: .: (0.000780) test_evalue: .: (0.000757) test_gaps: .: (0.000749) test_hit_from: .: (0.000736) test_hit_to: .: (0.000706) test_hseq: .: (0.000685) test_identity: .: (0.000684) test_midline: .: (0.000701) test_percent_identity: .: (0.000779) test_positive: .: (0.000721) test_qseq: .: (0.000743) test_query_from: .: (0.002070) test_query_to: .: (0.000841) test_score: .: (0.000726) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000794) test_hits_size: .: (0.001254) test_iterations_size: .: (0.001203) test_program: .: (0.000452) test_query_def: .: (0.000895) test_query_len: .: (0.000863) test_version: .: (0.000389) test_version_date: .: (0.000367) test_version_number: .: (0.000398) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000852) test_definition: .: (0.000493) test_evalue: .: (0.000436) test_hsps_size: .: (0.000421) test_identity: .: (0.000438) test_lap_at: .: (0.000547) test_len: .: (0.000470) test_midline: .: (0.000726) test_overlap: .: (0.000515) test_query_end: .: (0.000476) test_query_seq: .: (0.000480) test_query_start: .: (0.000438) test_target_def: .: (0.000424) test_target_end: .: (0.000487) test_target_len: .: (0.000437) test_target_seq: .: (0.000697) test_target_start: .: (0.000476) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000378) test_get_entry: .: (0.000295) test_rewind: .: (0.000065) test_skip_leader: .: (0.000115) Bio::TestReference: test_abstract: .: (0.000167) test_affiliations: .: (0.000049) test_authors: .: (0.000042) test_format_bibitem: .: (0.000088) test_format_bibtex: .: (0.000159) test_format_bibtex_with_arguments: .: (0.000131) test_format_cell: .: (0.000094) test_format_current: .: (0.000057) test_format_endnote: .: (0.000097) test_format_general: .: (0.000065) test_format_genome_biol: .: (0.000077) test_format_genome_res: .: (0.000061) test_format_nar: .: (0.000072) test_format_nature: .: (0.000066) test_format_rd: .: (0.000090) test_format_science: .: (0.000087) test_format_trends: .: (0.000330) test_issue: .: (0.000058) test_journal: .: (0.000043) test_mesh: .: (0.000090) test_pages: .: (0.000040) test_pubmed: .: (0.000038) test_pubmed_url: .: (0.000048) test_url: .: (0.000039) test_volume: .: (0.000041) test_year: .: (0.000039) Bio::TestReference_noURL: test_format_endnote: .: (0.000204) test_url: .: (0.000042) Bio::TestReferences: test_append: .: (0.000184) test_each: .: (0.000083) Bio::TestRelation: test_comparison_operator: .: (0.000136) test_uniq: .: (0.000079) Bio::TestResidue: test_addAtom: .: (0.000258) test_each: .: (0.000140) test_each_atom: .: (0.000116) test_get_residue_id_from_atom: .: (0.000089) test_het_atom: .: (0.000095) test_iCode: .: (0.000078) test_inspect: .: (0.000112) test_resSeq: .: (0.000107) test_sort: .: (0.000108) test_square_bracket: .: (0.000100) test_to_s: .: (0.000174) test_update_resudue_id: .: (0.000082) Bio::TestResidueFinder: test_each_residue: .: (0.000409) test_find_residue: .: (0.000133) test_residues: .: (0.000083) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.073924) test_cut_from_bio_sequence_na: .: (0.022247) test_cut_without_permutations: .: (0.013944) test_view_ranges: .: (0.014886) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000880) test_cuts_after_remove_incomplete_cuts: .: (0.000582) test_strands_for_display: .: (0.002060) test_strands_for_display_current: .: (0.000550) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000473) test_fragments_for_display_1: .: (0.000471) test_fragments_for_display_10: .: (0.000986) test_fragments_for_display_2: .: (0.000732) test_fragments_for_display_3: .: (0.001079) test_fragments_for_display_4: .: (0.000828) test_fragments_for_display_5: .: (0.000771) test_fragments_for_display_6: .: (0.000549) test_fragments_for_display_7: .: (0.000549) test_fragments_for_display_8: .: (0.000712) test_fragments_for_display_9: .: (0.000518) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000324) test_obj_3: .: (0.000159) test_obj_7: .: (0.000128) test_obj_z: .: (0.000238) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000225) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000170) test_bracket_eq: .: (0.000110) test_concat: .: (0.000070) test_delete: .: (0.000065) test_dup: .: (0.000103) test_each: .: (0.000088) test_eqeq: .: (0.000063) test_eqeq_false: .: (0.000055) test_eqeq_other: .: (0.000050) test_eqeq_self: .: (0.000042) test_include?: .: (0.000052) test_internal_data: .: (0.000051) test_internal_data_eq: .: (0.000058) test_length: .: (0.000049) test_ltlt: .: (0.000083) test_ltlt_larger: .: (0.000064) test_ltlt_middle: .: (0.000055) test_plus: .: (0.000072) test_plus_error: .: (0.000102) test_push: .: (0.000064) test_reverse_each: .: (0.000083) test_self_bracket: .: (0.000142) test_self_new: .: (0.000074) test_size: .: (0.000047) test_sort!: .: (0.000044) test_to_a: .: (0.000049) test_uniq!: .: (0.000121) test_unshift: .: (0.000113) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003409) test_complement: .: (0.002755) test_complement_with_cut_symbols: .: (0.002961) test_cut_locations: .: (0.002881) test_cut_locations_in_enzyme_notation: .: (0.002560) test_primary: .: (0.003173) test_primary_with_cut_symbols: .: (0.003051) test_to_re: .: (0.002807) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000774) test_align_with_cuts: .: (0.000469) test_argument_error: .: (0.000843) test_ds: .: (0.000700) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000402) test_complement: .: (0.000119) test_contents: .: (0.000109) test_primary: .: (0.000109) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000272) test_complement: .: (0.000217) test_contents: .: (0.000101) test_primary: .: (0.000099) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000164) test_contents: .: (0.000076) test_primary: .: (0.000074) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000157) test_complement_to_array_index: .: (0.000135) test_complement_to_array_index_class: .: (0.000238) test_contents: .: (0.000087) test_primary: .: (0.000076) test_primary_to_array_index: .: (0.000157) test_primary_to_array_index_class: .: (0.000115) test_to_array_index: .: (0.000263) test_to_array_index_class: .: (0.000228) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000586) test_rebase: .: (0.000250) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000635) test_creation_with_no_cuts: .: (0.000291) test_cut_locations: .: (0.000375) test_cut_locations_in_enzyme_notation: .: (0.000261) test_orientation: .: (0.000239) test_pattern: .: (0.000383) test_pattern_palindromic?: .: (0.000319) test_stripped: .: (0.000237) test_to_re: .: (0.000604) test_with_cut_symbols: .: (0.000299) test_with_spaces: .: (0.000345) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000676) test_creation_with_no_cuts: .: (0.000277) test_cut_locations: .: (0.000257) test_cut_locations_in_enzyme_notation: .: (0.000349) test_orientation: .: (0.000263) test_pattern: .: (0.000267) test_pattern_palindromic?: .: (0.000390) test_stripped: .: (0.000476) test_to_re: .: (0.000280) test_with_cut_symbols: .: (0.000365) test_with_spaces: .: (0.000294) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000351) test_initialize_with_pattern: .: (0.000187) test_max: .: (0.000165) test_min: .: (0.000066) test_to_array_index: .: (0.000081) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000174) test_bracket_eq: .: (0.000099) test_concat: .: (0.000071) test_delete: .: (0.000052) test_dup: .: (0.000116) test_each: .: (0.000083) test_eqeq: .: (0.000053) test_eqeq_false: .: (0.000047) test_eqeq_other: .: (0.000155) test_eqeq_self: .: (0.000041) test_include?: .: (0.000044) test_internal_data_hash: .: (0.000044) test_internal_data_hash_eq: .: (0.000054) test_length: .: (0.000041) test_ltlt: .: (0.000049) test_ltlt_noeffect: .: (0.000045) test_plus: .: (0.000050) test_plus_error: .: (0.000363) test_private_push_element: .: (0.000084) test_private_push_element_intermediate: .: (0.000071) test_private_push_element_last: .: (0.000068) test_private_push_element_noeffect: .: (0.000060) test_private_sorted_keys: .: (0.000062) test_private_unshift_element: .: (0.000213) test_private_unshift_element_first: .: (0.000055) test_private_unshift_element_intermediate: .: (0.000048) test_private_unshift_element_noeffect: .: (0.000043) test_push: .: (0.000051) test_reverse_each: .: (0.000077) test_self_bracket: .: (0.000041) test_self_new: .: (0.000072) test_size: .: (0.000043) test_sort!: .: (0.000041) test_to_a: .: (0.000042) test_uniq!: .: (0.000040) test_unshift: .: (0.000049) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000178) test_left_padding: .: (0.000174) test_right_padding: .: (0.000058) test_strip_padding: .: (0.000062) Bio::TestSOFT: test_dataset: .: (0.010032) test_series: .: (0.005534) Bio::TestSOSUIReport: test_entry_id: .: (0.000435) test_prediction: .: (0.000219) test_tmh: .: (0.000205) test_tmhs: .: (0.000240) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000409) test_rs: .: (0.000151) Bio::TestSOSUITMH: test_grade: .: (0.000371) test_range: .: (0.000208) test_sequence: .: (0.000224) Bio::TestSampleGraph: test_bellman_ford: .: (0.000497) test_bfs_shortest_path: .: (0.000155) test_breadth_first_search: .: (0.000105) test_depth_first_search: .: (0.000326) test_dijkstra: .: (0.000161) test_dump_list: .: (0.000148) test_dump_matrix: .: (0.000235) test_extract_subgraph_by_label: .: (0.000126) test_extract_subgraph_by_list: .: (0.000115) test_extract_subgraph_retains_disconnected_nodes: .: (0.000086) test_small_world_aka_node_degree_histogram: .: (0.000263) test_to_matrix: .: (0.000231) test_to_matrix_fixed_index: .: (0.000151) test_undirected_cliquishness: .: (0.000198) Bio::TestScf_version_2: test_complement: .: (0.007392) test_seq: .: (0.006995) test_to_biosequence: .: (0.007130) Bio::TestScf_version_3: test_complement: .: (0.021090) test_seq: .: (0.020902) test_to_biosequence: .: (0.020808) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000350) test_AA_new_sequence_all_legal_symbols: .: (0.000170) test_AA_new_sequence_removes_whitespace: .: (0.000165) test_AA_new_sequence_upcases_symbols: .: (0.000156) test_DNA_new_blank_sequence: .: (0.000323) test_DNA_new_sequence_downcases_symbols: .: (0.000168) test_DNA_new_sequence_removes_whitespace: .: (0.000171) test_NA_randomize_with_counts: .: (0.000747) test_NA_randomize_with_counts_and_block: .: (0.000926) test_RNA_new_sequence: .: (0.000178) test_ambiguous_dna_sequence_complement: .: (0.000178) test_ambiguous_rna_sequence_complement: .: (0.000158) test_amino_acid_codes: .: (0.000380) test_amino_acid_molecular_weight: .: (0.000277) test_amino_acid_names: .: (0.000194) test_amino_acid_randomize_can_be_chained: .: (0.000960) test_amino_acid_randomize_has_same_composition: .: (0.000509) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000635) test_dna_composition: .: (0.000197) test_dna_gc_percent: .: (0.000211) test_dna_molecular_weight: .: (0.000218) test_dna_pikachu: .: (0.000177) test_dna_sequence_complement: .: (0.000311) test_dna_sequence_translate: .: (0.000579) test_dna_to_re: .: (0.000237) test_element_reference_operator_with_one_argument: .: (0.000156) test_element_reference_operator_with_two_arguments: .: (0.000167) test_invalid_nucleic_acid_illegal_bases: .: (0.000213) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000236) test_nucleic_acid_names: .: (0.000193) test_randomize_dna_can_be_chained: .: (0.000359) test_randomize_dna_retains_composition: .: (0.000456) test_randomize_dna_with_block: .: (0.000341) test_rna_composition: .: (0.000216) test_rna_gc_percent: .: (0.000208) test_rna_molecular_weight: .: (0.000226) test_rna_pikachu: .: (0.000168) test_rna_sequence_complement: .: (0.000156) test_rna_sequence_translate: .: (0.000384) test_rna_to_re: .: (0.000238) test_total: .: (0.000172) test_two_consecutive_dna_randomizations_not_equal: .: (0.000274) test_valid_dna_sequence_illegal_bases: .: (0.000172) Bio::TestSequenceAA: test_codes: .: (0.000214) test_molecular_weight: .: (0.000098) test_names: .: (0.000066) test_to_re: .: (0.000105) test_to_s: .: (0.000044) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000191) Bio::TestSequenceAANew: test_new: .: (0.000099) test_new_n: .: (0.000172) test_new_r: .: (0.000043) test_new_t: .: (0.000037) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000149) test_concat: .: (0.000051) test_push: .: (0.000042) test_seq: .: (0.000039) test_splicing: .: (0.000131) test_sum: .: (0.000046) test_to_s: .: (0.000037) test_to_str: .: (0.000046) test_total: .: (0.000053) test_window_search: .: (0.000139) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000198) test_normalize_A: .: (0.000047) test_normalize_a: .: (0.000041) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000715) test_randomize_with_block: .: (0.002699) test_randomize_with_hash: .: (0.001050) test_randomize_with_hash_block: .: (0.004074) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.001418) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.001067) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000459) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000461) test_subseq_returns_subsequence: .: (0.000194) test_to_s_returns_self_as_string: .: (0.000192) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000312) test_window_search_with_width_3_step_two_with_residual: .: (0.000178) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000341) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000361) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000369) test_na_self_randomize: .: (0.000243) Bio::TestSequenceDBLink: test_database: .: (0.000344) test_id: .: (0.000152) test_secondary_ids: .: (0.000156) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000313) test_parse_uniprot_DR_line: .: (0.000198) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000967) test_output_width_35: .: (0.000407) test_output_width_nil: .: (0.000384) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000667) test_output_after_adding_sequence: .: (0.000265) test_output_after_truncating_sequence: .: (0.000131) test_output_from_error_probabilities: .: (0.002164) test_output_width45: .: (0.021030) test_output_with_converting_score_phred2solexa: .: (0.000583) test_output_with_converting_score_solexa2phred: .: (0.000278) test_output_with_default_score: .: (0.000203) Bio::TestSequenceMasker: test_mask: .: (0.000266) test_mask_with_enumerator: .: (0.000345) test_mask_with_enumerator_empty_mask_char: .: (0.000096) test_mask_with_enumerator_excess: .: (0.000370) test_mask_with_enumerator_longer_mask_char: .: (0.000089) test_mask_with_enumerator_shorter: .: (0.000116) test_mask_with_error_probability: .: (0.000085) test_mask_with_quality_score: .: (0.000078) Bio::TestSequenceNA: test_at_content: .: (0.000286) test_at_skew: .: (0.000129) test_codon_usage: .: (0.000090) test_complement: .: (0.000215) test_dna: .: (0.000055) test_dna!: .: (0.000042) test_forward_complement: .: (0.008380) test_gc_content: .: (0.000264) test_gc_percent: .: (0.000143) test_gc_skew: .: (0.000242) test_iliegal_bases: .: (0.000066) test_molecular_weight: .: (0.000091) test_names: .: (0.000118) test_reverse_complement: .: (0.000272) test_rna: .: (0.000048) test_rna!: .: (0.000042) test_splicing: .: (0.000111) test_to_re: .: (0.000104) test_to_s: .: (0.000040) Bio::TestSequenceNACommon: test_composition: .: (0.000192) test_concat: .: (0.000049) test_push: .: (0.000040) test_seq: .: (0.000045) test_splicing: .: (0.000103) test_sum: .: (0.000044) test_to_s: .: (0.000065) test_to_str: .: (0.000247) test_total: .: (0.000059) test_window_search: .: (0.000144) Bio::TestSequenceNANew: test_new: .: (0.000144) test_new_n: .: (0.000045) test_new_r: .: (0.000039) test_new_t: .: (0.000042) Bio::TestSequenceNATranslation: test_translate: .: (0.000306) test_translate_0: .: (0.000679) test_translate_1: .: (0.000132) test_translate_2: .: (0.000114) test_translate_3: .: (0.000115) test_translate_4: .: (0.000125) test_translate_5: .: (0.000115) test_translate_6: .: (0.000114) test_translate_7: .: (0.000282) test_translate_given_codon_table: .: (0.042302) test_translate_n1: .: (0.000390) test_translate_n2: .: (0.000273) test_translate_n3: .: (0.000447) test_translate_unknown_o: .: (0.000148) test_translate_unknown_x: .: (0.000134) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000164) test_convert_scores_from_phred_to_solexa: .: (0.000315) test_convert_scores_from_solexa_to_phred: .: (0.000111) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000144) test_convert_scores_from_phred: .: (0.000053) test_convert_scores_from_phred_to_solexa: .: (0.000357) test_convert_scores_from_solexa: .: (0.000108) test_convert_scores_from_solexa_to_phred: .: (0.000092) test_convert_scores_to_phred: .: (0.000035) test_convert_scores_to_solexa: .: (0.000338) test_p2q: .: (0.000107) test_phred_p2q: .: (0.000083) test_phred_q2p: .: (0.001572) test_q2p: .: (0.001565) test_quality_score_type: .: (0.000066) test_self_convert_scores_to_solexa: .: (0.000252) test_self_p2q: .: (0.000225) test_self_q2p: .: (0.001438) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000484) test_convert_scores_from_phred: .: (0.000254) test_convert_scores_from_phred_to_solexa: .: (0.000227) test_convert_scores_from_solexa: .: (0.000071) test_convert_scores_from_solexa_to_phred: .: (0.000100) test_convert_scores_to_phred: .: (0.000111) test_convert_scores_to_solexa: .: (0.000038) test_p2q: .: (0.000128) test_q2p: .: (0.001610) test_quality_score_type: .: (0.000067) test_self_convert_scores_to_phred: .: (0.000126) test_self_p2q: .: (0.000121) test_self_q2p: .: (0.026033) test_solexa_p2q: .: (0.004622) test_solexa_q2p: .: (0.022724) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.003829) test_center: .: (0.000091) test_chomp: .: (0.008088) test_chop: .: (0.000165) test_delete: .: (0.000056) test_delete_prefix: .: (0.000058) test_delete_suffix: .: (0.000078) test_downcase: .: (0.000061) test_each_char: .: (0.000116) test_each_char_enum: .: (0.000180) test_each_grapheme_cluster: .: (0.000472) test_each_grapheme_cluster_enum: .: (0.000110) test_each_line: .: (0.000105) test_each_line_enum: .: (0.000089) test_gsub: .: (0.000088) test_gsub_with_block: .: (0.000311) test_ljust: .: (0.000063) test_lstrip: .: (0.000060) test_multiply: .: (0.000056) test_next: .: (0.000060) test_reverse: .: (0.000063) test_rjust: .: (0.000056) test_rstrip: .: (0.000055) test_slice: .: (0.000062) test_slice2: .: (0.000193) test_split: .: (0.000094) test_squeeze: .: (0.000073) test_strip: .: (0.000062) test_sub: .: (0.000073) test_sub_with_block: .: (0.000200) test_succ: .: (0.000061) test_swapcase: .: (0.000058) test_tr: .: (0.000058) test_tr_s: .: (0.000055) test_upcase: .: (0.000057) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.002108) test_partition_nomatch: .: (0.000114) test_partition_sep_TSeq: .: (0.000076) test_partition_sep_regexp: .: (0.000073) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000190) test_rpartition_nomatch: .: (0.000075) test_rpartition_sep_TSeq: .: (0.000075) test_rpartition_sep_regexp: .: (0.000077) Bio::TestShRNA: test_blocK_it: .: (0.019603) test_blocK_it_: .: (0.016436) test_blocK_it_BLOCK_IT: .: (0.018860) test_blocK_it_BLOCK_iT: .: (0.021165) test_blocK_it_piGene: .: (0.015164) test_bottom_strand: .: (0.016300) test_bottom_strand_class: .: (0.016428) test_bottom_strand_nil: .: (0.020600) test_design: .: (0.021559) test_design_BLOCK_IT: .: (0.019657) test_report: .: (0.015707) test_report_before_design: .: (0.015703) test_top_strand: .: (0.017683) test_top_strand_class: .: (0.015279) test_top_strand_nil: .: (0.016372) Bio::TestShRNANew: test_new: .: (0.000556) Bio::TestSiRNA: test_antisense_size: .: (0.000279) test_design: .: (0.018314) test_design_reynolds: .: (0.018846) test_design_uitei: .: (0.017739) test_max_gc_percent: .: (0.000211) test_min_gc_percent: .: (0.000172) test_reynolds: .: (0.020435) test_reynolds?: .: (0.000239) test_uitei: .: (0.015434) test_uitei?: .: (0.000222) Bio::TestSiRNANew: test_new: .: (0.000848) Bio::TestSiRNAPair: test_antisense: .: (0.017574) test_gc_percent: .: (0.015874) test_report: .: (0.015648) test_rule: .: (0.017573) test_sense: .: (0.015892) test_start: .: (0.015029) test_stop: .: (0.018039) test_target: .: (0.017442) Bio::TestSiRNAPairNew: test_new: .: (0.000539) Bio::TestSim4Report: test_all_hits: .: (0.000747) test_each: .: (0.000375) test_each_hit: .: (0.000307) test_hits: .: (0.000319) test_num_hits: .: (0.000274) test_query_def: .: (0.000266) test_query_id: .: (0.000256) test_query_len: .: (0.000258) test_seq1: .: (0.000305) Bio::TestSim4Report2: test_all_hits: .: (0.000571) test_each: .: (0.000306) test_each_hit: .: (0.000310) test_hits: .: (0.000346) test_num_hits: .: (0.000275) test_query_def: .: (0.000268) test_query_id: .: (0.000264) test_query_len: .: (0.000256) test_seq1: .: (0.000301) Bio::TestSim4Report4: test_all_hits: .: (0.000564) test_each: .: (0.000324) test_each_hit: .: (0.000330) test_hits: .: (0.000303) test_num_hits: .: (0.000279) test_query_def: .: (0.000293) test_query_id: .: (0.000281) test_query_len: .: (0.000298) test_seq1: .: (0.000348) Bio::TestSim4ReportHit: test_align: .: (0.000684) test_complement?: .: (0.000302) test_definition: .: (0.000296) test_each: .: (0.000511) test_exons: .: (0.000494) test_hit_id: .: (0.000277) test_hsps: .: (0.000441) test_introns: .: (0.000486) test_len: .: (0.000219) test_query_def: .: (0.000109) test_query_id: .: (0.000088) test_query_len: .: (0.000084) test_segmentpairs: .: (0.000238) test_seq1: .: (0.000148) test_seq2: .: (0.000126) test_target_def: .: (0.000092) test_target_id: .: (0.000081) test_target_len: .: (0.000081) Bio::TestSim4ReportHit2: test_align: .: (0.000381) test_complement?: .: (0.000114) test_definition: .: (0.000095) test_each: .: (0.000224) test_exons: .: (0.000185) test_hit_id: .: (0.000164) test_hsps: .: (0.000295) test_introns: .: (0.000211) test_len: .: (0.000109) test_query_def: .: (0.000097) test_query_id: .: (0.000089) test_query_len: .: (0.000084) test_segmentpairs: .: (0.000178) test_seq1: .: (0.000118) test_seq2: .: (0.000213) test_target_def: .: (0.000121) test_target_id: .: (0.000085) test_target_len: .: (0.000090) Bio::TestSim4ReportHit4: test_align: .: (0.000336) test_complement?: .: (0.000117) test_definition: .: (0.000098) test_each: .: (0.000293) test_exons: .: (0.000374) test_hit_id: .: (0.000142) test_hsps: .: (0.000262) test_introns: .: (0.000874) test_len: .: (0.000284) test_query_def: .: (0.000251) test_query_id: .: (0.000255) test_query_len: .: (0.000243) test_segmentpairs: .: (0.000659) test_seq1: .: (0.000324) test_seq2: .: (0.000333) test_target_def: .: (0.000243) test_target_id: .: (0.000250) test_target_len: .: (0.000252) Bio::TestSim4ReportSegment: test_from: .: (0.000285) test_self_new: .: (0.000194) test_seq: .: (0.000153) test_to: .: (0.000291) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000723) test_direction: .: (0.000377) test_hit_from: .: (0.000349) test_hit_to: .: (0.000327) test_hseq: .: (0.000368) test_midline: .: (0.000328) test_percent_identity: .: (0.000456) test_qseq: .: (0.000424) test_query_from: .: (0.000348) test_query_to: .: (0.000406) test_seq1: .: (0.000400) test_seq2: .: (0.000357) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000493) test_direction: .: (0.000356) test_hit_from: .: (0.000323) test_hit_to: .: (0.000298) test_hseq: .: (0.000319) test_midline: .: (0.000307) test_percent_identity: .: (0.000306) test_qseq: .: (0.000314) test_query_from: .: (0.000482) test_query_to: .: (0.000360) test_seq1: .: (0.000392) test_seq2: .: (0.000411) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000583) test_direction: .: (0.000533) test_hit_from: .: (0.000497) test_hit_to: .: (0.000382) test_hseq: .: (0.000369) test_midline: .: (0.000339) test_percent_identity: .: (0.000435) test_qseq: .: (0.000381) test_query_from: .: (0.000344) test_query_to: .: (0.000356) test_seq1: .: (0.000412) test_seq2: .: (0.000576) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000505) test_direction: .: (0.000355) test_hit_from: .: (0.000335) test_hit_to: .: (0.000436) test_hseq: .: (0.000395) test_midline: .: (0.000344) test_percent_identity: .: (0.000346) test_qseq: .: (0.000341) test_query_from: .: (0.000488) test_query_to: .: (0.000425) test_seq1: .: (0.000401) test_seq2: .: (0.000435) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000712) test_direction: .: (0.000488) test_hit_from: .: (0.000409) test_hit_to: .: (0.000384) test_hseq: .: (0.000371) test_midline: .: (0.000394) test_percent_identity: .: (0.000691) test_qseq: .: (0.000377) test_query_from: .: (0.000383) test_query_to: .: (0.000337) test_seq1: .: (0.000393) test_seq2: .: (0.000632) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000489) test_direction: .: (0.000317) test_hit_from: .: (0.000302) test_hit_to: .: (0.000323) test_hseq: .: (0.000436) test_midline: .: (0.000311) test_percent_identity: .: (0.000317) test_qseq: .: (0.000381) test_query_from: .: (0.000311) test_query_to: .: (0.000343) test_seq1: .: (0.000482) test_seq2: .: (0.000402) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000482) test_direction: .: (0.000376) test_hit_from: .: (0.000332) test_hit_to: .: (0.000350) test_hseq: .: (0.000426) test_midline: .: (0.000339) test_percent_identity: .: (0.000328) test_qseq: .: (0.000366) test_query_from: .: (0.000352) test_query_to: .: (0.000338) test_seq1: .: (0.000372) test_seq2: .: (0.000448) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000346) test_entry_id: .: (0.000174) test_filename: .: (0.000188) test_len: .: (0.000156) test_self_new: .: (0.000216) test_self_parse: .: (0.000208) Bio::TestTMHMMReport: test_entry_id: .: (0.000510) test_exp_aas_in_tmhs: .: (0.000402) test_exp_first_60aa: .: (0.000306) test_helix: .: (0.000346) test_predicted_tmhs: .: (0.000313) test_query_len: .: (0.000436) test_tmhs: .: (0.000336) test_to_s: .: (0.000464) test_total_prob_of_N_in: .: (0.000311) Bio::TestTMHMMReport_reports: test_reports: .: (0.000309) Bio::TestTMHMMTMH: test_entry_id: .: (0.000534) test_pos: .: (0.000316) test_range: .: (0.000395) test_status: .: (0.000297) test_version: .: (0.000429) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000482) test_cutoff: .: (0.000279) test_entry_id: .: (0.000250) test_length: .: (0.000248) test_loc: .: (0.000236) test_name: .: (0.000253) test_networks: .: (0.000246) test_prediction: .: (0.000286) test_query_len: .: (0.000344) test_query_sequences: .: (0.000233) test_rc: .: (0.000243) test_version: .: (0.000254) Bio::TestTargetPReportConst: test_delimiter: .: (0.000277) test_rs: .: (0.000143) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000322) test_togows_access_wait: .: (2.009777) Bio::TestTogoWSREST: test_debug: .: (0.000624) test_debug_default: .: (0.000114) test_internal_http: .: (0.000109) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000137) test_entry: .: (0.000045) test_entry_database_list: .: (0.000038) test_new: .: (0.000121) test_new_with_uri_object: .: (0.000126) test_new_with_uri_string: .: (0.000106) test_retrieve: .: (0.000041) test_search: .: (0.000041) test_search_database_list: .: (0.000039) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000536) test_prepare_return_value: .: (0.000166) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000272) Bio::TestTree: test_get_edge_distance: .: (0.000163) test_get_edge_distance_string: .: (0.000079) test_get_node_name: .: (0.000057) test_initialize: .: (0.000116) test_options: .: (0.000054) test_root: .: (0.000039) test_root=: .: (0.000263) Bio::TestTree2: test_add_edge: .: (0.000262) test_add_node: .: (0.000128) test_adjacency_matrix: .: (0.000151) test_adjacency_matrix_with_block: .: (0.000125) test_adjacent_nodes: .: (0.000125) test_adjacent_nodes_nonexistent: .: (0.000075) test_ancestors: .: (0.000105) test_children: .: (0.000089) test_clear: .: (0.000271) test_clear_node: .: (0.000112) test_clear_node_nonexistent: .: (0.000190) test_collect_edge!: .: (0.000174) test_collect_node!: .: (0.000166) test_concat: .: (0.000183) test_descendents: .: (0.000125) test_distance_matrix: .: (0.000329) test_each_edge: .: (0.000241) test_each_node: .: (0.000107) test_each_out_edge: .: (0.016415) test_each_out_edge_chimpanzee: .: (0.000123) test_each_out_edge_human: .: (0.000098) test_each_out_edge_mammals: .: (0.000124) test_each_out_edge_nonexistent: .: (0.000088) test_each_out_edge_primates: .: (0.000119) test_each_out_edge_rat: .: (0.000097) test_each_out_edge_rodents: .: (0.000181) test_edges: .: (0.000099) test_get_edge: .: (0.013416) test_get_edge_indirect: .: (0.000177) test_get_edge_merged: .: (0.000127) test_get_edge_nonexistent: .: (0.000098) test_get_node_bootstrap: .: (0.000112) test_get_node_bootstrap_string=: .: (0.000112) test_get_node_by_name: .: (0.000174) test_get_node_by_name_noexistent: .: (0.000258) test_include?: .: (0.000182) test_include_nonexistent: .: (0.000323) test_insert_node: .: (0.000206) test_leaves: .: (0.000145) test_leaves_noargs: .: (0.000101) test_lowest_common_ancestor: .: (0.000115) test_nodes: .: (0.000097) test_number_of_edges: .: (0.000085) test_number_of_nodes: .: (0.000087) test_out_degree: .: (0.000122) test_out_degree_nonexistent: .: (0.000088) test_out_edges: .: (0.000357) test_out_edges_mammals: .: (0.000150) test_out_edges_nonexistent: .: (0.000088) test_out_edges_primates: .: (0.000132) test_out_edges_rodents: .: (0.000173) test_parent: .: (0.000137) test_path: .: (0.000105) test_remove_edge: .: (0.000111) test_remove_edge_if: .: (0.000128) test_remove_edge_if_nothing_removed: .: (0.000419) test_remove_edge_nonexistent: .: (0.000371) test_remove_node: .: (0.000156) test_remove_node_if: .: (0.000101) test_remove_node_if_false: .: (0.000118) test_remove_node_nonexistent: .: (0.000135) test_remove_nonsense_nodes: .: (0.000129) test_subtree: .: (0.000162) test_subtree_with_all_paths: .: (0.000214) test_total_distance: .: (0.000293) Bio::TestTreeEdge: test_distance: .: (0.000175) test_distance=: .: (0.000081) test_distance_string: .: (0.000050) test_distance_string=: .: (0.000075) test_initialize: .: (0.000077) test_inspect: .: (0.000054) test_to_s: .: (0.000052) Bio::TestTreeNode: test_bootstrap: .: (0.000166) test_bootstrap=: .: (0.000075) test_bootstrap_string: .: (0.000048) test_bootstrap_string=: .: (0.000086) test_initialize: .: (0.000295) test_inspect: .: (0.004379) test_name: .: (0.000158) test_to_s: .: (0.000050) Bio::TestUniProt: test_gene_name: .: (0.019740) Bio::TestUniProtKB: test_ac: .: (0.003220) test_accession: .: (0.002911) test_cc: .: (0.024329) test_cc_alternative_products: .: (0.017068) test_cc_database: .: (0.017023) test_cc_mass_spectrometry: .: (0.004605) test_de: .: (0.019174) test_dr: .: (0.016473) test_dr_with_key: .: (0.012317) test_dr_with_key_empty: .: (0.042417) test_dt: .: (0.096422) test_dt_annotation: .: (0.106903) test_dt_created: .: (0.003204) test_dt_sequence: .: (0.003136) test_entry: .: (0.023338) test_ft: .: (0.015833) test_gene_name: .: (0.011364) test_gene_names: .: (0.007807) test_gn: .: (0.011630) test_gn_old_parser: .: (0.007680) test_gn_uniprot_parser: .: (0.003132) test_id_line: .: (0.016264) test_id_line_data_class: .: (0.011773) test_id_line_entry_name: .: (0.002851) test_id_line_molecule_type: .: (0.007224) test_id_line_sequence_length: .: (0.011668) test_kw: .: (0.013562) test_molecule: .: (0.003200) test_oc: .: (0.007542) test_og_1: .: (0.007334) test_og_2: .: (0.013620) test_og_3: .: (0.003370) test_og_4: .: (0.007734) test_og_5: .: (0.008120) test_og_6: .: (0.007956) test_os: .: (0.007673) test_os_access: .: (0.007737) test_os_access2: .: (0.003137) test_ox: .: (0.011053) test_protein_name: .: (0.007392) test_ref: .: (0.037851) test_seq: .: (0.003633) test_sequence_length: .: (0.028150) test_sq: .: (0.003209) test_sq_crc64: .: (0.017021) test_sq_len: .: (0.011272) test_sq_mw: .: (0.007637) test_synonyms: .: (0.007722) Bio::TestUniProtKB_CC: test_allergen: .: (0.000513) test_alternative_products_access_as_hash: .: (0.000358) test_alternative_products_ai: .: (0.000598) test_alternative_products_apu: .: (0.000610) test_alternative_products_as: .: (0.004534) test_alternative_products_rf: .: (0.000264) test_biophysicochemical_properties: .: (0.000481) test_biotechnology: .: (0.000286) test_catalytic_activity: .: (0.000575) test_caution: .: (0.000267) test_cofactor: .: (0.000258) test_developmental_stage: .: (0.000252) test_disease: .: (0.000399) test_domain: .: (0.003847) test_enzyme_regulation: .: (0.000277) test_function: .: (0.000136) test_induction: .: (0.000091) test_interaction: .: (0.000162) test_mass_spectrometry: .: (0.000158) test_miscellaneous: .: (0.000091) test_pathway: .: (0.000118) test_pharmaceutical: .: (0.000154) test_polymorphism: .: (0.000175) test_ptm: .: (0.000098) test_rna_editing: .: (0.000176) test_similarity: .: (0.000286) test_subcellular_location: .: (0.000133) test_subunit: .: (0.000078) test_tissue_specificity: .: (0.000194) test_toxic_dose: .: (0.000096) test_web_resource: .: (0.000165) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000295) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.005074) test_protein_name: .: (0.000487) test_synonyms: .: (0.004652) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000513) test_entry: .: (0.000211) test_entry_id: .: (0.000206) test_entry_name: .: (0.000182) test_id_line: .: (0.000456) test_molecule: .: (0.000200) test_sequence_length: .: (0.000199) Bio::TestUniProtKB_P03589: test_ac: .: (0.001550) test_accession: .: (0.003674) test_cc: .: (0.001050) test_cc_alternative_products: .: (0.000820) test_cc_database: .: (0.005403) test_cc_mass_spectrometry: .: (0.003694) test_de: .: (0.000615) test_dr: .: (0.001074) test_dr_with_key: .: (0.009629) test_dr_with_key_empty: .: (0.000956) test_dt: .: (0.000536) test_dt_annotation: .: (0.000484) test_dt_created: .: (0.000717) test_dt_sequence: .: (0.004213) test_entry: .: (0.002284) test_ft: .: (0.001082) test_gene_name: .: (0.000662) test_gene_names: .: (0.002870) test_gn: .: (0.000818) test_gn_old_parser: .: (0.006727) test_gn_uniprot_parser: .: (0.000716) test_id_line: .: (0.000651) test_id_line_data_class: .: (0.000466) test_id_line_entry_name: .: (0.000490) test_id_line_sequence_length: .: (0.000607) test_kw: .: (0.000482) test_oc: .: (0.000457) test_oh: .: (0.006857) test_os: .: (0.000667) test_os_access: .: (0.000772) test_os_access2: .: (0.000598) test_ox: .: (0.000532) test_protein_name: .: (0.000710) test_protein_name_after_calling_de: .: (0.000523) test_ref: .: (0.002674) test_seq: .: (0.001140) test_sequence_length: .: (0.006249) test_sq: .: (0.000875) test_sq_crc64: .: (0.000558) test_sq_len: .: (0.000515) test_sq_mw: .: (0.000739) test_synonyms: .: (0.000627) Bio::TestUniProtKB_P28907: test_ac: .: (0.003203) test_accession: .: (0.003617) test_cc: .: (0.007710) test_cc_alternative_products: .: (0.001954) test_cc_database: .: (0.006342) test_cc_mass_spectrometry: .: (0.002922) test_de: .: (0.003673) test_dr: .: (0.007979) test_dr_with_key: .: (0.007645) test_dr_with_key_empty: .: (0.007701) test_dt: .: (0.007356) test_dt_annotation: .: (0.001501) test_dt_created: .: (0.001470) test_dt_sequence: .: (0.008272) test_entry: .: (0.001461) test_ft: .: (0.002545) test_gene_name: .: (0.007236) test_gene_names: .: (0.001802) test_gn: .: (0.001652) test_gn_old_parser: .: (0.007773) test_gn_uniprot_parser: .: (0.001633) test_id_line: .: (0.001558) test_id_line_data_class: .: (0.008118) test_id_line_entry_name: .: (0.001639) test_id_line_sequence_length: .: (0.001809) test_kw: .: (0.007895) test_oc: .: (0.001752) test_os: .: (0.001644) test_os_access: .: (0.007932) test_os_access2: .: (0.001587) test_ox: .: (0.001763) test_protein_name: .: (0.007917) test_protein_name_after_calling_de: .: (0.001548) test_ref: .: (0.002094) test_seq: .: (0.007645) test_sequence_length: .: (0.001508) test_sq: .: (0.001561) test_sq_crc64: .: (0.008049) test_sq_len: .: (0.001641) test_sq_mw: .: (0.001455) test_synonyms: .: (0.008108) test_synonyms_after_calling_de: .: (0.002010) Bio::TestUniProtKB_P49144: test_ac: .: (0.001026) test_accession: .: (0.000950) test_cc: .: (0.006437) test_cc_alternative_products: .: (0.001936) test_cc_database: .: (0.005470) test_cc_mass_spectrometry: .: (0.009435) test_de: .: (0.009848) test_dr: .: (0.001594) test_dr_with_key: .: (0.001321) test_dr_with_key_empty: .: (0.009637) test_dt: .: (0.000886) test_dt_annotation: .: (0.001018) test_dt_created: .: (0.004796) test_dt_sequence: .: (0.001162) test_entry: .: (0.000764) test_ft: .: (0.014330) test_gene_name: .: (0.000946) test_gene_names: .: (0.005718) test_gn: .: (0.007628) test_gn_old_parser: .: (0.001157) test_gn_uniprot_parser: .: (0.000891) test_id_line: .: (0.005157) test_id_line_data_class: .: (0.001022) test_id_line_entry_name: .: (0.000775) test_id_line_sequence_length: .: (0.005435) test_kw: .: (0.007596) test_oc: .: (0.000872) test_os: .: (0.000514) test_os_access: .: (0.000642) test_os_access2: .: (0.000470) test_ox: .: (0.000728) test_protein_name: .: (0.000756) test_protein_name_after_calling_de: .: (0.000555) test_ref: .: (0.000768) test_seq: .: (0.000606) test_sequence_length: .: (0.000678) test_sq: .: (0.000508) test_sq_crc64: .: (0.020918) test_sq_len: .: (0.000760) test_sq_mw: .: (0.000553) test_synonyms: .: (0.000802) test_synonyms_after_calling_de: .: (0.000658) Bio::TestUniProtKB_Ref: test_RA: .: (0.000707) test_RC: .: (0.000190) test_RG: .: (0.000155) test_RL: .: (0.000150) test_RN: .: (0.000308) test_RP: .: (0.000153) test_RT: .: (0.000138) test_RX: .: (0.000146) test_ref: .: (0.000152) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000406) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000366) test_alternative_products_with_ft: .: (0.000588) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.020795) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000316) test_RL_lines: .: (0.000107) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000409) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000156) test_RG_line: .: (0.000083) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000397) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000200) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000165) test_RL_line: .: (0.000086) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000751) test_RP_line: .: (0.000182) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000104) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000196) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000130) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000104) test_CC_interaction_isoform: .: (0.000101) test_CC_interaction_no_gene_name: .: (0.000096) test_CC_interaction_self_association: .: (0.000130) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000180) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000179) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000232) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000190) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000259) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000185) test_DT_line: .: (0.000102) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.031291) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000711) test_CC_web_resource: .: (0.000058) test_FT_VER_SEQ: .: (0.000121) test_OH_line_exception: .: (0.000233) test_OH_lines: .: (0.000413) Bio::TestUtils: test_centreOfGravity: .: (0.000381) test_dihedral_angle: .: (0.000226) test_distance: .: (0.000220) test_geometricCentre: .: (0.000143) test_rad2deg: .: (0.000088) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000377) test_dijkstra_on_weighted_graph: .: (0.000086) Finished in 15.061329167 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 261.66 tests/s, 1434.20 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.5-1_arm64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3036177/tmp/hooks/B01_cleanup finished 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/3036177 and its subdirectories I: Current time: Fri Feb 7 10:59:03 +14 2025 I: pbuilder-time-stamp: 1738875543