I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 6 12:16:49 +14 2025 I: pbuilder-time-stamp: 1751753809 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ruby-bio_2.0.5-1.dsc] I: copying [./ruby-bio_2.0.5.orig.tar.gz] I: copying [./ruby-bio_2.0.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Mar 3 13:24:05 2024 gpgv: using RSA key FEDEC1CB337BCF509F43C2243914B532F4DFBE99 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.5-1.dsc: no acceptable signature found dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.5 dpkg-source: info: unpacking ruby-bio_2.0.5.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable_tests_using_chi2.patch dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/761875/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. 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 Jul 5 22:16 /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/761875/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/761875/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=e637f8c0bbf743559e69f8f1da5f058e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=761875 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.YvZYz0iV/pbuilderrc_Rmnd --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.YvZYz0iV/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jul 4 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/761875/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19719 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libb-hooks-op-check-perl{a} libbsd0{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap-2.5-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato gnupg-utils gpg-wks-client libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc strace unzip wget zip 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 43.6 MB of archives. After unpacking 165 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-4 [95.7 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.43-7 [119 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.43-7 [363 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.43-7 [701 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.43-7 [523 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.43-7 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.43-7 [250 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.43-7 [375 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 92 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.23.7 [1068 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-46 [73.3 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 120 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 122 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 gem2deb-test-runner amd64 2.2.3 [17.8 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 ruby3.1-dev amd64 3.1.2-8.3 [1001 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 ruby-all-dev amd64 1:3.1+nmu1 [5672 B] Get: 128 http://deb.debian.org/debian unstable/main amd64 gem2deb amd64 2.2.3 [47.8 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 ruby-libxml amd64 3.2.4-2+b2 [83.5 kB] Fetched 43.6 MB in 4s (10.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19719 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21027 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sgml-base. 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Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../078-perl-openssl-defaults_7+b2_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:amd64. Preparing to unpack .../079-libnet-ssleay-perl_1.94-1+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.94-1+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../080-libio-socket-ssl-perl_2.085-1_all.deb ... Unpacking libio-socket-ssl-perl (2.085-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../081-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../082-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. 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Selecting previously unselected package sgml-data. Preparing to unpack .../090-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../091-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../092-libosp5_1.5.2-15_amd64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../093-opensp_1.5.2-15_amd64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../094-docbook-to-man_1%3a2.0.0-46_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-46) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../095-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../096-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../097-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../098-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../099-ruby-sdbm_1.0.0-5+b4_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../100-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../101-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../102-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../103-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../104-libruby3.1t64_3.1.2-8.3_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../105-ruby3.1_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../106-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../107-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../108-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../109-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../110-gem2deb-test-runner_2.2.3_amd64.deb ... Unpacking gem2deb-test-runner (2.2.3) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../111-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../112-libgmp-dev_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package ruby3.1-dev:amd64. Preparing to unpack .../113-ruby3.1-dev_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1-dev:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby-all-dev:amd64. Preparing to unpack .../114-ruby-all-dev_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:3.1+nmu1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../115-gem2deb_2.2.3_amd64.deb ... Unpacking gem2deb (2.2.3) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../116-ruby-rd_0.6.38-4.1_all.deb ... Unpacking ruby-rd (0.6.38-4.1) ... Selecting previously unselected package rdtool. Preparing to unpack .../117-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:amd64. Preparing to unpack .../118-ruby-libxml_3.2.4-2+b2_amd64.deb ... Unpacking ruby-libxml:amd64 (3.2.4-2+b2) ... Setting up libksba8:amd64 (1.6.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:amd64 (1.6-3.1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-4) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-3) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libosp5 (1.5.2-15) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 5 22:17:16 UTC 2025. Universal Time is now: Sat Jul 5 22:17:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up gnupg-l10n (2.2.43-7) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up liburi-perl (5.28-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.43-7) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.43-7) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.43-7) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.43-7) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.43-7) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gnupg (2.2.43-7) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up devscripts (2.23.7) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up ruby3.1-dev:amd64 (3.1.2-8.3) ... Setting up ruby-libxml:amd64 (3.2.4-2+b2) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-all-dev:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.2.1-1) ... Setting up rdtool (0.6.38-4.1) ... Setting up gem2deb-test-runner (2.2.3) ... Setting up gem2deb (2.2.3) ... Processing triggers for libc-bin (2.38-12) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-46) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/761875/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/761875/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 amd64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/brite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/compound.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/drug.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/expression.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genes.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/genome.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/glycan.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/keggtab.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/kgml.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/module.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/orthology.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/kegg/reaction.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/lasergene.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/litdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/medline.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nbrf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/newick.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/nexus.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/atom.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chain.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/chemicalcomponent.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/model.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/residue.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb/utils.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/pdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/prosite.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/rebase.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/abif.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/sanger_chromatogram/scf.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/soft.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db/transfac.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/db.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/feature.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/das.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fastacmd.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/fetch.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/autodetection.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/bdb.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/buffer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/index.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/indexer.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile/splitter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/flatfile.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/hinv.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/ncbirest.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/pubmed.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/registry.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/io/togows.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/location.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/map.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/pathway.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/reference.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/aa.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/adapter.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/common.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/compat.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/dblink.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/format_raw.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/generic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/na.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/quality_score.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence/sequence_masker.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/sequence.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree/output.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/tree.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/buried.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.5.gemspec /usr/bin/ruby3.1 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.1 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.5/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.1.0:/var/lib/gems/3.1.0:/usr/local/lib/ruby/gems/3.1.0:/usr/lib/ruby/gems/3.1.0:/usr/lib/x86_64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000389) test_dbs: .: (0.000140) test_go_ids: .: (0.000144) test_go_terms: .: (0.000254) test_parser: .: (0.000293) test_set_date: .: (0.000134) test_set_desc: .: (0.000287) test_to_str: .: (0.000261) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000700) test_mktmpdir_without_block: .: (0.000524) test_remove_entry_secure: .: (0.000369) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.003936) test_call_command_fork: .: (0.000249) test_call_command_open3: .: (0.002946) test_call_command_popen: .: (0.002765) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.002774) test_call_command_fork: .: (0.000176) test_call_command_open3: .: (0.002602) test_call_command_popen: .: (0.002408) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.002517) test_call_command_fork: .: (0.000181) test_call_command_open3: .: (0.002415) test_call_command_popen: .: (0.002948) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.001872) test_call_command_fork_chdir: .: (0.000333) test_call_command_popen_chdir: .: (0.001415) test_query_command_chdir: .: (0.001574) test_query_command_fork_chdir: .: (0.000335) test_query_command_popen_chdir: .: (0.001576) Bio::FuncTestCommandQuery: test_query_command: .: (0.006717) test_query_command_fork: .: (0.001879) test_query_command_open3: .: (0.006102) test_query_command_popen: .: (0.005854) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000716) test_initialize: .: (0.000345) test_path: .: (0.000293) test_path_after_close: .: (0.000870) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.008717) test_output_fasta: .: (0.004913) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000288) test_accession: .: (0.000173) test_accessions: .: (0.000173) test_comment: .: (0.000154) test_common_name: .: (0.000170) test_definition: .: (0.000201) test_features: .: (0.000329) test_gi: .: (0.000170) test_keywords: .: (0.000166) test_locus: .: (0.000129) test_nid: .: (0.000171) test_organism: .: (0.000185) test_origin: .: (0.000161) test_references: .: (0.000530) test_segment: .: (0.000173) test_source: .: (0.000241) test_taxonomy: .: (0.000158) test_version: .: (0.000189) test_versions: .: (0.000169) Bio::TestAA: test_13: .: (0.000203) test_1n: .: (0.000118) test_name2one: .: (0.000198) test_name2three: .: (0.000160) test_one2name: .: (0.000288) test_one2three: .: (0.000107) test_three2name: .: (0.000135) test_three2one: .: (0.000164) test_to_1_1: .: (0.000113) test_to_1_3: .: (0.000145) test_to_1_name: .: (0.000146) test_to_3_1: .: (0.000117) test_to_3_3: .: (0.000124) test_to_3_name: .: (0.000144) test_to_re: .: (0.000199) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000197) Bio::TestAAindex: test_api: .: (0.000166) test_auto_aax1: .: (0.000191) test_auto_aax2: .: (0.000357) Bio::TestAAindex1: test_author: .: (0.000233) test_comment: .: (0.000146) test_correlation_coefficient: .: (0.000275) test_dblinks: .: (0.000145) test_definition: .: (0.000139) test_entry_id: .: (0.000133) test_index: .: (0.000193) test_journal: .: (0.000161) test_title: .: (0.000315) Bio::TestAAindex2: test_access_A_R: .: (0.000753) test_access_R_A: .: (0.000507) test_author: .: (0.000220) test_cols: .: (0.000338) test_comment: .: (0.000220) test_dblinks: .: (0.000206) test_definition: .: (0.000211) test_entry_id: .: (0.000218) test_journal: .: (0.000243) test_matrix: .: (0.000534) test_matrix_1_2: .: (0.000517) test_matrix_2_2: .: (0.004068) test_matrix_A_R: .: (0.000513) test_matrix_R_A: .: (0.000832) test_matrix_determinant: .: (0.002665) test_matrix_rank: .: (0.002757) test_matrix_transpose: .: (0.000679) test_rows: .: (0.000211) test_title: .: (0.000221) Bio::TestAAindexConstant: test_delimiter: .: (0.000201) test_tagsize: .: (0.000116) Bio::TestAbif: test_complement: .: (0.008486) test_seq: .: (0.007521) test_to_biosequence: .: (0.008151) Bio::TestActsLikeMap: test_mixin: .: (0.000268) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000268) Bio::TestActsLikeMarker: test_mixin: .: (0.000322) Bio::TestAlignment: test_add_seq_no_key: .: (0.000306) test_add_seq_using_seq_with_aaseq_method: .: (0.000161) test_add_seq_using_seq_with_definition_method: .: (0.000136) test_add_seq_using_seq_with_entry_id_method: .: (0.000167) test_add_seq_using_seq_with_naseq_method: .: (0.000154) test_add_seq_using_seq_with_seq_method: .: (0.000150) test_consensus_iupac_gap_modes: .: (0.000397) test_consensus_iupac_missing_char: .: (0.000175) test_consensus_iupac_missing_char_option: .: (0.000405) test_consensus_iupac_no_gaps: .: (0.000212) test_consensus_iupac_of_ambiguous_bases: .: (0.000318) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.003583) test_consensus_opt_gap_mode: .: (0.000791) test_consensus_opt_missing_char: .: (0.000221) test_consensus_string_no_gaps: .: (0.000215) test_consensus_threshold_four_sequences: .: (0.000289) test_consensus_threshold_two_sequences: .: (0.000291) test_convert_match: .: (0.000437) test_convert_unmatch: .: (0.000164) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000159) test_convert_unmatch_different_match_char: .: (0.000157) test_convert_unmatch_multiple_sequences: .: (0.000198) test_default_gap_char: .: (0.000121) test_default_gap_regexp_matches_default_gap_char: .: (0.000133) test_default_missing_char: .: (0.000134) test_each_site_equal_length: .: (0.000178) test_each_site_unequal_length: .: (0.000412) test_equals: .: (0.000234) test_match_line_protein: .: (0.000372) test_normalizebang_extends_sequences_with_gaps: .: (0.000164) test_seq_length_is_max_seq_length: .: (0.000148) test_seq_length_when_one_sequence: .: (0.000113) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000110) test_seqclass_when_seqclass_set: .: (0.000131) test_seqclass_when_sequence_used: .: (0.000124) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000124) test_set_and_get_gap_char: .: (0.000115) test_store_cannot_override_key: .: (0.000132) test_store_with_default_keys_and_user_defined_keys: .: (0.000141) test_store_with_nil_key_uses_next_number_for_key: .: (0.000360) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000217) test_alignment_concat: .: (0.000167) test_alignment_length: .: (0.000124) test_alignment_lstrip!: .: (0.000205) test_alignment_lstrip_nil: .: (0.000155) test_alignment_normalize!: .: (0.000126) test_alignment_rstrip!: .: (0.000202) test_alignment_rstrip_nil: .: (0.000144) test_alignment_site: .: (0.000176) test_alignment_slice: .: (0.000132) test_alignment_strip!: .: (0.000228) test_alignment_strip_nil: .: (0.000164) test_alignment_subseq: .: (0.000271) test_alignment_window: .: (0.000111) test_collect_each_site: .: (0.000152) test_consensus_each_site_default: .: (0.000195) test_consensus_each_site_gap_mode_1: .: (0.002613) test_consensus_each_site_gap_mode_minus1: .: (0.000180) test_consensus_iupac: .: (0.000307) test_consensus_string_default: .: (0.000168) test_consensus_string_half: .: (0.000174) test_convert_match: .: (0.000158) test_convert_unmatch: .: (0.000147) test_each_seq: .: (0.000152) test_each_site: .: (0.000237) test_each_site_step: .: (0.000182) test_each_window: .: (0.000198) test_match_line: .: (0.000690) test_match_line_amino: .: (0.001265) test_match_line_nuc: .: (0.000195) test_private_alignment_site: .: (0.000134) test_remove_all_gaps!: .: (0.000156) test_seqclass: .: (0.000132) test_seqclass=: .: (0.000163) test_seqclass_default: .: (0.000120) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002884) test_determine_seq_method: .: (0.001322) test_entries: .: (0.000307) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000265) test_avoid_same_name_numbering: .: (0.000161) test_clustal_have_same_name_true: .: (0.000143) test_have_same_name_false: .: (0.000144) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000208) test_gap_char_default: .: (0.000141) test_gap_char_never_nil: .: (0.000304) test_gap_regexp: .: (0.000126) test_gap_regexp=: .: (0.000127) test_gap_regexp_never_nil: .: (0.000150) test_get_all_property_default: .: (0.000119) test_get_all_property_nodefault: .: (0.000142) test_is_gap_default_false: .: (0.000142) test_is_gap_default_true: .: (0.000163) test_is_gap_nodefault_false: .: (0.000156) test_is_gap_nodefault_true: .: (0.000154) test_missing_char=: .: (0.000135) test_missing_char_default: .: (0.000146) test_missing_char_never_nil: .: (0.000109) test_seqclass=: .: (0.000078) test_seqclass_default: .: (0.000161) test_seqclass_never_nil: .: (0.000065) test_set_all_property: .: (0.000169) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000472) test_consensus_string_50percent: .: (0.000135) test_consensus_string_50percent_nil: .: (0.000131) test_consensus_string_default: .: (0.000117) test_consensus_string_default_nil: .: (0.000128) test_has_gap_false: .: (0.000127) test_has_gap_true: .: (0.000121) test_match_line_amino_100percent: .: (0.000164) test_match_line_amino_missing: .: (0.000359) test_match_line_amino_strong: .: (0.000149) test_match_line_amino_weak: .: (0.000166) test_match_line_nuc_100percent: .: (0.000143) test_match_line_nuc_missing: .: (0.000145) test_remove_gaps!: .: (0.000140) test_remove_gaps_bang_not_removed: .: (0.000116) Bio::TestAtomFinder: test_atoms: .: (0.039580) test_each_atom: .: (0.010435) test_find_atom: .: (0.000241) Bio::TestBioFastaDefline: test_acc_version: .: (0.000412) test_accession: .: (0.000436) test_accessions: .: (0.000336) test_description: .: (0.000598) test_descriptions: .: (0.000293) test_entry_id: .: (0.000260) test_get: .: (0.000314) test_get_all_by_type: .: (0.000503) test_get_by_type: .: (0.000268) test_gi: .: (0.000251) test_id_strings: .: (0.000509) test_locus: .: (0.000748) test_method_missing: .: (0.000312) test_to_s: .: (0.000293) test_words: .: (0.000980) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000701) test_goid2term: .: (0.000349) test_parse_goids: .: (0.000328) Bio::TestBioGenBank: test_basecount: .: (0.000713) test_circular: .: (0.000313) test_classification: .: (0.000296) test_date: .: (0.000253) test_date_modified: .: (0.000673) test_division: .: (0.000251) test_each_cds_feature: .: (0.000912) test_each_cds_qualifiers: .: (0.000582) test_each_gene: .: (0.000585) test_entry_id: .: (0.000291) test_length: .: (0.000234) test_locus_circular: .: (0.000279) test_locus_class: .: (0.000270) test_locus_date: .: (0.000267) test_locus_division: .: (0.000263) test_locus_entry_id: .: (0.000251) test_locus_length: .: (0.000262) test_locus_natype: .: (0.000491) test_locus_strand: .: (0.000279) test_natype: .: (0.000227) test_seq: .: (0.000295) test_seq_len: .: (0.000259) test_strand: .: (0.000246) test_strandedness: .: (0.000285) test_to_biosequence: .: (0.001738) Bio::TestBioGenPept: test_circular: .: (0.000384) test_date: .: (0.000217) test_dbsource: .: (0.000204) test_division: .: (0.000210) test_entry_id: .: (0.000209) test_length: .: (0.000216) test_locus: .: (0.000239) test_seq: .: (0.000266) test_seq_len: .: (0.000260) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000417) test_aaseq: .: (0.000496) test_chromosome: .: (0.000237) test_codon_usage: .: (0.000331) test_cu_list: .: (0.000207) test_dblinks_as_hash: .: (0.000253) test_dblinks_as_strings: .: (0.000225) test_definition: .: (0.000250) test_division: .: (0.000245) test_eclinks: .: (0.000669) test_entry: .: (0.000216) test_entry_id: .: (0.000212) test_gbposition: .: (0.000238) test_gene: .: (0.000251) test_genes: .: (0.000265) test_keggclass: .: (0.000306) test_keggclasses: .: (0.000286) test_locations: .: (0.000636) test_motifs_as_hash: .: (0.000310) test_motifs_as_strings: .: (0.000220) test_name: .: (0.000226) test_names_as_array: .: (0.000243) test_new: .: (0.000232) test_ntlen: .: (0.000310) test_ntseq: .: (0.000315) test_organism: .: (0.000252) test_orthologs_as_hash: .: (0.000235) test_orthologs_as_strings: .: (0.000274) test_pathway: .: (0.000257) test_pathway_after_pathways_as_strings: .: (0.000294) test_pathway_before_pathways_as_strings: .: (0.000313) test_pathways_as_hash: .: (0.000269) test_pathways_as_strings: .: (0.000209) test_position: .: (0.000281) test_structure: .: (0.000238) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001014) test_comment: .: (0.000385) test_data_source: .: (0.000370) test_definition: .: (0.000362) test_disease: .: (0.000369) test_entry_id: .: (0.000352) test_lineage: .: (0.000397) test_nalen: .: (0.000344) test_name: .: (0.000348) test_new: .: (0.000362) test_num_gene: .: (0.000363) test_num_rna: .: (0.000382) test_original_databases: .: (0.000340) test_original_db: .: (0.000346) test_plasmids: .: (0.000336) test_references: .: (0.001963) test_statistics: .: (0.000396) test_taxid: .: (0.000397) test_taxonomy: .: (0.000367) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000414) test_comment: .: (0.000292) test_data_source: .: (0.000259) test_definition: .: (0.000290) test_disease: .: (0.000280) test_entry_id: .: (0.000227) test_lineage: .: (0.000302) test_nalen: .: (0.000285) test_name: .: (0.000229) test_new: .: (0.000250) test_num_gene: .: (0.000265) test_num_rna: .: (0.000214) test_original_databases: .: (0.000249) test_original_db: .: (0.000260) test_plasmids: .: (0.000323) test_references: .: (0.000349) test_statistics: .: (0.000227) test_taxid: .: (0.000326) test_taxonomy: .: (0.000303) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000385) test_compounds_as_strings: .: (0.000206) test_dblinks_as_hash: .: (0.000229) test_dblinks_as_strings: .: (0.000190) test_description: .: (0.000251) test_diseases_as_hash: .: (0.000212) test_diseases_as_strings: .: (0.000263) test_entry_id: .: (0.000258) test_enzymes_as_strings: .: (0.000288) test_genes_as_hash: .: (0.000189) test_genes_as_strings: .: (0.000217) test_keggclass: .: (0.000216) test_ko_pathway: .: (0.000247) test_modules_as_hash: .: (0.000227) test_modules_as_strings: .: (0.000279) test_name: .: (0.000205) test_new: .: (0.000238) test_organism: .: (0.000230) test_orthologs_as_hash: .: (0.000230) test_orthologs_as_strings: .: (0.000208) test_pathways_as_hash: .: (0.000300) test_pathways_as_strings: .: (0.000193) test_reactions_as_hash: .: (0.000258) test_reactions_as_strings: .: (0.000206) test_references: .: (0.000245) test_rel_pathways_as_hash: .: (0.000262) test_rel_pathways_as_strings: .: (0.000304) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000488) test_compounds_as_strings: .: (0.000299) test_dblinks_as_hash: .: (0.000219) test_dblinks_as_strings: .: (0.000243) test_description: .: (0.000222) test_diseases_as_hash: .: (0.000269) test_diseases_as_strings: .: (0.000254) test_entry_id: .: (0.000285) test_enzymes_as_strings: .: (0.000234) test_genes_as_hash: .: (0.000269) test_genes_as_strings: .: (0.000261) test_keggclass: .: (0.000265) test_ko_pathway: .: (0.000242) test_modules_as_hash: .: (0.000257) test_modules_as_strings: .: (0.000215) test_name: .: (0.000234) test_new: .: (0.000281) test_organism: .: (0.000223) test_orthologs_as_hash: .: (0.000268) test_orthologs_as_strings: .: (0.000205) test_pathways_as_hash: .: (0.000264) test_pathways_as_strings: .: (0.000208) test_reactions_as_hash: .: (0.000251) test_reactions_as_strings: .: (0.000218) test_references: .: (0.000241) test_rel_pathways_as_hash: .: (0.000309) test_rel_pathways_as_strings: .: (0.000262) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000331) test_compounds_as_strings: .: (0.000230) test_dblinks_as_hash: .: (0.000227) test_dblinks_as_strings: .: (0.000192) test_description: .: (0.000239) test_diseases_as_hash: .: (0.000210) test_diseases_as_strings: .: (0.000267) test_entry_id: .: (0.000246) test_enzymes_as_strings: .: (0.000217) test_genes_as_hash: .: (0.000186) test_genes_as_strings: .: (0.000226) test_keggclass: .: (0.000222) test_ko_pathway: .: (0.000252) test_modules_as_hash: .: (0.000221) test_modules_as_strings: .: (0.000260) test_name: .: (0.000264) test_new: .: (0.000235) test_organism: .: (0.000256) test_orthologs_as_hash: .: (0.000317) test_orthologs_as_strings: .: (0.000209) test_pathways_as_hash: .: (0.000230) test_pathways_as_strings: .: (0.000195) test_reactions_as_hash: .: (0.000224) test_reactions_as_strings: .: (0.000206) test_references: .: (0.000256) test_rel_pathways_as_hash: .: (0.000235) test_rel_pathways_as_strings: .: (0.000262) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000350) test_compounds_as_strings: .: (0.000232) test_dblinks_as_hash: .: (0.000282) test_dblinks_as_strings: .: (0.000221) test_description: .: (0.000372) test_diseases_as_hash: .: (0.000263) test_diseases_as_strings: .: (0.000225) test_entry_id: .: (0.000267) test_enzymes_as_strings: .: (0.000215) test_genes_as_hash: .: (0.000260) test_genes_as_strings: .: (0.000257) test_keggclass: .: (0.000321) test_ko_pathway: .: (0.000224) test_modules_as_hash: .: (0.000267) test_modules_as_strings: .: (0.000286) test_name: .: (0.000297) test_new: .: (0.000216) test_organism: .: (0.000262) test_orthologs_as_hash: .: (0.000223) test_orthologs_as_strings: .: (0.000263) test_pathways_as_hash: .: (0.000229) test_pathways_as_strings: .: (0.000247) test_reactions_as_hash: .: (0.000251) test_reactions_as_strings: .: (0.000251) test_references: .: (0.000705) test_rel_pathways_as_hash: .: (0.000290) test_rel_pathways_as_strings: .: (0.000290) Bio::TestBioKeggDRUG: test_activity: .: (0.000404) test_comment: .: (0.000277) test_dblinks_as_hash: .: (0.000327) test_dblinks_as_strings: .: (0.000280) test_entry_id: .: (0.000299) test_formula: .: (0.000263) test_kcf: .: (0.000258) test_mass: .: (0.000259) test_name: .: (0.000293) test_names: .: (0.000284) test_pathways_as_hash: .: (0.000261) test_pathways_as_strings: .: (0.000262) test_products: .: (0.000270) test_remark: .: (0.000284) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000401) test_composition: .: (0.000299) test_compounds: .: (0.000236) test_dblinks_as_hash: .: (0.000440) test_dblinks_as_strings: .: (0.000274) test_entry_id: .: (0.000264) test_enzymes: .: (0.000278) test_kcf: .: (0.000216) test_keggclass: .: (0.000264) test_mass: .: (0.000246) test_name: .: (0.000269) test_orthologs_as_hash: .: (0.000369) test_orthologs_as_strings: .: (0.000256) test_pathways_as_hash: .: (0.000225) test_pathways_as_strings: .: (0.000191) test_reactions: .: (0.000181) test_references: .: (0.000232) test_remark: .: (0.000226) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000273) test_composition: .: (0.000161) test_compounds: .: (0.000169) test_dblinks_as_hash: .: (0.000164) test_dblinks_as_strings: .: (0.000165) test_entry_id: .: (0.000146) test_enzymes: .: (0.000164) test_kcf: .: (0.000125) test_keggclass: .: (0.000159) test_mass: .: (0.000141) test_name: .: (0.000163) test_orthologs_as_hash: .: (0.000271) test_orthologs_as_strings: .: (0.000255) test_pathways_as_hash: .: (0.000226) test_pathways_as_strings: .: (0.000261) test_reactions: .: (0.000197) test_references: .: (0.000223) test_remark: .: (0.000204) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000502) test_compounds_as_strings: .: (0.000321) test_dblinks_as_hash: .: (0.000280) test_dblinks_as_strings: .: (0.000265) test_description: .: (0.000252) test_diseases_as_hash: .: (0.000311) test_diseases_as_strings: .: (0.000275) test_entry_id: .: (0.000257) test_enzymes_as_strings: .: (0.000260) test_genes_as_hash: .: (0.000234) test_genes_as_strings: .: (0.000262) test_keggclass: .: (0.000253) test_ko_pathway: .: (0.000281) test_modules_as_hash: .: (0.000342) test_modules_as_strings: .: (0.000289) test_name: .: (0.000258) test_new: .: (0.000290) test_organism: .: (0.000248) test_orthologs_as_hash: .: (0.000261) test_orthologs_as_strings: .: (0.000233) test_pathways_as_hash: .: (0.000273) test_pathways_as_strings: .: (0.000269) test_reactions_as_hash: .: (0.004442) test_reactions_as_strings: .: (0.000354) test_references: .: (0.000464) test_rel_pathways_as_hash: .: (0.000351) test_rel_pathways_as_strings: .: (0.000551) Bio::TestBioLITDB: test_author: .: (0.000327) test_entry_id: .: (0.000232) test_field: .: (0.000207) test_journal: .: (0.000207) test_keyword: .: (0.000244) test_reference: .: (0.000357) test_title: .: (0.000467) test_volume: .: (0.000320) Bio::TestBioNBRF: test_aalen: .: (0.000254) test_aaseq: .: (0.000120) test_entry: .: (0.000104) test_length: .: (0.000111) test_nalen: .: (0.000160) test_naseq: .: (0.000134) test_seq: .: (0.000106) test_seq_class: .: (0.000104) test_to_nbrf: .: (0.000116) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000483) test_to_newick_format_leaf: .: (0.000223) test_to_newick_format_leaf_NHX: .: (0.000129) Bio::TestBl2seqReport: test_db_len: .: (0.000538) test_db_num: .: (0.000334) test_new: .: (0.000363) test_undefed_methods: .: (0.001179) test_undefed_methods_for_iteration: .: (0.000745) Bio::TestBl2seqReportConstants: test_rs: .: (0.000184) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000369) test_hits: .: (0.000294) Bio::TestBlast: test_blast_reports_format0: .: (0.004927) test_blast_reports_format0_with_block: .: (0.000641) test_blast_reports_format7: .: (0.010836) test_blast_reports_format7_with_block: .: (0.009333) test_blast_reports_format7_with_parser: .: (0.009207) test_blast_reports_format7_with_parser_with_block: .: (0.015130) test_blast_reports_format8: .: (0.002575) test_blast_reports_format8_with_block: .: (0.000449) test_blast_reports_format8_with_parser: .: (0.002139) test_blast_reports_format8_with_parser_with_block: .: (0.000273) test_blast_reports_xml: .: (0.038714) test_blast_reports_xml_with_block: .: (0.010331) test_blastll: .: (0.000201) test_db: .: (0.000180) test_exec_genomenet: .: (0.000169) test_exec_local: .: (0.000376) test_exec_ncbi: .: (0.000165) test_filter: .: (0.000180) test_format: .: (0.000190) test_make_command_line: .: (0.000435) test_make_command_line_2: .: (0.000337) test_matrix: .: (0.000179) test_new: .: (0.000385) test_new_opt_string: .: (0.000270) test_option: .: (0.000198) test_option_set: .: (0.000283) test_option_set_m0: .: (0.000239) test_options: .: (0.000191) test_output: .: (0.000198) test_parse_result: .: (0.009031) test_parser: .: (0.000192) test_program: .: (0.000190) test_query: .: (0.000167) test_self_local: .: (0.000298) test_self_remote: .: (0.001575) test_server: .: (0.000220) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000377) test_delete: .: (0.000299) test_equal_equal: .: (0.000398) test_get: .: (0.000309) test_make_command_line_options: .: (0.000298) test_normalize!: .: (0.000209) test_parse: .: (0.000217) test_set: .: (0.000469) Bio::TestBlastReport: test_db: .: (0.009092) test_db_len: .: (0.008996) test_db_num: .: (0.010475) test_each_hit: .: (0.009416) test_each_iteration: .: (0.009310) test_eff_space: .: (0.009001) test_entrez_query: .: (0.008896) test_entropy: .: (0.008679) test_expect: .: (0.009952) test_filter: .: (0.009291) test_gap_extend: .: (0.009123) test_gap_open: .: (0.008869) test_hits: .: (0.008745) test_hsp_len: .: (0.008751) test_inclusion: .: (0.010128) test_iterations: .: (0.009267) test_kappa: .: (0.009142) test_lambda: .: (0.008910) test_matrix: .: (0.008779) test_message: .: (0.008928) test_parameters: .: (0.010686) test_pattern: .: (0.009914) test_program: .: (0.009427) test_query_def: .: (0.008933) test_query_id: .: (0.008641) test_query_len: .: (0.008836) test_reference: .: (0.010014) test_sc_match: .: (0.009305) test_sc_mismatch: .: (0.008906) test_statistics: .: (0.008838) test_version: .: (0.008805) Bio::TestBlastReportDefault: test_db: .: (0.000583) test_db_len: .: (0.000408) test_db_num: .: (0.000378) test_each_hit: .: (0.000392) test_each_iteration: .: (0.000351) test_eff_space: .: (0.000441) test_entropy: .: (0.000514) test_expect: .: (0.000453) test_gap_extend: .: (0.000411) test_gap_open: .: (0.000416) test_gapped_entropy: .: (0.000382) test_gapped_kappa: .: (0.000382) test_gapped_lambda: .: (0.000375) test_hits: .: (0.000375) test_iterations: .: (0.000420) test_kappa: .: (0.000399) test_lambda: .: (0.000383) test_matrix: .: (0.000421) test_message: .: (0.000391) test_pattern: .: (0.000353) test_program: .: (0.000361) test_query_def: .: (0.000385) test_query_len: .: (0.000370) test_reference: .: (0.000466) test_sc_match: .: (0.000449) test_sc_mismatch: .: (0.000420) test_version: .: (0.000358) Bio::TestBlastReportHit: test_Hit_accession: .: (0.010552) test_Hit_bit_score: .: (0.009582) test_Hit_definition: .: (0.009461) test_Hit_evalue: .: (0.009485) test_Hit_hit_id: .: (0.009251) test_Hit_hsps: .: (0.009553) test_Hit_identity: .: (0.010417) test_Hit_lap_at: .: (0.009110) test_Hit_len: .: (0.008931) test_Hit_midline: .: (0.008830) test_Hit_num: .: (0.008750) test_Hit_overlap: .: (0.008819) test_Hit_query_def: .: (0.010027) test_Hit_query_end: .: (0.009204) test_Hit_query_id: .: (0.008766) test_Hit_query_len: .: (0.008849) test_Hit_query_seq: .: (0.008769) test_Hit_query_start: .: (0.009736) test_Hit_taeget_def: .: (0.009272) test_Hit_target_end: .: (0.008982) test_Hit_target_id: .: (0.008879) test_Hit_target_len: .: (0.008928) test_Hit_target_seq: .: (0.008801) test_Hit_target_start: .: (0.009886) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000635) test_Hit_definition: .: (0.000414) test_Hit_evalue: .: (0.000412) test_Hit_hsps: .: (0.000362) test_Hit_identity: .: (0.000387) test_Hit_lap_at: .: (0.000503) test_Hit_len: .: (0.000386) test_Hit_midline: .: (0.000616) test_Hit_overlap: .: (0.000392) test_Hit_query_end: .: (0.000483) test_Hit_query_seq: .: (0.000482) test_Hit_query_start: .: (0.000467) test_Hit_taeget_def: .: (0.000376) test_Hit_target_end: .: (0.000600) test_Hit_target_id: .: (0.000383) test_Hit_target_len: .: (0.000377) test_Hit_target_seq: .: (0.000475) test_Hit_target_start: .: (0.000457) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.025987) test_Hit_bit_score: .: (0.027936) test_Hit_definition: .: (0.025457) test_Hit_evalue: .: (0.027310) test_Hit_hit_id: .: (0.025752) test_Hit_hsps: .: (0.028471) test_Hit_identity: .: (0.026864) test_Hit_lap_at: .: (0.026706) test_Hit_len: .: (0.027034) test_Hit_midline: .: (0.025972) test_Hit_num: .: (0.027405) test_Hit_overlap: .: (0.025850) test_Hit_query_def: .: (0.027291) test_Hit_query_end: .: (0.025916) test_Hit_query_id: .: (0.027670) test_Hit_query_len: .: (0.026992) test_Hit_query_seq: .: (0.026451) test_Hit_query_start: .: (0.027358) test_Hit_taeget_def: .: (0.026193) test_Hit_target_end: .: (0.027877) test_Hit_target_id: .: (0.025924) test_Hit_target_len: .: (0.027406) test_Hit_target_seq: .: (0.025704) test_Hit_target_start: .: (0.027338) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.027163) test_Hit_bit_score: .: (0.026126) test_Hit_definition: .: (0.027273) test_Hit_evalue: .: (0.025825) test_Hit_hit_id: .: (0.027238) test_Hit_hsps: .: (0.025565) test_Hit_identity: .: (0.027323) test_Hit_lap_at: .: (0.027252) test_Hit_len: .: (0.026817) test_Hit_midline: .: (0.027631) test_Hit_num: .: (0.025989) test_Hit_overlap: .: (0.027717) test_Hit_query_def: .: (0.025979) test_Hit_query_end: .: (0.027521) test_Hit_query_id: .: (0.026830) test_Hit_query_len: .: (0.026603) test_Hit_query_seq: .: (0.028091) test_Hit_query_start: .: (0.027670) test_Hit_taeget_def: .: (0.028131) test_Hit_target_end: .: (0.026111) test_Hit_target_id: .: (0.028167) test_Hit_target_len: .: (0.027327) test_Hit_target_seq: .: (0.027834) test_Hit_target_start: .: (0.027320) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.009676) test_Hit_bit_score: .: (0.008906) test_Hit_definition: .: (0.009040) test_Hit_evalue: .: (0.008949) test_Hit_hit_id: .: (0.008720) test_Hit_hsps: .: (0.010470) test_Hit_identity: .: (0.009361) test_Hit_lap_at: .: (0.008796) test_Hit_len: .: (0.008997) test_Hit_midline: .: (0.009080) test_Hit_num: .: (0.009924) test_Hit_overlap: .: (0.009317) test_Hit_query_def: .: (0.009173) test_Hit_query_end: .: (0.008801) test_Hit_query_id: .: (0.008932) test_Hit_query_len: .: (0.008957) test_Hit_query_seq: .: (0.010094) test_Hit_query_start: .: (0.009129) test_Hit_taeget_def: .: (0.008945) test_Hit_target_end: .: (0.008782) test_Hit_target_id: .: (0.008873) test_Hit_target_len: .: (0.010048) test_Hit_target_seq: .: (0.009296) test_Hit_target_start: .: (0.009022) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000392) test_Hit_bit_score: .: (0.000185) test_Hit_definition: .: (0.000172) test_Hit_evalue: .: (0.000177) test_Hit_hit_id: .: (0.000182) test_Hit_hsps: .: (0.000187) test_Hit_identity: .: (0.000193) test_Hit_lap_at: .: (0.000196) test_Hit_len: .: (0.000195) test_Hit_midline: .: (0.000193) test_Hit_num: .: (0.000309) test_Hit_overlap: .: (0.000218) test_Hit_query_def: .: (0.000177) test_Hit_query_end: .: (0.000173) test_Hit_query_id: .: (0.000177) test_Hit_query_len: .: (0.000184) test_Hit_query_seq: .: (0.000193) test_Hit_query_start: .: (0.000192) test_Hit_taeget_def: .: (0.000189) test_Hit_target_end: .: (0.000192) test_Hit_target_id: .: (0.000211) test_Hit_target_len: .: (0.000195) test_Hit_target_seq: .: (0.000194) test_Hit_target_start: .: (0.000193) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.009113) test_Hsp_bit_score: .: (0.008876) test_Hsp_density: .: (0.009885) test_Hsp_evalue: .: (0.009519) test_Hsp_gaps: .: (0.009110) test_Hsp_hit_frame: .: (0.009183) test_Hsp_hit_from: .: (0.009012) test_Hsp_hit_to: .: (0.009152) test_Hsp_hseq: .: (0.010856) test_Hsp_identity: .: (0.009809) test_Hsp_midline: .: (0.009460) test_Hsp_mismatch_count: .: (0.008985) test_Hsp_num: .: (0.008836) test_Hsp_pattern_from: .: (0.008898) test_Hsp_pattern_to: .: (0.010345) test_Hsp_percent_identity: .: (0.009165) test_Hsp_positive: .: (0.008923) test_Hsp_qseq: .: (0.008817) test_Hsp_query_frame: .: (0.008868) test_Hsp_query_from: .: (0.010103) test_Hsp_query_to: .: (0.009158) test_Hsp_score: .: (0.008987) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000600) test_Hsp_bit_score: .: (0.000399) test_Hsp_evalue: .: (0.000428) test_Hsp_gaps: .: (0.000413) test_Hsp_hit_frame: .: (0.000387) test_Hsp_hit_from: .: (0.000483) test_Hsp_hit_to: .: (0.000489) test_Hsp_hseq: .: (0.000473) test_Hsp_identity: .: (0.000376) test_Hsp_midline: .: (0.000619) test_Hsp_percent_identity: .: (0.000382) test_Hsp_positive: .: (0.000381) test_Hsp_qseq: .: (0.000478) test_Hsp_query_frame: .: (0.000381) test_Hsp_query_from: .: (0.000472) test_Hsp_query_to: .: (0.000562) test_Hsp_score: .: (0.000417) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.027592) test_Hsp_bit_score: .: (0.026602) test_Hsp_density: .: (0.028203) test_Hsp_evalue: .: (0.026503) test_Hsp_gaps: .: (0.066633) test_Hsp_hit_frame: .: (0.026658) test_Hsp_hit_from: .: (0.027296) test_Hsp_hit_to: .: (0.025675) test_Hsp_hseq: .: (0.027210) test_Hsp_identity: .: (0.025678) test_Hsp_midline: .: (0.026805) test_Hsp_mismatch_count: .: (0.026165) test_Hsp_num: .: (0.026309) test_Hsp_pattern_from: .: (0.026638) test_Hsp_pattern_to: .: (0.026182) test_Hsp_percent_identity: .: (0.026730) test_Hsp_positive: .: (0.026054) test_Hsp_qseq: .: (0.027253) test_Hsp_query_frame: .: (0.026427) test_Hsp_query_from: .: (0.028121) test_Hsp_query_to: .: (0.026424) test_Hsp_score: .: (0.028318) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.026241) test_Hsp_bit_score: .: (0.027708) test_Hsp_density: .: (0.025278) test_Hsp_evalue: .: (0.027306) test_Hsp_gaps: .: (0.025520) test_Hsp_hit_frame: .: (0.027534) test_Hsp_hit_from: .: (0.025880) test_Hsp_hit_to: .: (0.027538) test_Hsp_hseq: .: (0.025664) test_Hsp_identity: .: (0.027894) test_Hsp_midline: .: (0.027670) test_Hsp_mismatch_count: .: (0.026752) test_Hsp_num: .: (0.026521) test_Hsp_pattern_from: .: (0.026489) test_Hsp_pattern_to: .: (0.027180) test_Hsp_percent_identity: .: (0.026026) test_Hsp_positive: .: (0.027703) test_Hsp_qseq: .: (0.026169) test_Hsp_query_frame: .: (0.027948) test_Hsp_query_from: .: (0.027302) test_Hsp_query_to: .: (0.027612) test_Hsp_score: .: (0.025954) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.010496) test_Hsp_bit_score: .: (0.009268) test_Hsp_density: .: (0.009083) test_Hsp_evalue: .: (0.008959) test_Hsp_gaps: .: (0.008631) test_Hsp_hit_frame: .: (0.008908) test_Hsp_hit_from: .: (0.010220) test_Hsp_hit_to: .: (0.009527) test_Hsp_hseq: .: (0.009583) test_Hsp_identity: .: (0.009679) test_Hsp_midline: .: (0.009697) test_Hsp_mismatch_count: .: (0.009164) test_Hsp_num: .: (0.010223) test_Hsp_pattern_from: .: (0.009306) test_Hsp_pattern_to: .: (0.009081) test_Hsp_percent_identity: .: (0.008882) test_Hsp_positive: .: (0.008859) test_Hsp_qseq: .: (0.008927) test_Hsp_query_frame: .: (0.010006) test_Hsp_query_from: .: (0.009462) test_Hsp_query_to: .: (0.008944) test_Hsp_score: .: (0.008813) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000332) test_Hsp_bit_score: .: (0.000180) test_Hsp_density: .: (0.000183) test_Hsp_evalue: .: (0.000243) test_Hsp_gaps: .: (0.000196) test_Hsp_hit_frame: .: (0.000196) test_Hsp_hit_from: .: (0.000194) test_Hsp_hit_to: .: (0.000193) test_Hsp_hseq: .: (0.000206) test_Hsp_identity: .: (0.000195) test_Hsp_midline: .: (0.000190) test_Hsp_mismatch_count: .: (0.000191) test_Hsp_num: .: (0.000196) test_Hsp_pattern_from: .: (0.000199) test_Hsp_pattern_to: .: (0.000189) test_Hsp_percent_identity: .: (0.000187) test_Hsp_positive: .: (0.000191) test_Hsp_qseq: .: (0.000191) test_Hsp_query_frame: .: (0.000362) test_Hsp_query_from: .: (0.000171) test_Hsp_query_to: .: (0.000176) test_Hsp_score: .: (0.000193) Bio::TestBlastReportIteration: test_hits: .: (0.009001) test_message: .: (0.008931) test_num: .: (0.010549) test_statistics: .: (0.009226) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000567) test_message: .: (0.000363) test_num: .: (0.000347) Bio::TestBlastReportIterationMulti: test_each: .: (0.025954) test_hits: .: (0.027707) test_message: .: (0.026106) test_num: .: (0.027490) test_query_def: .: (0.026449) test_query_id: .: (0.028059) test_query_len: .: (0.026014) test_statistics: .: (0.027657) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.027672) test_hits: .: (0.026678) test_message: .: (0.027536) test_num: .: (0.026693) test_query_def: .: (0.027979) test_query_id: .: (0.026133) test_query_len: .: (0.027660) test_statistics: .: (0.026112) Bio::TestBlastReportIterationREXML: test_hits: .: (0.009461) test_message: .: (0.009949) test_num: .: (0.009247) test_statistics: .: (0.008910) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000326) test_message: .: (0.000301) test_num: .: (0.000204) test_statistics: .: (0.000180) Bio::TestBlastReportMulti: test_db: .: (0.026815) test_db_len: .: (0.026475) test_db_num: .: (0.027484) test_each_hit: .: (0.026530) test_each_iteration: .: (0.027712) test_eff_space: .: (0.026081) test_entropy: .: (0.027496) test_expect: .: (0.025662) test_filter: .: (0.027304) test_gap_extend: .: (0.025838) test_gap_open: .: (0.027659) test_hits: .: (0.026921) test_hsp_len: .: (0.026936) test_iterations: .: (0.028462) test_kappa: .: (0.027198) test_lambda: .: (0.027759) test_matrix: .: (0.026203) test_message: .: (0.027722) test_parameters: .: (0.026244) test_pattern: .: (0.027642) test_program: .: (0.026179) test_query_def: .: (0.027453) test_query_id: .: (0.026576) test_query_len: .: (0.026160) test_reference: .: (0.026850) test_reports: .: (0.025462) test_statistics: .: (0.027473) test_version: .: (0.025688) Bio::TestBlastReportMultiREXML: test_db: .: (0.027435) test_db_len: .: (0.026847) test_db_num: .: (0.028302) test_each_hit: .: (0.027154) test_each_iteration: .: (0.026120) test_eff_space: .: (0.027541) test_entropy: .: (0.026227) test_expect: .: (0.028241) test_filter: .: (0.026021) test_gap_extend: .: (0.027998) test_gap_open: .: (0.027296) test_hits: .: (0.026678) test_hsp_len: .: (0.028402) test_iterations: .: (0.026801) test_kappa: .: (0.028042) test_lambda: .: (0.026377) test_matrix: .: (0.028180) test_message: .: (0.027342) test_parameters: .: (0.027025) test_pattern: .: (0.027990) test_program: .: (0.026649) test_query_def: .: (0.027884) test_query_id: .: (0.026300) test_query_len: .: (0.027795) test_reference: .: (0.027598) test_reports: .: (0.026716) test_statistics: .: (0.028120) test_version: .: (0.026574) Bio::TestBlastReportREXML: test_db: .: (0.010222) test_db_len: .: (0.009301) test_db_num: .: (0.009408) test_each_hit: .: (0.008754) test_each_iteration: .: (0.008749) test_eff_space: .: (0.009116) test_entrez_query: .: (0.010155) test_entropy: .: (0.009153) test_expect: .: (0.008893) test_filter: .: (0.008873) test_gap_extend: .: (0.008839) test_gap_open: .: (0.010016) test_hits: .: (0.009157) test_hsp_len: .: (0.009106) test_inclusion: .: (0.008922) test_iterations: .: (0.009003) test_kappa: .: (0.009036) test_lambda: .: (0.010179) test_matrix: .: (0.009243) test_message: .: (0.008868) test_parameters: .: (0.008924) test_pattern: .: (0.008936) test_program: .: (0.010085) test_query_def: .: (0.009282) test_query_id: .: (0.008961) test_query_len: .: (0.008926) test_reference: .: (0.008884) test_sc_match: .: (0.010039) test_sc_mismatch: .: (0.009525) test_statistics: .: (0.009894) test_version: .: (0.009583) Bio::TestBlastReportTabular: test_db: .: (0.000437) test_db_len: .: (0.000179) test_db_num: .: (0.000198) test_each_hit: .: (0.000188) test_each_iteration: .: (0.000199) test_eff_space: .: (0.000193) test_entrez_query: .: (0.000208) test_entropy: .: (0.000201) test_expect: .: (0.000197) test_filter: .: (0.000193) test_gap_extend: .: (0.000197) test_gap_open: .: (0.000198) test_hits: .: (0.000356) test_hsp_len: .: (0.000175) test_inclusion: .: (0.000174) test_iterations: .: (0.000174) test_kappa: .: (0.000184) test_lambda: .: (0.000190) test_matrix: .: (0.000215) test_message: .: (0.000205) test_parameters: .: (0.000201) test_pattern: .: (0.000198) test_program: .: (0.000196) test_query_def: .: (0.000214) test_query_id: .: (0.000204) test_query_len: .: (0.000201) test_reference: .: (0.000408) test_sc_match: .: (0.000245) test_sc_mismatch: .: (0.000177) test_statistics: .: (0.000178) test_version: .: (0.000177) Bio::TestChain: test_aaseq: .: (0.000432) test_addLigand: .: (0.000141) test_addResidue: .: (0.000151) test_atom_seq: .: (0.000145) test_comp: .: (0.000176) test_each: .: (0.000176) test_each_heterogen: .: (0.000159) test_each_residue: .: (0.000157) test_get_heterogen_by_id: .: (0.000376) test_get_residue_by_id: .: (0.000136) test_inspect: .: (0.000165) test_rehash: .: (0.000139) test_rehash_heterogens: .: (0.000134) test_rehash_residues: .: (0.000139) test_square_brace: .: (0.000143) test_to_s: .: (0.000175) Bio::TestChainFinder: test_chains: .: (0.000315) test_each_chain: .: (0.000152) test_find_chain: .: (0.000144) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005892) test_header: .: (0.000560) test_match_line: .: (0.000471) test_sequence0: .: (0.000536) test_sequence1: .: (0.000445) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.006182) test_header: .: (0.000632) test_match_line: .: (0.002246) test_sequence0: .: (0.000601) test_sequence1: .: (0.000833) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.007926) test_header: .: (0.000608) test_match_line: .: (0.000708) test_sequence0: .: (0.000511) test_sequence1: .: (0.000467) Bio::TestCodonTable: test_Tables: .: (0.000235) test_accessor: .: (0.000148) test_definition: .: (0.000125) test_each: .: (0.000148) test_revtrans: .: (0.000235) test_self_accessor: .: (0.000129) test_self_copy: .: (0.000720) test_set_accessor: .: (0.104884) test_start: .: (0.000160) test_start_codon?: .: (0.000139) test_stop: .: (0.000101) test_stop_codon?: .: (0.000141) test_table: .: (0.000129) Bio::TestCodonTableConstants: test_Definitions: .: (0.000268) test_Starts: .: (0.000148) test_Tables: .: (0.000117) test_stops: .: (0.000136) Bio::TestColorScheme: test_buried: .: (0.001207) Bio::TestCommand: test_command_constants: .: (0.000224) test_escape_shell: .: (0.000232) test_escape_shell_unix: .: (0.000109) test_escape_shell_windows: .: (0.000140) test_make_cgi_params_by_array_of_array: .: (0.000346) test_make_cgi_params_by_array_of_hash: .: (0.000277) test_make_cgi_params_by_array_of_string: .: (0.000471) test_make_cgi_params_by_hash_in_string: .: (0.000366) test_make_cgi_params_by_hash_in_symbol: .: (0.000344) test_make_cgi_params_by_string: .: (0.000272) test_make_command_line: .: (0.000149) test_make_command_line_unix: .: (0.000150) test_make_command_line_windows: .: (0.000147) test_safe_command_line_array: .: (0.000168) test_safe_command_line_array_passthrough: .: (0.000346) Bio::TestContingencyTable: test_lite_example: .: (0.108805) Bio::TestDB: test_entry_id: .: (0.000367) test_exists: .: (0.000123) test_fetch: .: (0.000324) test_get: .: (0.000163) test_open: .: (0.000126) test_tags: .: (0.000121) Bio::TestDataType: test_const_like_method: .: (0.000525) test_pdb_achar: .: (0.000239) test_pdb_atom: .: (0.000212) test_pdb_character: .: (0.000210) test_pdb_date: .: (0.000219) test_pdb_idcode: .: (0.000225) test_pdb_integer: .: (0.000126) test_pdb_list: .: (0.000139) test_pdb_lstring: .: (0.000232) test_pdb_real: .: (0.000197) test_pdb_resudue_name: .: (0.000338) test_pdb_slist: .: (0.000132) test_pdb_string: .: (0.000223) test_pdb_stringrj: .: (0.000130) test_pdb_symop: .: (0.000231) test_specification_list: .: (0.000155) Bio::TestEMBL: test_ac: .: (0.000530) test_accession: .: (0.000313) test_cc: .: (0.000294) test_de: .: (0.000338) test_division: .: (0.000357) test_dr: .: (0.000301) test_dt: .: (0.000343) test_dt_created: .: (0.000405) test_dt_iterator: .: (0.000292) test_dt_updated: .: (0.000281) test_each_cds: .: (0.000445) test_each_gene: .: (0.000383) test_entry: .: (0.000350) test_fh: .: (0.000293) test_ft: .: (0.000397) test_ft_accessor: .: (0.000483) test_ft_iterator: .: (0.000409) test_id_line: .: (0.000306) test_id_line_data_class: .: (0.000302) test_id_line_division: .: (0.000327) test_id_line_entry_name: .: (0.000381) test_id_line_iterator: .: (0.000301) test_id_line_molecule_type: .: (0.000298) test_id_line_sequence_length: .: (0.000295) test_kw: .: (0.000384) test_molecule: .: (0.000331) test_oc: .: (0.000340) test_og: .: (0.000271) test_os: .: (0.000327) test_ref: .: (0.000432) test_references: .: (0.000484) test_seq: .: (0.000580) test_sequence_length: .: (0.000312) test_sq: .: (0.000306) test_sq_get: .: (0.000313) test_sv: .: (0.000277) test_version: .: (0.000359) Bio::TestEMBL89: test_ac: .: (0.000393) test_accession: .: (0.000286) test_cc: .: (0.000291) test_de: .: (0.000288) test_division: .: (0.000324) test_dr: .: (0.000262) test_dt: .: (0.000293) test_dt_created: .: (0.000266) test_dt_iterator: .: (0.000373) test_dt_updated: .: (0.000262) test_each_cds: .: (0.000381) test_each_gene: .: (0.000361) test_entry: .: (0.000428) test_fh: .: (0.000286) test_ft: .: (0.000382) test_ft_accessor: .: (0.000393) test_ft_iterator: .: (0.000478) test_id_line: .: (0.000306) test_id_line_data_class: .: (0.000300) test_id_line_division: .: (0.000301) test_id_line_entry_name: .: (0.000368) test_id_line_iterator: .: (0.000296) test_id_line_molecule_type: .: (0.000301) test_id_line_sequence_length: .: (0.000296) test_id_line_sequence_version: .: (0.000322) test_kw: .: (0.000377) test_molecule: .: (0.000309) test_oc: .: (0.000334) test_og: .: (0.000256) test_os: .: (0.000294) test_ref: .: (0.000411) test_references: .: (0.000428) test_seq: .: (0.000463) test_sequence_length: .: (0.000377) test_sq: .: (0.000307) test_sq_get: .: (0.000289) test_sv: .: (0.000316) test_version: .: (0.000312) Bio::TestEMBLAPI: test_ac: .: (0.000282) test_accessions: .: (0.000183) Bio::TestEMBLCommon: test_ac: .: (0.000236) test_accession: .: (0.000130) test_accessions: .: (0.000119) test_de: .: (0.000126) test_definition: .: (0.000120) test_description: .: (0.000120) test_dr: .: (0.000125) test_keywords: .: (0.000132) test_kw: .: (0.000118) test_oc: .: (0.000126) test_og: .: (0.000125) test_os: .: (0.000119) test_ref: .: (0.000236) test_references: .: (0.000135) Bio::TestEMBLDB: test_fetch: .: (0.000312) test_p_entry2hash: .: (0.000110) Bio::TestEMBLToBioSequence: test_classification: .: (0.002583) test_date_created: .: (0.000466) test_date_modified: .: (0.000385) test_definition: .: (0.000407) test_division: .: (0.000343) test_entry_id: .: (0.000338) test_entry_version: .: (0.000331) test_features: .: (0.000520) test_keywords: .: (0.000329) test_molecule_type: .: (0.000335) test_primary_accession: .: (0.000319) test_references: .: (0.000548) test_release_created: .: (0.000322) test_release_modified: .: (0.000318) test_secondary_accessions: .: (0.000321) test_sequence_version: .: (0.000445) test_species: .: (0.000324) test_topology: .: (0.000338) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.004759) test_date_created: .: (0.002055) test_date_modified: .: (0.002067) test_definition: .: (0.002022) test_division: .: (0.001941) test_entry_id: .: (0.001901) test_entry_version: .: (0.002020) test_features: .: (0.002316) test_keywords: .: (0.002288) test_molecule_type: .: (0.002239) test_primary_accession: .: (0.002066) test_references: .: (0.002312) test_release_created: .: (0.002157) test_release_modified: .: (0.002092) test_secondary_accessions: .: (0.002142) test_sequence_version: .: (0.002013) test_species: .: (0.002134) test_topology: .: (0.002106) Bio::TestFasta: test_db: .: (0.000241) test_format: .: (0.000127) test_format_arg_integer: .: (0.000147) test_format_arg_str: .: (0.000134) test_ktup: .: (0.000130) test_matrix: .: (0.000129) test_option: .: (0.000176) test_options: .: (0.000149) test_output: .: (0.000118) test_program: .: (0.000144) test_server: .: (0.000258) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000249) test_accession: .: (0.000162) test_accessions: .: (0.000165) test_description: .: (0.000150) test_descriptions: .: (0.000147) test_entry_id: .: (0.000143) test_get_all_by_type: .: (0.000166) test_gi: .: (0.000151) test_id_strings: .: (0.000213) test_list_ids: .: (0.000148) test_locus: .: (0.000149) test_words: .: (0.000193) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000399) test_accession: .: (0.000154) test_accessions: .: (0.000156) test_description: .: (0.000146) test_descriptions: .: (0.000152) test_emb: .: (0.000174) test_entry_id: .: (0.000156) test_get_all_by_type: .: (0.000159) test_get_emb: .: (0.000183) test_gi: .: (0.000161) test_id_strings: .: (0.000214) test_list_ids: .: (0.000160) test_locus: .: (0.000160) test_words: .: (0.000208) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000446) test_accession: .: (0.000147) test_accessions: .: (0.000148) test_description: .: (0.000138) test_descriptions: .: (0.000140) test_entry_id: .: (0.000144) test_get_all_by_type: .: (0.000145) test_gi: .: (0.000152) test_id_strings: .: (0.000193) test_list_ids: .: (0.000165) test_locus: .: (0.000148) test_sp: .: (0.000161) test_words: .: (0.000190) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000432) test_accession: .: (0.000178) test_accessions: .: (0.000188) test_description: .: (0.000173) test_descriptions: .: (0.000177) test_entry_id: .: (0.000185) test_get_all_by_type: .: (0.000196) test_gi: .: (0.000193) test_id_strings: .: (0.000304) test_list_ids: .: (0.000175) test_locus: .: (0.000688) test_words: .: (0.000322) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000307) test_accession: .: (0.000165) test_accessions: .: (0.000161) test_description: .: (0.000181) test_descriptions: .: (0.000163) test_entry_id: .: (0.000176) test_get_all_by_type: .: (0.000176) test_gi: .: (0.000173) test_id_strings: .: (0.000418) test_list_ids: .: (0.000162) test_locus: .: (0.000156) test_words: .: (0.000213) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000261) test_accession: .: (0.000145) test_accessions: .: (0.000138) test_description: .: (0.000133) test_descriptions: .: (0.000135) test_entry_id: .: (0.000131) test_get_all_by_type: .: (0.000132) test_gi: .: (0.000130) test_id_strings: .: (0.000164) test_list_ids: .: (0.000326) test_locus: .: (0.000122) test_words: .: (0.000160) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000209) test_accession: .: (0.000122) test_accessions: .: (0.000114) test_description: .: (0.000109) test_descriptions: .: (0.000140) test_entry_id: .: (0.000150) test_get: .: (0.000166) test_get_all_by_type: .: (0.000146) test_id_strings: .: (0.000225) test_list_ids: .: (0.000146) test_locus: .: (0.000146) test_sp: .: (0.000342) test_words: .: (0.000187) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000218) test_accession: .: (0.000164) test_accessions: .: (0.000154) test_description: .: (0.000149) test_descriptions: .: (0.000150) test_entry_id: .: (0.000141) test_get: .: (0.000161) test_get_all_by_type: .: (0.000148) test_id_strings: .: (0.000251) test_list_ids: .: (0.000150) test_locus: .: (0.000348) test_tr: .: (0.000153) test_words: .: (0.000207) Bio::TestFastaFirstName: test_first_name1: .: (0.000255) test_first_name_multi_identifier: .: (0.000140) test_first_name_single_worded_defintion: .: (0.000156) test_no_definition: .: (0.000133) test_space_before_first_name: .: (0.000142) test_tabbed_defintion: .: (0.000134) Bio::TestFastaFormat: test_aalen: .: (0.000280) test_aaseq: .: (0.000148) test_acc_version: .: (0.000181) test_accession: .: (0.000195) test_accessions: .: (0.000295) test_data: .: (0.000154) test_definition: .: (0.000141) test_entry: .: (0.000143) test_entry_id: .: (0.000174) test_entry_overrun: .: (0.000146) test_first_name: .: (0.000149) test_gi: .: (0.003722) test_identifiers: .: (0.000226) test_length: .: (0.000176) test_query: .: (0.000160) test_seq: .: (0.000152) Bio::TestFastaFormatConst: test_delimiter: .: (0.000221) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000320) test_data: .: (0.000140) test_definition: .: (0.000136) test_entry: .: (0.000160) test_entry_id: .: (0.000190) test_first_name: .: (0.000162) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000526) test_naseq: .: (0.000129) test_naseq_class: .: (0.000262) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000302) Bio::TestFastaInitialize: test_new_1: .: (0.000483) test_option: .: (0.000128) test_option_backward_compatibility: .: (0.000164) Bio::TestFastaNumericFormat: test_arg: .: (0.000288) test_data: .: (0.000161) test_definition: .: (0.000105) test_each: .: (0.000137) test_entry: .: (0.000119) test_entry_id: .: (0.000132) test_length: .: (0.000160) test_to_biosequence: .: (0.000781) Bio::TestFastaQuery: test_query: .: (0.000163) test_self_local: .: (0.000083) test_self_parser: .: (0.000079) test_self_remote: .: (0.000080) Bio::TestFastacmd: test_database: .: (0.000184) test_fastacmd: .: (0.000107) test_methods: .: (0.000343) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000578) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000435) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000975) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000571) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000432) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000420) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000537) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000439) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000391) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000378) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000554) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000382) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000373) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000944) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000928) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000400) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001088) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000645) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.003823) test_error_probabilities_as_sanger: .: (0.003704) test_error_probabilities_as_solexa: .: (0.003670) test_quality_scores_as_illumina: .: (0.000495) test_quality_scores_as_sanger: .: (0.000285) test_quality_scores_as_solexa: .: (0.000309) test_validate_format: .: (0.000463) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000899) test_entry_id: .: (0.000902) test_error_probabilities: .: (0.122507) test_nalen: .: (0.000822) test_naseq: .: (0.000829) test_quality_scores: .: (0.001345) test_quality_string: .: (0.000728) test_roundtrip: .: (0.089870) test_seq: .: (0.000869) test_sequence_string: .: (0.000597) test_to_biosequence: .: (0.084086) test_to_biosequence_and_output: .: (0.003827) test_to_s: .: (0.000781) test_validate_format: .: (0.000745) test_validate_format_with_array: .: (0.000686) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000476) test_mask_20_with_empty_string: .: (0.000329) test_mask_20_with_longer_string: .: (0.000495) test_mask_20_with_x: .: (0.000325) test_mask_60: .: (0.000379) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.004490) test_error_probabilities_as_sanger: .: (0.004374) test_error_probabilities_as_solexa: .: (0.005706) test_quality_scores_as_illumina: .: (0.000360) test_quality_scores_as_sanger: .: (0.000280) test_quality_scores_as_solexa: .: (0.000358) test_validate_format: .: (0.000666) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.003471) test_error_probabilities_as_sanger: .: (0.003533) test_error_probabilities_as_solexa: .: (0.003296) test_quality_scores_as_illumina: .: (0.000365) test_quality_scores_as_sanger: .: (0.000331) test_quality_scores_as_solexa: .: (0.000262) test_validate_format: .: (0.000628) Bio::TestFeature: test_append: .: (0.000224) test_append_nil: .: (0.000142) test_assoc: .: (0.000128) test_each: .: (0.000118) test_feature: .: (0.000104) test_locations: .: (0.000181) test_new: .: (0.000110) test_position: .: (0.000103) test_qualifiers: .: (0.000103) Bio::TestFeatures: test_append: .: (0.000286) test_arg: .: (0.000114) test_each: .: (0.000124) test_features: .: (0.000130) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000803) test_aaindex2: .: (0.000238) test_blast: .: (0.000228) test_blastxml: .: (0.000668) test_embl: .: (0.000261) test_embl_oldrelease: .: (0.000250) test_fastaformat: .: (0.000402) test_fastanumericformat: .: (0.000159) test_fastq: .: (0.000319) test_genbank: .: (0.000218) test_genpept: .: (0.000229) test_hmmer: .: (0.000278) test_maxml_cluster: .: (0.002321) test_maxml_sequence: .: (0.000308) test_medline: .: (0.000171) test_prosite: .: (0.003570) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002833) test_transfac: .: (0.001142) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000261) test_auto_1arg_filename: .: (0.000648) test_auto_1arg_io: .: (0.000388) test_auto_1arg_io_with_block: .: (0.000552) test_auto_1arg_with_block: .: (0.000467) test_auto_2arg_filename_mode: .: (0.000292) test_auto_2arg_filename_mode_with_block: .: (0.000672) test_auto_3arg: .: (0.000337) test_auto_3arg_with_block: .: (0.000462) test_foreach: .: (0.000406) test_new_2arg_class: .: (0.000179) test_new_2arg_nil: .: (0.000425) test_open_0arg: .: (0.000186) test_open_1arg_class: .: (0.000155) test_open_1arg_filename: .: (0.000285) test_open_1arg_io: .: (0.000277) test_open_1arg_io_with_block: .: (0.000478) test_open_1arg_nil: .: (0.000139) test_open_1arg_with_block: .: (0.000623) test_open_2arg_autodetect: .: (0.000324) test_open_2arg_autodetect_io: .: (0.000280) test_open_2arg_autodetect_io_with_block: .: (0.000470) test_open_2arg_autodetect_with_block: .: (0.000467) test_open_2arg_class: .: (0.000297) test_open_2arg_class_io: .: (0.000206) test_open_2arg_class_io_with_block: .: (0.000379) test_open_2arg_class_with_block: .: (0.000370) test_open_2arg_filename_mode: .: (0.000286) test_open_2arg_filename_mode_with_block: .: (0.000595) test_open_3arg: .: (0.000550) test_open_3arg_with_block: .: (0.001226) test_open_4arg: .: (0.000960) test_to_a: .: (0.000423) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000498) test_close: .: (0.000163) test_dbclass: .: (0.000153) test_dbclass_eq: .: (0.000179) test_dbclass_nil: .: (0.000213) test_each: .: (0.000276) test_each_entry: .: (0.000355) test_ended_pos: .: (0.000246) test_entry_pos_flag: .: (0.000173) test_entry_raw: .: (0.000290) test_eof?: .: (0.000383) test_next_entry: .: (0.000305) test_path: .: (0.000157) test_pos: .: (0.000220) test_raw: .: (0.000277) test_rewind: .: (0.000224) test_start_pos: .: (0.000240) test_start_pos_ended_pos_not_recorded: .: (0.000238) test_to_io: .: (0.000177) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000426) test_simpleformat2: .: (0.000222) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000203) test_eof_false_after_prefetch: .: (0.000193) test_eof_false_first: .: (0.000132) test_eof_true: .: (0.000214) test_getc: .: (0.000145) test_getc_after_prefetch: .: (0.000137) test_gets: .: (0.000139) test_gets_equal_prefetch_gets: .: (0.000153) test_gets_paragraph_mode: .: (0.000190) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000302) test_gets_paragraph_mode_within_buffer: .: (0.000388) test_gets_rs: .: (0.000182) test_gets_rs_equal_prefetch_gets: .: (0.000167) test_gets_rs_within_buffer: .: (0.000280) test_pos: .: (0.000131) test_pos=: .: (0.000143) test_prefetch_buffer: .: (0.000132) test_prefetch_gets: .: (0.000148) test_prefetch_gets_with_arg: .: (0.000167) test_rewind: .: (0.000135) test_skip_spaces: .: (0.000153) test_to_io: .: (0.000147) test_ungetc: .: (0.000151) test_ungetc_after_prefetch: .: (0.000158) test_ungets: .: (0.000178) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000371) test_self_open_file: .: (0.000156) test_self_open_file_with_block: .: (0.000170) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000209) test_parse_file_open_arg_int_perm: .: (0.000119) test_parse_file_open_arg_int_perm_opt: .: (0.000126) test_parse_file_open_arg_integer: .: (0.000113) test_parse_file_open_arg_nil: .: (0.000104) test_parse_file_open_arg_opt: .: (0.000146) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000134) test_parse_file_open_arg_str: .: (0.000127) test_parse_file_open_arg_str_opt: .: (0.000133) test_parse_file_open_arg_str_perm: .: (0.000123) test_parse_file_open_arg_str_perm_opt: .: (0.000127) test_parse_file_open_arg_str_with_enc: .: (0.000130) test_parse_file_open_arg_str_with_ext_enc: .: (0.000128) test_parse_file_open_mode_integer: .: (0.000108) test_parse_file_open_mode_nil: .: (0.000261) test_parse_file_open_mode_str: .: (0.000135) test_parse_file_open_mode_str_with_enc: .: (0.000118) test_parse_file_open_mode_str_with_ext_enc: .: (0.000120) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000197) test_entry: .: (0.000142) test_entry_ended_pos: .: (0.000126) test_entry_pos_flag: .: (0.000131) test_entry_start_pos: .: (0.000124) test_get_entry: .: (0.000172) test_rewind: .: (0.000138) test_skip_leader: .: (0.000144) test_stream: .: (0.000116) test_stream_pos: .: (0.000138) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000248) test_delimiter_overrun: .: (0.000222) test_entry: .: (0.000137) test_entry_ended_pos: .: (0.000143) test_entry_ended_pos_default_nil: .: (0.000157) test_entry_start_pos: .: (0.000157) test_entry_start_pos_default_nil: .: (0.000145) test_get_entry: .: (0.000240) test_get_parsed_entry: .: (0.000259) test_header: .: (0.000120) test_skip_leader: .: (0.000163) test_skip_leader_without_header: .: (0.000167) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000443) test_entry_ended_pos: .: (0.000208) test_entry_start_pos: .: (0.000190) test_flag_to_fetch_header: .: (0.000185) test_get_entry: .: (0.000260) test_get_parsed_entry: .: (0.000307) test_rewind: .: (0.000329) test_skip_leader: .: (0.000144) Bio::TestGCGMsf: test_alignment: .: (0.000784) test_checksum: .: (0.000206) test_compcheck: .: (0.000203) test_date: .: (0.000329) test_description: .: (0.000206) test_entry_id: .: (0.000218) test_gap_length_weight: .: (0.000201) test_gap_weight: .: (0.000214) test_heading: .: (0.000242) test_length: .: (0.000246) test_seq_type: .: (0.000369) test_symbol_comparison_table: .: (0.000203) test_validate_checksum: .: (0.001205) Bio::TestGFF: test_record_class: .: (0.000407) test_records: .: (0.000294) Bio::TestGFF2: test_const_version: .: (0.000420) test_gff_version: .: (0.003127) test_metadata: .: (0.000339) test_metadata_size: .: (0.000308) test_records_size: .: (0.000323) test_to_s: .: (0.000716) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000233) test_attributes_case2: .: (0.000181) test_attributes_incompatible_backslash_semicolon: .: (0.000227) Bio::TestGFF2MetaData: test_data: .: (0.000441) test_directive: .: (0.000107) test_parse: .: (0.000119) Bio::TestGFF2Record: test_attribute: .: (0.000348) test_attribute_nonexistent: .: (0.000208) test_attributes: .: (0.000232) test_attributes_to_hash: .: (0.000441) test_comment_only?: .: (0.000215) test_delete_attribute: .: (0.000237) test_delete_attribute_multiple: .: (0.000248) test_delete_attribute_multiple2: .: (0.000272) test_delete_attribute_multiple_nil: .: (0.000229) test_delete_attribute_nil: .: (0.000381) test_delete_attribute_nonexistent: .: (0.000247) test_delete_attributes: .: (0.000241) test_delete_attributes_multiple: .: (0.000242) test_delete_attributes_nonexistent: .: (0.000246) test_end: .: (0.000274) test_eqeq: .: (0.000571) test_eqeq_false: .: (0.000406) test_feature: .: (0.000214) test_frame: .: (0.000344) test_get_attribute: .: (0.000262) test_get_attribute_nonexistent: .: (0.000210) test_get_attributes: .: (0.000278) test_get_attributes_nonexistent: .: (0.000232) test_replace_attributes: .: (0.000374) test_replace_attributes_multiple_multiple_over: .: (0.000248) test_replace_attributes_multiple_multiple_same: .: (0.000242) test_replace_attributes_multiple_multiple_two: .: (0.000263) test_replace_attributes_multiple_single: .: (0.000235) test_replace_attributes_nonexistent: .: (0.000234) test_replace_attributes_nonexistent_multiple: .: (0.000377) test_replace_attributes_single_multiple: .: (0.000235) test_score: .: (0.000206) test_self_parse: .: (0.000425) test_seqname: .: (0.000209) test_set_attribute: .: (0.000387) test_set_attribute_multiple: .: (0.000237) test_set_attribute_nonexistent: .: (0.000234) test_sort_attributes_by_tag!: .: (0.000290) test_sort_attributes_by_tag_bang_test2: .: (0.000279) test_sort_attributes_by_tag_bang_with_block: .: (0.000416) test_source: .: (0.000212) test_start: .: (0.000206) test_strand: .: (0.000209) test_to_s: .: (0.000320) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000195) test_comment_eq: .: (0.000287) test_comment_only?: .: (0.000132) test_comment_only_false: .: (0.000115) test_to_s: .: (0.000124) test_to_s_not_empty: .: (0.000183) Bio::TestGFF3: test_const_version: .: (0.000571) test_gff_version: .: (0.000539) test_records: .: (0.000479) test_sequence_regions: .: (0.000509) test_sequences: .: (0.000455) test_to_s: .: (0.000934) Bio::TestGFF3MetaData: test_data: .: (0.000184) test_directive: .: (0.000107) test_parse: .: (0.000118) Bio::TestGFF3Record: test_attributes: .: (0.000488) test_end: .: (0.000205) test_feature: .: (0.000205) test_frame: .: (0.000209) test_id: .: (0.000221) test_score: .: (0.000229) test_seqname: .: (0.000448) test_source: .: (0.000201) test_start: .: (0.000222) test_strand: .: (0.000243) test_to_s: .: (0.000348) test_to_s_attr_order_changed: .: (0.000617) Bio::TestGFF3RecordEscape: test_escape: .: (0.000221) test_escape_attribute: .: (0.000160) test_escape_seqid: .: (0.000166) test_unescape: .: (0.000170) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000324) test_eqeq: .: (0.000191) test_new_from_sequences_na: .: (0.000433) test_new_from_sequences_na_aa: .: (0.000270) test_new_from_sequences_na_aa_boundary_gap: .: (0.000370) test_new_from_sequences_na_aa_example: .: (0.000280) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000257) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000224) test_process_sequences_na: .: (0.000456) test_process_sequences_na_aa: .: (0.000226) test_process_sequences_na_aa_reverse_frameshift: .: (0.000196) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000212) test_process_sequences_na_aa_tooshort: .: (0.000303) test_process_sequences_na_tooshort: .: (0.000236) test_to_s: .: (0.000187) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000460) test_attributes_one: .: (0.000142) test_attributes_with_escaping: .: (0.000156) test_id_multiple: .: (0.000220) test_id_multiple2: .: (0.000215) test_id_replace: .: (0.000174) test_id_set: .: (0.000200) test_initialize_9: .: (0.000114) test_phase: .: (0.000172) test_score: .: (0.000345) test_to_s_void: .: (0.000130) Bio::TestGFF3RecordTarget: test_end: .: (0.000200) test_parse: .: (0.000179) test_start: .: (0.000128) test_strand: .: (0.000121) test_target_id: .: (0.000143) test_to_s: .: (0.000205) Bio::TestGFF3SequenceRegion: test_end: .: (0.000237) test_parse: .: (0.000212) test_seqid: .: (0.000130) test_start: .: (0.000123) test_to_s: .: (0.000394) Bio::TestGFFRecord: test_attributes: .: (0.000229) test_comment: .: (0.000138) test_end: .: (0.000141) test_feature: .: (0.000147) test_frame: .: (0.000143) test_score: .: (0.000141) test_seqname: .: (0.000151) test_source: .: (0.000142) test_start: .: (0.000141) test_strand: .: (0.000140) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000171) Bio::TestGeneAssociation: test_aspect: .: (0.000396) test_assigned_by: .: (0.000085) test_date: .: (0.000081) test_db: .: (0.000077) test_db_object_id: .: (0.000074) test_db_object_name: .: (0.000077) test_db_object_symbol: .: (0.000074) test_db_object_synonym: .: (0.000080) test_db_object_type: .: (0.000077) test_db_reference: .: (0.000078) test_evidence: .: (0.000078) test_goid: .: (0.000089) test_parser: .: (0.000552) test_qualifier: .: (0.000083) test_taxon: .: (0.000075) test_to_str: .: (0.000079) test_with: .: (0.000078) Bio::TestGenscanReport: test_date_run: .: (0.000705) test_gccontent: .: (0.000718) test_genscan_version: .: (0.000487) test_isochore: .: (0.000694) test_length: .: (0.000478) test_matrix: .: (0.000476) test_predictions_size: .: (0.000500) test_query_name: .: (0.000495) test_time: .: (0.000646) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000582) test_donor_score: .: (0.000629) test_exon_type: .: (0.000475) test_exon_type_long: .: (0.000471) test_first: .: (0.000618) test_initiation_score: .: (0.000488) test_last: .: (0.000690) test_number: .: (0.000526) test_p_value: .: (0.000462) test_phase: .: (0.000664) test_range: .: (0.000477) test_score: .: (0.000666) test_strand: .: (0.000525) test_t_score: .: (0.000454) test_termination_score: .: (0.002413) Bio::TestGenscanReportGene: test_aaseq: .: (0.006312) test_naseq: .: (0.002902) test_number: .: (0.002749) test_polyA: .: (0.002006) test_promoter: .: (0.002899) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.002155) test_reports_ary_contents: .: (0.000559) Bio::TestHMMERReportConstants: test_rs: .: (0.002570) Bio::TestHMMERReportHit: test_accession: .: (0.003049) test_append_hsp: .: (0.002357) test_bit_score: .: (0.013894) test_definition: .: (0.000573) test_description: .: (0.000491) test_each: .: (0.000551) test_each_hsp: .: (0.000688) test_entry_id: .: (0.000509) test_evalue: .: (0.000482) test_hit: .: (0.000628) test_hit_id: .: (0.000496) test_hsps: .: (0.000480) test_num: .: (0.000494) test_score: .: (0.000640) test_target_def: .: (0.000493) test_target_id: .: (0.000475) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000742) test_each: .: (0.000492) test_each_hit: .: (0.000492) test_histogram: .: (0.000479) test_hits: .: (0.000614) test_hsps: .: (0.000489) test_parameter: .: (0.000504) test_program: .: (0.000651) test_query_info: .: (0.000535) test_statistical_detail: .: (0.000496) test_total_seq_searched: .: (0.000473) test_whole_seq_top_hits: .: (0.000622) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000717) test_histogram: .: (0.000560) test_statistical_detail: .: (0.000690) test_total_seq_searched: .: (0.000555) test_whole_seq_top_hit: .: (0.000595) Bio::TestHMMERReportHsp: test_accession: .: (0.000679) test_bit_score: .: (0.000503) test_csline: .: (0.000476) test_domain: .: (0.000476) test_evalue: .: (0.000586) test_flatseq: .: (0.000499) test_hmm_f: .: (0.000466) test_hmm_t: .: (0.000465) test_hmmseq: .: (0.000648) test_hsp: .: (0.000477) test_midline: .: (0.000469) test_query_frame: .: (0.000648) test_query_from: .: (0.000491) test_query_seq: .: (0.000491) test_query_to: .: (0.000469) test_rfline: .: (0.000629) test_score: .: (0.000481) test_seq_f: .: (0.000469) test_seq_ft: .: (0.000474) test_seq_t: .: (0.000586) test_set_alignment: .: (0.000485) test_targat_to: .: (0.000470) test_target_frame: .: (0.000591) test_target_from: .: (0.000491) test_target_seq: .: (0.000472) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000327) test_find_hetatm: .: (0.000332) test_hetatms: .: (0.000213) Bio::TestHeterogen: test_addAtom: .: (0.000237) test_each: .: (0.000161) test_each_hetatm: .: (0.000126) test_get_residue_id_from_atom: .: (0.000115) test_het_atom: .: (0.000254) test_iCode: .: (0.000106) test_inspect: .: (0.000149) test_resSeq: .: (0.000102) test_sort: .: (0.000127) test_square_bracket: .: (0.000118) test_to_s: .: (0.000179) test_update_resudue_id: .: (0.000110) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000172) test_find_heterogen: .: (0.000096) test_heterogens: .: (0.000097) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000202) test_match_description: .: (0.000103) test_match_evalue: .: (0.000098) test_match_ipr_description: .: (0.000099) test_match_ipr_id: .: (0.000098) test_match_match_end: .: (0.000099) test_match_match_start: .: (0.000097) test_match_method: .: (0.000323) test_matches_size: .: (0.000097) test_query_id: .: (0.000101) test_query_length: .: (0.000095) Bio::TestIprscanRawReport: test_entry_id: .: (0.001724) test_match_accession: .: (0.001420) test_match_crc64: .: (0.001671) test_match_date: .: (0.001707) test_match_description: .: (0.001631) test_match_evalue: .: (0.001761) test_match_go_terms: .: (0.001517) test_match_ipr_description: .: (0.001568) test_match_ipr_id: .: (0.003540) test_match_match_end: .: (0.001963) test_match_match_start: .: (0.001584) test_match_method: .: (0.001538) test_match_query_id: .: (0.001689) test_match_query_length: .: (0.001593) test_match_status: .: (0.001442) test_obj: .: (0.001433) test_query_id: .: (0.001393) test_query_length: .: (0.001359) test_self_reports_in_raw: .: (0.002778) Bio::TestIprscanReport: test_output_raw: .: (0.000497) test_to_raw: .: (0.000511) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000418) test_match_accession: .: (0.000329) test_match_date: .: (0.000314) test_match_description: .: (0.000431) test_match_evalue: .: (0.000324) test_match_go_terms: .: (0.000312) test_match_ipr_description: .: (0.000301) test_match_ipr_id: .: (0.000302) test_match_match_end: .: (0.000343) test_match_match_start: .: (0.000306) test_match_method: .: (0.000301) test_match_status: .: (0.000402) test_matches_size: .: (0.000324) test_query_id: .: (0.000304) test_query_length: .: (0.000304) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000603) test_to_hash_match?: .: (0.000430) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.000974) Bio::TestKeggCompound: test_comment: .: (0.000392) test_dblinks_as_hash: .: (0.000288) test_dblinks_as_strings: .: (0.000206) test_entry_id: .: (0.000205) test_enzymes: .: (0.000552) test_formula: .: (0.000230) test_kcf: .: (0.000187) test_mass: .: (0.000200) test_name: .: (0.000212) test_names: .: (0.000211) test_pathways_as_hash: .: (0.000329) test_pathways_as_strings: .: (0.000422) test_reactions: .: (0.000450) test_remark: .: (0.000227) test_rpairs: .: (0.000207) Bio::TestKeggEnzyme: test_all_reac: .: (0.000492) test_classes: .: (0.000367) test_cofactors: .: (0.000353) test_comment: .: (0.000369) test_dblinks_as_hash: .: (0.000377) test_dblinks_as_strings: .: (0.000343) test_diseases: .: (0.000320) test_entry: .: (0.000390) test_entry_id: .: (0.000432) test_genes: .: (0.008867) test_genes_as_hash: .: (0.008254) test_genes_as_strings: .: (0.002940) test_inhibitors: .: (0.000481) test_iubmb_reactions: .: (0.000521) test_kegg_reactions: .: (0.000507) test_motifs: .: (0.000453) test_name: .: (0.000789) test_names: .: (0.000519) test_obsolete?: .: (0.000500) test_orthologs_as_hash: .: (0.000466) test_orthologs_as_strings: .: (0.000434) test_pathways_as_hash: .: (0.000506) test_pathways_as_strings: .: (0.000826) test_products: .: (0.000537) test_reaction: .: (0.000464) test_structures: .: (0.000588) test_substrates: .: (0.000446) test_sysname: .: (0.000460) Bio::TestKeggGenesDblinks: test_data: .: (0.000302) test_dblinks_0: .: (0.000120) test_dblinks_1: .: (0.000092) test_dblinks_2: .: (0.000083) Bio::TestKeggGenesStructure: test_data: .: (0.000169) test_ids: .: (0.000127) test_ids_in_array: .: (0.000108) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.009182) test_graphics__size: .: (0.005796) test_id: .: (0.005984) test_link: .: (0.005968) test_name: .: (0.005910) test_reaction: .: (0.006276) test_type: .: (0.006566) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.005887) test_graphics__size: .: (0.005766) test_id: .: (0.005523) test_link: .: (0.005512) test_name: .: (0.005792) test_reaction: .: (0.005536) test_type: .: (0.006740) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.005867) test_category: .: (0.005806) test_entry_id: .: (0.005521) test_fgcolor=: .: (0.005539) test_height=: .: (0.005503) test_label=: .: (0.006680) test_shape=: .: (0.005858) test_width=: .: (0.005615) test_x=: .: (0.005563) test_y=: .: (0.005799) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.005646) test_graphics__size: .: (0.006786) test_id: .: (0.005687) test_link: .: (0.005762) test_name: .: (0.005793) test_reaction: .: (0.005592) test_type: .: (0.005586) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000258) test_graphics=: .: (0.000131) test_id=: .: (0.000152) test_link=: .: (0.000320) test_name=: .: (0.000132) test_reaction=: .: (0.000127) test_type=: .: (0.000132) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000249) test_category=: .: (0.000184) test_entry_id=: .: (0.000166) test_fgcolor=: .: (0.000193) test_height=: .: (0.000172) test_label=: .: (0.000186) test_pathway=: .: (0.000155) test_shape=: .: (0.000246) test_width=: .: (0.000173) test_x=: .: (0.000171) test_y=: .: (0.000181) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.005988) test_coords: .: (0.005673) test_fgcolor: .: (0.005792) test_height: .: (0.005587) test_name: .: (0.005619) test_type: .: (0.005458) test_width: .: (0.006650) test_x: .: (0.005824) test_y: .: (0.005523) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.005918) test_coords: .: (0.005632) test_fgcolor: .: (0.005551) test_height: .: (0.006631) test_name: .: (0.005616) test_type: .: (0.005794) test_width: .: (0.005486) test_x: .: (0.005586) test_y: .: (0.005793) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000252) test_coords=: .: (0.000126) test_fgcolor=: .: (0.000130) test_height=: .: (0.000129) test_name=: .: (0.000136) test_type=: .: (0.000145) test_width=: .: (0.000141) test_x=: .: (0.000136) test_y=: .: (0.000139) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.007025) test_entries__size: .: (0.005632) test_image: .: (0.005549) test_link: .: (0.005659) test_name: .: (0.005582) test_number: .: (0.005485) test_org: .: (0.006636) test_reactions=: .: (0.005907) test_reactions__size: .: (0.005580) test_relations=: .: (0.005514) test_relations__size: .: (0.005605) test_title: .: (0.005769) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.012595) test_name: .: (0.011170) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000284) test_initialize_0: .: (0.000123) test_initialize_1: .: (0.000132) test_initialize_2: .: (0.000135) test_name=: .: (0.000705) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.007255) test_name: .: (0.007450) test_products: .: (0.006109) test_substrates: .: (0.006414) test_type: .: (0.005861) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000246) test_name=: .: (0.000141) test_products=: .: (0.000145) test_substraces=: .: (0.000154) test_type=: .: (0.000170) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000265) test_entry_id=: .: (0.000302) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.006148) test_entry2: .: (0.005687) test_name: .: (0.053167) test_type: .: (0.006164) test_value: .: (0.006016) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000232) test_node1=: .: (0.000149) test_node2=: .: (0.000342) test_rel=: .: (0.000150) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000216) test_entry2=: .: (0.000145) test_name=: .: (0.000155) test_type=: .: (0.000156) test_value=: .: (0.000158) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.012153) test_name: .: (0.011285) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000211) test_initialize_0: .: (0.000117) test_initialize_1: .: (0.000122) test_initialize_2: .: (0.000125) test_name=: .: (0.000156) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000409) test_initialize_0: .: (0.000112) test_initialize_1: .: (0.000148) test_initialize_2: .: (0.000121) test_name=: .: (0.000148) Bio::TestKeggModule: test_compounds: .: (0.000432) test_compounds_as_hash: .: (0.000260) test_compounds_as_strings: .: (0.000233) test_definition: .: (0.000244) test_entry_id: .: (0.000316) test_keggclass: .: (0.000276) test_name: .: (0.000271) test_new: .: (0.000257) test_orthologs: .: (0.000367) test_orthologs_as_array: .: (0.000377) test_orthologs_as_hash: .: (0.000306) test_orthologs_as_strings: .: (0.000276) test_pathways: .: (0.000520) test_pathways_as_hash: .: (0.000220) test_pathways_as_strings: .: (0.000215) test_reactions: .: (0.000271) test_reactions_as_hash: .: (0.000315) test_reactions_as_strings: .: (0.000296) Bio::TestKeggOrthology: test_dblinks: .: (0.000593) test_dblinks_as_hash: .: (0.000621) test_dblinks_as_strings: .: (0.000390) test_definition: .: (0.000407) test_entry_id: .: (0.000402) test_genes_as_hash: .: (0.010032) test_genes_as_strings: .: (0.002791) test_keggclass: .: (0.000476) test_keggclasses: .: (0.000472) test_modules: .: (0.000521) test_modules_as_hash: .: (0.000362) test_modules_as_strings: .: (0.000425) test_name: .: (0.000459) test_names: .: (0.000470) test_pathways_as_strings: .: (0.000469) test_pathways_in_keggclass: .: (0.000541) test_references: .: (0.000608) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000381) test_compounds_as_strings: .: (0.000232) test_dblinks_as_hash: .: (0.000222) test_dblinks_as_strings: .: (0.000221) test_description: .: (0.000278) test_diseases_as_hash: .: (0.000259) test_diseases_as_strings: .: (0.000268) test_entry_id: .: (0.000292) test_enzymes_as_strings: .: (0.000262) test_genes_as_hash: .: (0.000260) test_genes_as_strings: .: (0.000311) test_keggclass: .: (0.000289) test_ko_pathway: .: (0.000242) test_modules_as_hash: .: (0.000280) test_modules_as_strings: .: (0.000266) test_name: .: (0.000250) test_organism: .: (0.000279) test_orthologs_as_hash: .: (0.000282) test_orthologs_as_strings: .: (0.000261) test_pathways_as_hash: .: (0.000497) test_pathways_as_strings: .: (0.000299) test_reactions_as_hash: .: (0.000225) test_reactions_as_strings: .: (0.000220) test_references: .: (0.000246) test_rel_pathways_as_hash: .: (0.000309) test_rel_pathways_as_strings: .: (0.000241) Bio::TestKeggReaction: test_definition: .: (0.000408) test_entry_id: .: (0.000447) test_enzymes: .: (0.000305) test_equation: .: (0.000248) test_name: .: (0.000267) test_orthologs_as_hash: .: (0.000274) test_orthologs_as_strings: .: (0.000238) test_pathways_as_hash: .: (0.000256) test_pathways_as_strings: .: (0.000246) test_rpairs_as_hash: .: (0.000503) test_rpairs_as_strings: .: (0.000274) test_rpairs_as_tokens: .: (0.000299) Bio::TestLasergene: test_methods: .: (0.004839) Bio::TestLocations: test_complement: .: (0.000289) test_hat: .: (0.000162) test_normal: .: (0.000155) test_replace_single_base: .: (0.000290) test_should_not_modify_argument: .: (0.000138) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002491) test_locations_to_s: .: (0.001100) Bio::TestMEDLINE: test_authors: .: (0.000643) test_authors_with_last_name_all_caps: .: (0.000135) test_authors_with_suffix: .: (0.000142) Bio::TestMEDLINE_20146148: test_ab: .: (0.000454) test_ad: .: (0.000470) test_au: .: (0.000320) test_authors: .: (0.000300) test_doi: .: (0.000296) test_dp: .: (0.000394) test_ip: .: (0.000299) test_mh: .: (0.000347) test_pages: .: (0.000311) test_pg: .: (0.000428) test_pii: .: (0.000310) test_pmid: .: (0.000287) test_pt: .: (0.000317) test_reference: .: (0.000643) test_self_new: .: (0.000318) test_so: .: (0.000303) test_ta: .: (0.000310) test_ti: .: (0.000518) test_ui: .: (0.000349) test_vi: .: (0.000334) test_year: .: (0.000318) Bio::TestMapSimple: test_attributes: .: (0.000257) Bio::TestMapping: test_add_mapping_as_map: .: (0.000433) test_add_mapping_as_marker: .: (0.000192) test_contains_marker?: .: (0.000154) test_mapped_to?: .: (0.000149) test_mapping_location_comparison: .: (0.000342) test_mappings_as_map_each: .: (0.000167) test_mappings_as_marker_each: .: (0.000225) test_mappings_on: .: (0.000220) test_multiple_mappings_between_same_marker_and_map: .: (0.000327) test_positions_on: .: (0.000362) test_raise_error_kind_of: .: (0.000332) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000325) test_check_options_with_invalid_opts: .: (0.000200) test_check_options_with_valid_opts: .: (0.000223) test_command_to_be_run: .: (0.000199) test_config_defaults: .: (0.000201) test_minimal_config: .: (0.000204) test_more_config: .: (0.000196) test_run: .: (0.000143) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000610) test_report_has_motifs: .: (0.000265) Bio::TestModel: test_addChain: .: (0.000208) test_comp: .: (0.000214) test_each: .: (0.000156) test_each_chain: .: (0.000172) test_inspect: .: (0.000153) test_rehash: .: (0.000127) test_square_brace: .: (0.000163) test_to_s: .: (0.000141) Bio::TestModelFinder: test_find_model: .: (0.000548) Bio::TestMotif: test_creation_and_attributes: .: (0.000260) test_length: .: (0.000142) Bio::TestMyGraph: test_cliquishness: .: (0.000503) Bio::TestNA: test_accessor: .: (0.000190) test_na: .: (0.000122) test_name: .: (0.000157) test_names: .: (0.000126) test_to_re: .: (0.000295) test_weight: .: (0.000156) test_weight_rna: .: (0.000406) Bio::TestNAConstants: test_NAMES: .: (0.000207) test_NAMES_1_to_name: .: (0.000119) test_WEIGHT: .: (0.000130) Bio::TestNATranslate: test_translate: .: (0.000377) test_translate_1: .: (0.000216) test_translate_2: .: (0.000148) test_translate_3: .: (0.000142) test_translate_4: .: (0.000218) test_translate_5: .: (0.000151) test_translate_6: .: (0.000165) Bio::TestNCBIDB: test_fetch: .: (0.000312) test_p_entry2hash: .: (0.000613) test_p_subtag2array: .: (0.000119) test_p_toptag2array: .: (0.000103) Bio::TestNewick: test_reparse: .: (0.001004) test_reparse_before_lazy_parsing: .: (0.000410) test_string_tree: .: (0.001161) Bio::TestNewick2: test_string_tree: .: (0.000586) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000210) test_parse_newick_leaf: .: (0.000245) test_parse_newick_tokenize: .: (0.000312) Bio::TestNexus: test_nexus: .: (0.011707) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000260) test_uncapitalized_letter_Q32725_9POAL: .: (0.000152) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000232) test_load_parameters: .: (0.000155) test_parameters: .: (0.000127) test_set_default_parameters: .: (0.000468) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000861) test_expected_parameters_set_in_control_file: .: (0.000924) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000228) test_new_with_parameters: .: (0.000189) test_new_with_two_argument: .: (0.000176) test_new_without_argument: .: (0.000141) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001351) test_rates_hundred_and_fiftieth_position: .: (0.001147) test_rates_last_position: .: (0.001059) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.006474) test_tree: .: (0.006580) test_tree_length: .: (0.006335) test_tree_log_likelihood: .: (0.006316) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000344) test_parameters_should_be_loaded_from_control: .: (0.000258) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.002062) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000284) test_dN_dS: .: (0.000181) test_kappa: .: (0.000185) test_lnL: .: (0.000178) test_m3_classes: .: (0.000276) test_m3_lnL: .: (0.000195) test_m3_to_s: .: (0.000185) test_m3_tree: .: (0.000564) test_omega: .: (0.000179) test_to_s: .: (0.000171) test_tree: .: (0.000490) test_tree_length: .: (0.000172) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000662) test_p: .: (0.000356) test_position: .: (0.000333) test_probability: .: (0.000574) test_w: .: (0.000316) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000473) test_graph_omega: .: (0.000670) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000310) test_footer: .: (0.000193) test_header: .: (0.000174) test_initialize: .: (0.000238) test_models: .: (0.000227) test_nb_sites: .: (0.000875) test_num_codons: .: (0.000211) test_num_sequences: .: (0.000197) test_significant: .: (0.000202) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000329) test_nb_sites: .: (0.000278) test_significant: .: (0.000191) test_sites: .: (0.001217) Bio::TestPDB: test_accession: .: (0.001295) test_addModel: .: (0.000615) test_authors: .: (0.000861) test_bracket: .: (0.000627) test_classification: .: (0.000780) test_dbref: .: (0.000771) test_definition: .: (0.000731) test_each: .: (0.000658) test_each_model: .: (0.000571) test_entry_id: .: (0.000738) test_helix: .: (0.000635) test_inspect: .: (0.000801) test_jrnl: .: (0.000683) test_keywords: .: (0.000865) test_record: .: (0.000608) test_remark: .: (0.000978) test_seqres: .: (0.000826) test_sheet: .: (0.001156) test_ssbond: .: (0.000606) test_to_s: .: (0.001072) test_turn: .: (0.000602) test_version: .: (0.000876) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000266) test_U12: .: (0.000160) test_U13: .: (0.000159) test_U22: .: (0.000177) test_U23: .: (0.000201) test_U33: .: (0.000180) test_altLoc: .: (0.000179) test_chainID: .: (0.000177) test_charge: .: (0.000179) test_element: .: (0.000175) test_iCode: .: (0.000341) test_name: .: (0.000153) test_resName: .: (0.000228) test_resSeq: .: (0.000180) test_segID: .: (0.000168) test_serial: .: (0.000171) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000287) test_anisou: .: (0.000142) test_chainID: .: (0.000118) test_charge: .: (0.000128) test_comparable: .: (0.000152) test_do_parse: .: (0.000166) test_element: .: (0.000164) test_iCode: .: (0.000157) test_name: .: (0.000330) test_occupancy: .: (0.000201) test_original_data: .: (0.000156) test_record_name: .: (0.000145) test_resName: .: (0.000118) test_resSeq: .: (0.000128) test_residue: .: (0.000134) test_segID: .: (0.000132) test_serial: .: (0.000132) test_sigatm: .: (0.000135) test_tempFactor: .: (0.000174) test_ter: .: (0.000138) test_to_a: .: (0.000141) test_to_s: .: (0.000169) test_x: .: (0.000175) test_xyz: .: (0.000181) test_y: .: (0.000440) test_z: .: (0.000187) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000302) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000273) test_idcode: .: (0.000141) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000243) test_chainID2: .: (0.000130) test_icode1: .: (0.000103) test_icode2: .: (0.000154) test_measure: .: (0.000176) test_modNum: .: (0.000168) test_pep1: .: (0.000168) test_pep2: .: (0.000372) test_seqNum1: .: (0.000162) test_seqNum2: .: (0.000169) test_serNum: .: (0.000166) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000285) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000227) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000223) test_alpha: .: (0.000125) test_b: .: (0.000128) test_beta: .: (0.000165) test_c: .: (0.000148) test_gamma: .: (0.000141) test_sGroup: .: (0.000377) test_z: .: (0.000146) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000266) test_database: .: (0.000192) test_dbAccession: .: (0.000184) test_dbIdCode: .: (0.000187) test_dbseqBegin: .: (0.000196) test_dbseqEnd: .: (0.000186) test_idCode: .: (0.000203) test_idbnsBeg: .: (0.000194) test_insertBegin: .: (0.000190) test_insertEnd: .: (0.000189) test_seqBegin: .: (0.000186) test_seqEnd: .: (0.000456) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000234) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000272) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000239) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000252) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000250) test_depDate: .: (0.000165) test_idCode: .: (0.000158) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000243) test_hetID: .: (0.000175) test_iCode: .: (0.000162) test_numHetAtoms: .: (0.000166) test_seqNum: .: (0.000177) test_text: .: (0.000164) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000265) test_anisou: .: (0.000142) test_chainID: .: (0.000135) test_charge: .: (0.000145) test_comparable: .: (0.000165) test_do_parse: .: (0.000135) test_element: .: (0.000136) test_iCode: .: (0.000131) test_name: .: (0.000135) test_occupancy: .: (0.000179) test_original_data: .: (0.000492) test_record_name: .: (0.000132) test_resName: .: (0.000127) test_resSeq: .: (0.000323) test_residue: .: (0.000131) test_segID: .: (0.000174) test_serial: .: (0.000151) test_sigatm: .: (0.000163) test_tempFactor: .: (0.000231) test_ter: .: (0.000164) test_to_a: .: (0.000173) test_to_s: .: (0.000221) test_x: .: (0.000199) test_xyz: .: (0.000200) test_y: .: (0.000199) test_z: .: (0.000194) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000368) test_ChainH: .: (0.000226) test_ICode1: .: (0.000181) test_altLoc1: .: (0.000190) test_altLoc2: .: (0.000196) test_altLocH: .: (0.000217) test_chainID2: .: (0.000236) test_iCode2: .: (0.000235) test_iCodeH: .: (0.000238) test_name1: .: (0.000234) test_name2: .: (0.000592) test_nameH: .: (0.000196) test_resName1: .: (0.000191) test_resName2: .: (0.000198) test_resSeq1: .: (0.000226) test_resSeq2: .: (0.000306) test_resSeqH: .: (0.000217) test_sym1: .: (0.000177) test_sym2: .: (0.000183) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000240) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.005683) test_altLoc2: .: (0.000189) test_chainID1: .: (0.000176) test_chainID2: .: (0.000179) test_iCode1: .: (0.000184) test_iCode2: .: (0.000202) test_name1: .: (0.000208) test_name2: .: (0.000209) test_resName1: .: (0.000229) test_resName2: .: (0.000215) test_resSeq1: .: (0.000274) test_resSeq2: .: (0.000219) test_sym1: .: (0.000463) test_sym2: .: (0.000167) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000245) test_numCoord: .: (0.000151) test_numHelix: .: (0.000155) test_numHet: .: (0.000168) test_numRemark: .: (0.000163) test_numSeq: .: (0.000162) test_numSheet: .: (0.000166) test_numSite: .: (0.000162) test_numTer: .: (0.000161) test_numTurn: .: (0.000176) test_numXform: .: (0.000163) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000256) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000635) test_comment: .: (0.000164) test_iCode: .: (0.000187) test_idCode: .: (0.000163) test_resName: .: (0.000169) test_seqNum: .: (0.000182) test_stdRes: .: (0.000186) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000277) test_Mn2: .: (0.000167) test_Mn3: .: (0.000146) test_Vn: .: (0.000141) test_iGiven: .: (0.000154) test_serial: .: (0.000162) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000541) test_Mn2: .: (0.000168) test_Mn3: .: (0.000146) test_Vn: .: (0.000146) test_iGiven: .: (0.000190) test_serial: .: (0.000166) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000290) test_Mn2: .: (0.000189) test_Mn3: .: (0.000161) test_Vn: .: (0.000158) test_iGiven: .: (0.000162) test_serial: .: (0.000158) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000303) test_rIdCode: .: (0.000184) test_repDate: .: (0.000392) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000257) test_On2: .: (0.000146) test_On3: .: (0.000160) test_Tn: .: (0.000156) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000276) test_modId: .: (0.000175) test_modNum: .: (0.000174) test_modType: .: (0.000172) test_record: .: (0.000171) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000271) test_text: .: (0.000143) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000310) test_Sn2: .: (0.000382) test_Sn3: .: (0.000146) test_Un: .: (0.000137) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000226) test_Sn2: .: (0.000153) test_Sn3: .: (0.000153) test_Un: .: (0.000149) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000239) test_Sn2: .: (0.000157) test_Sn3: .: (0.000152) test_Un: .: (0.000149) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000315) test_conflict: .: (0.000196) test_database: .: (0.000367) test_dbIdCode: .: (0.000218) test_dbRes: .: (0.000161) test_dbSeq: .: (0.000171) test_iCode: .: (0.000177) test_idCode: .: (0.000191) test_resName: .: (0.000193) test_seqNum: .: (0.000191) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000314) test_numRes: .: (0.000160) test_resName: .: (0.000172) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000297) test_curChainId: .: (0.000239) test_curICode: .: (0.000244) test_curResName: .: (0.000191) test_curResSeq: .: (0.000228) test_endChainID: .: (0.000190) test_endICode: .: (0.000208) test_endResName: .: (0.000224) test_endSeqNum: .: (0.000242) test_initChainID: .: (0.000241) test_initICode: .: (0.000241) test_initResName: .: (0.000493) test_initSeqNum: .: (0.000187) test_numStrands: .: (0.000225) test_prevAtom: .: (0.000227) test_prevChainId: .: (0.000196) test_prevICode: .: (0.000226) test_prevResName: .: (0.000245) test_prevResSeq: .: (0.000243) test_sense: .: (0.000238) test_sheetID: .: (0.000241) test_strand: .: (0.000466) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000316) test_chainID: .: (0.000168) test_charge: .: (0.000172) test_element: .: (0.000179) test_iCode: .: (0.000186) test_name: .: (0.000205) test_resName: .: (0.000200) test_resSeq: .: (0.000202) test_segID: .: (0.000199) test_serial: .: (0.000196) test_sigOcc: .: (0.000202) test_sigTemp: .: (0.000201) test_sigX: .: (0.000202) test_sigY: .: (0.000347) test_sigZ: .: (0.000172) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000328) test_SigmaU12: .: (0.000188) test_SigmaU13: .: (0.000202) test_SigmaU22: .: (0.000187) test_SigmaU23: .: (0.000199) test_SigmaU33: .: (0.000196) test_altLoc: .: (0.000197) test_chainID: .: (0.000196) test_charge: .: (0.000196) test_element: .: (0.000195) test_iCode: .: (0.000193) test_name: .: (0.000205) test_resName: .: (0.000198) test_resSeq: .: (0.000265) test_segID: .: (0.000201) test_serial: .: (0.000197) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000296) test_chainID2: .: (0.000214) test_chainID3: .: (0.000191) test_chainID4: .: (0.000205) test_iCode1: .: (0.000216) test_iCode2: .: (0.000214) test_iCode3: .: (0.000376) test_iCode4: .: (0.000173) test_numRes: .: (0.000175) test_resName1: .: (0.000227) test_resName2: .: (0.000205) test_resName3: .: (0.000218) test_resName4: .: (0.000215) test_seq1: .: (0.000214) test_seq2: .: (0.000214) test_seq3: .: (0.000235) test_seq4: .: (0.000214) test_seqNum: .: (0.000214) test_siteID: .: (0.000373) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000344) test_altLoc2: .: (0.000187) test_atom1: .: (0.000173) test_atom2: .: (0.000165) test_chainID1: .: (0.000174) test_chainID2: .: (0.000185) test_iCode1: .: (0.000188) test_iCode2: .: (0.000184) test_resName1: .: (0.000183) test_resName2: .: (0.000183) test_resSeq1: .: (0.000181) test_resSeq2: .: (0.000184) test_sym1: .: (0.000182) test_sym2: .: (0.000183) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000274) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000240) test_sIdCode: .: (0.000180) test_sprsdeDate: .: (0.000160) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000244) test_iCode: .: (0.000171) test_resName: .: (0.000166) test_resSeq: .: (0.000166) test_serial: .: (0.000163) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000250) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000445) test_t1: .: (0.000154) test_t2: .: (0.000167) test_t3: .: (0.000150) test_text: .: (0.000164) Bio::TestPROSITE: test_ac: .: (0.001396) test_cc: .: (0.001181) test_de: .: (0.001232) test_division: .: (0.001190) test_dr: .: (0.059016) test_dt: .: (0.001432) test_false_neg: .: (0.001359) test_false_pos: .: (0.001230) test_false_positive_sequences: .: (0.001273) test_list_falsenegative: .: (0.012679) test_list_falsepositive: .: (0.012676) test_list_potentialhit: .: (0.012766) test_list_truepositive: .: (0.015409) test_list_unknown: .: (0.012920) test_list_xref: .: (0.012820) test_ma: .: (0.001123) test_max_repeat: .: (0.001122) test_name: .: (0.001371) test_nr: .: (0.001181) test_pa: .: (0.001322) test_pa2re: .: (0.002981) test_partial: .: (0.001299) test_pdb_xref: .: (0.001376) test_pdoc_xref: .: (0.001376) test_positive: .: (0.001290) test_positive_hits: .: (0.001638) test_positive_sequences: .: (0.001749) test_release: .: (0.001315) test_ru: .: (0.001820) test_self_pa2re: .: (0.001503) test_site: .: (0.001686) test_skip_flag: .: (0.001202) test_swissprot_release_number: .: (0.001318) test_swissprot_release_sequences: .: (0.001435) test_taxon_range: .: (0.001490) test_total: .: (0.001471) test_total_hits: .: (0.001532) test_total_sequences: .: (0.001270) test_unknown: .: (0.001361) test_unknown_hits: .: (0.001303) test_unknown_sequences: .: (0.001147) Bio::TestPROSITEConst: test_delimiter: .: (0.000265) test_tagsize: .: (0.000125) Bio::TestPTS1: test_function_set: .: (0.000230) test_function_set_number_1: .: (0.000169) test_function_set_number_2: .: (0.000154) test_function_set_number_3: .: (0.000151) test_function_show: .: (0.000139) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000247) Bio::TestPTS1New: test_fungi: .: (0.000442) test_general: .: (0.000136) test_metazoa: .: (0.000131) Bio::TestQualifier: test_qualifier: .: (0.000221) test_value: .: (0.000131) Bio::TestREBASE: test_methods: .: (0.000726) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000975) test_bit_score: .: (0.000548) test_evalue: .: (0.000502) test_gaps: .: (0.000539) test_hit_from: .: (0.000731) test_hit_to: .: (0.000596) test_hseq: .: (0.000554) test_identity: .: (0.000575) test_midline: .: (0.000587) test_percent_identity: .: (0.000615) test_positive: .: (0.000535) test_qseq: .: (0.001941) test_query_from: .: (0.000595) test_query_to: .: (0.000552) test_score: .: (0.000556) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000605) test_hits_size: .: (0.001200) test_iterations_size: .: (0.001072) test_program: .: (0.000721) test_query_def: .: (0.001120) test_query_len: .: (0.001102) test_version: .: (0.000692) test_version_date: .: (0.000497) test_version_number: .: (0.000465) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000637) test_definition: .: (0.000582) test_evalue: .: (0.000769) test_hsps_size: .: (0.000519) test_identity: .: (0.000602) test_lap_at: .: (0.000593) test_len: .: (0.000562) test_midline: .: (0.000876) test_overlap: .: (0.000513) test_query_end: .: (0.000570) test_query_seq: .: (0.000572) test_query_start: .: (0.000761) test_target_def: .: (0.000545) test_target_end: .: (0.000595) test_target_len: .: (0.000535) test_target_seq: .: (0.000763) test_target_start: .: (0.000589) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000439) test_get_entry: .: (0.000415) test_rewind: .: (0.000171) test_skip_leader: .: (0.000223) Bio::TestReference: test_abstract: .: (0.000483) test_affiliations: .: (0.000121) test_authors: .: (0.000117) test_format_bibitem: .: (0.000186) test_format_bibtex: .: (0.000241) test_format_bibtex_with_arguments: .: (0.000248) test_format_cell: .: (0.000174) test_format_current: .: (0.000172) test_format_endnote: .: (0.000193) test_format_general: .: (0.000190) test_format_genome_biol: .: (0.000175) test_format_genome_res: .: (0.000218) test_format_nar: .: (0.000178) test_format_nature: .: (0.000200) test_format_rd: .: (0.000179) test_format_science: .: (0.000236) test_format_trends: .: (0.000152) test_issue: .: (0.000134) test_journal: .: (0.000134) test_mesh: .: (0.000148) test_pages: .: (0.000136) test_pubmed: .: (0.000132) test_pubmed_url: .: (0.000141) test_url: .: (0.000133) test_volume: .: (0.000168) test_year: .: (0.000160) Bio::TestReference_noURL: test_format_endnote: .: (0.000249) test_url: .: (0.000140) Bio::TestReferences: test_append: .: (0.000277) test_each: .: (0.000146) Bio::TestRelation: test_comparison_operator: .: (0.000320) test_uniq: .: (0.000186) Bio::TestResidue: test_addAtom: .: (0.000538) test_each: .: (0.000216) test_each_atom: .: (0.000210) test_get_residue_id_from_atom: .: (0.000195) test_het_atom: .: (0.000190) test_iCode: .: (0.000207) test_inspect: .: (0.000241) test_resSeq: .: (0.000218) test_sort: .: (0.000451) test_square_bracket: .: (0.000195) test_to_s: .: (0.000247) test_update_resudue_id: .: (0.000186) Bio::TestResidueFinder: test_each_residue: .: (0.000273) test_find_residue: .: (0.000179) test_residues: .: (0.000229) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.136301) test_cut_from_bio_sequence_na: .: (0.023979) test_cut_without_permutations: .: (0.017517) test_view_ranges: .: (0.017952) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.001090) test_cuts_after_remove_incomplete_cuts: .: (0.000598) test_strands_for_display: .: (0.002139) test_strands_for_display_current: .: (0.000596) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000507) test_fragments_for_display_1: .: (0.000707) test_fragments_for_display_10: .: (0.000814) test_fragments_for_display_2: .: (0.000686) test_fragments_for_display_3: .: (0.000994) test_fragments_for_display_4: .: (0.005002) test_fragments_for_display_5: .: (0.000554) test_fragments_for_display_6: .: (0.000935) test_fragments_for_display_7: .: (0.000512) test_fragments_for_display_8: .: (0.000474) test_fragments_for_display_9: .: (0.000483) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000437) test_obj_3: .: (0.000243) test_obj_7: .: (0.000233) test_obj_z: .: (0.000230) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000331) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000463) test_bracket_eq: .: (0.000235) test_concat: .: (0.000158) test_delete: .: (0.000163) test_dup: .: (0.000228) test_each: .: (0.000199) test_eqeq: .: (0.000172) test_eqeq_false: .: (0.000153) test_eqeq_other: .: (0.000185) test_eqeq_self: .: (0.000149) test_include?: .: (0.000139) test_internal_data: .: (0.000159) test_internal_data_eq: .: (0.000152) test_length: .: (0.000168) test_ltlt: .: (0.000400) test_ltlt_larger: .: (0.000148) test_ltlt_middle: .: (0.000141) test_plus: .: (0.000160) test_plus_error: .: (0.000205) test_push: .: (0.000175) test_reverse_each: .: (0.000234) test_self_bracket: .: (0.000154) test_self_new: .: (0.000194) test_size: .: (0.000148) test_sort!: .: (0.000144) test_to_a: .: (0.000149) test_uniq!: .: (0.000142) test_unshift: .: (0.000186) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003694) test_complement: .: (0.003265) test_complement_with_cut_symbols: .: (0.003217) test_cut_locations: .: (0.003090) test_cut_locations_in_enzyme_notation: .: (0.003290) test_primary: .: (0.003213) test_primary_with_cut_symbols: .: (0.003362) test_to_re: .: (0.003243) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000818) test_align_with_cuts: .: (0.000752) test_argument_error: .: (0.001129) test_ds: .: (0.000654) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000643) test_complement: .: (0.000215) test_contents: .: (0.000204) test_primary: .: (0.000203) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000367) test_complement: .: (0.000201) test_contents: .: (0.000200) test_primary: .: (0.000203) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000481) test_contents: .: (0.000183) test_primary: .: (0.000166) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000268) test_complement_to_array_index: .: (0.000243) test_complement_to_array_index_class: .: (0.000226) test_contents: .: (0.000202) test_primary: .: (0.000201) test_primary_to_array_index: .: (0.000265) test_primary_to_array_index_class: .: (0.000468) test_to_array_index: .: (0.000372) test_to_array_index_class: .: (0.000346) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000412) test_rebase: .: (0.000175) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001100) test_creation_with_no_cuts: .: (0.000423) test_cut_locations: .: (0.000429) test_cut_locations_in_enzyme_notation: .: (0.000758) test_orientation: .: (0.000429) test_pattern: .: (0.000411) test_pattern_palindromic?: .: (0.000649) test_stripped: .: (0.000421) test_to_re: .: (0.000354) test_with_cut_symbols: .: (0.000419) test_with_spaces: .: (0.000716) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000701) test_creation_with_no_cuts: .: (0.000514) test_cut_locations: .: (0.000401) test_cut_locations_in_enzyme_notation: .: (0.000408) test_orientation: .: (0.000408) test_pattern: .: (0.000516) test_pattern_palindromic?: .: (0.000468) test_stripped: .: (0.000385) test_to_re: .: (0.000368) test_with_cut_symbols: .: (0.000445) test_with_spaces: .: (0.000478) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000405) test_initialize_with_pattern: .: (0.000408) test_max: .: (0.000167) test_min: .: (0.000168) test_to_array_index: .: (0.000194) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000278) test_bracket_eq: .: (0.000201) test_concat: .: (0.000170) test_delete: .: (0.000151) test_dup: .: (0.000205) test_each: .: (0.000233) test_eqeq: .: (0.000175) test_eqeq_false: .: (0.000145) test_eqeq_other: .: (0.000134) test_eqeq_self: .: (0.000131) test_include?: .: (0.000267) test_internal_data_hash: .: (0.000133) test_internal_data_hash_eq: .: (0.000147) test_length: .: (0.000129) test_ltlt: .: (0.000149) test_ltlt_noeffect: .: (0.000155) test_plus: .: (0.000155) test_plus_error: .: (0.000193) test_private_push_element: .: (0.000151) test_private_push_element_intermediate: .: (0.000154) test_private_push_element_last: .: (0.000156) test_private_push_element_noeffect: .: (0.000148) test_private_sorted_keys: .: (0.000142) test_private_unshift_element: .: (0.000150) test_private_unshift_element_first: .: (0.000160) test_private_unshift_element_intermediate: .: (0.000157) test_private_unshift_element_noeffect: .: (0.000150) test_push: .: (0.000159) test_reverse_each: .: (0.000314) test_self_bracket: .: (0.000144) test_self_new: .: (0.000145) test_size: .: (0.000128) test_sort!: .: (0.000133) test_to_a: .: (0.000139) test_uniq!: .: (0.000133) test_unshift: .: (0.000155) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000273) test_left_padding: .: (0.000207) test_right_padding: .: (0.000148) test_strip_padding: .: (0.000161) Bio::TestSOFT: test_dataset: .: (0.004821) test_series: .: (0.004587) Bio::TestSOSUIReport: test_entry_id: .: (0.000290) test_prediction: .: (0.000191) test_tmh: .: (0.000187) test_tmhs: .: (0.000216) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000300) test_rs: .: (0.000122) Bio::TestSOSUITMH: test_grade: .: (0.000267) test_range: .: (0.000181) test_sequence: .: (0.000187) Bio::TestSampleGraph: test_bellman_ford: .: (0.000439) test_bfs_shortest_path: .: (0.000201) test_breadth_first_search: .: (0.000199) test_depth_first_search: .: (0.000299) test_dijkstra: .: (0.000334) test_dump_list: .: (0.000293) test_dump_matrix: .: (0.000336) test_extract_subgraph_by_label: .: (0.000228) test_extract_subgraph_by_list: .: (0.000228) test_extract_subgraph_retains_disconnected_nodes: .: (0.000194) test_small_world_aka_node_degree_histogram: .: (0.000199) test_to_matrix: .: (0.000361) test_to_matrix_fixed_index: .: (0.000336) test_undirected_cliquishness: .: (0.000317) Bio::TestScf_version_2: test_complement: .: (0.007956) test_seq: .: (0.007373) test_to_biosequence: .: (0.007607) Bio::TestScf_version_3: test_complement: .: (0.023575) test_seq: .: (0.023185) test_to_biosequence: .: (0.023267) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000283) test_AA_new_sequence_all_legal_symbols: .: (0.000142) test_AA_new_sequence_removes_whitespace: .: (0.000148) test_AA_new_sequence_upcases_symbols: .: (0.000146) test_DNA_new_blank_sequence: .: (0.000142) test_DNA_new_sequence_downcases_symbols: .: (0.000141) test_DNA_new_sequence_removes_whitespace: .: (0.000271) test_NA_randomize_with_counts: .: (0.000520) test_NA_randomize_with_counts_and_block: .: (0.000666) test_RNA_new_sequence: .: (0.000131) test_ambiguous_dna_sequence_complement: .: (0.000137) test_ambiguous_rna_sequence_complement: .: (0.000136) test_amino_acid_codes: .: (0.000169) test_amino_acid_molecular_weight: .: (0.000253) test_amino_acid_names: .: (0.000180) test_amino_acid_randomize_can_be_chained: .: (0.000857) test_amino_acid_randomize_has_same_composition: .: (0.000515) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000525) test_dna_composition: .: (0.000150) test_dna_gc_percent: .: (0.000164) test_dna_molecular_weight: .: (0.000193) test_dna_pikachu: .: (0.000146) test_dna_sequence_complement: .: (0.000141) test_dna_sequence_translate: .: (0.000395) test_dna_to_re: .: (0.000190) test_element_reference_operator_with_one_argument: .: (0.000136) test_element_reference_operator_with_two_arguments: .: (0.000135) test_invalid_nucleic_acid_illegal_bases: .: (0.000173) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000201) test_nucleic_acid_names: .: (0.000166) test_randomize_dna_can_be_chained: .: (0.000485) test_randomize_dna_retains_composition: .: (0.000235) test_randomize_dna_with_block: .: (0.000267) test_rna_composition: .: (0.000160) test_rna_gc_percent: .: (0.000170) test_rna_molecular_weight: .: (0.000217) test_rna_pikachu: .: (0.000146) test_rna_sequence_complement: .: (0.000140) test_rna_sequence_translate: .: (0.000338) test_rna_to_re: .: (0.000182) test_total: .: (0.000146) test_two_consecutive_dna_randomizations_not_equal: .: (0.000232) test_valid_dna_sequence_illegal_bases: .: (0.000142) Bio::TestSequenceAA: test_codes: .: (0.000209) test_molecular_weight: .: (0.000187) test_names: .: (0.000163) test_to_re: .: (0.000168) test_to_s: .: (0.000114) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000257) Bio::TestSequenceAANew: test_new: .: (0.000184) test_new_n: .: (0.000120) test_new_r: .: (0.000124) test_new_t: .: (0.000119) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000235) test_concat: .: (0.000132) test_push: .: (0.000119) test_seq: .: (0.000117) test_splicing: .: (0.000260) test_sum: .: (0.000122) test_to_s: .: (0.000218) test_to_str: .: (0.000120) test_total: .: (0.000130) test_window_search: .: (0.000293) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000177) test_normalize_A: .: (0.000126) test_normalize_a: .: (0.000123) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000750) test_randomize_with_block: .: (0.008349) test_randomize_with_hash: .: (0.000952) test_randomize_with_hash_block: .: (0.003076) 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' =============================================================================== : (0.001100) 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' =============================================================================== : (0.000553) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000250) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000159) test_subseq_returns_subsequence: .: (0.000127) test_to_s_returns_self_as_string: .: (0.000145) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000252) test_window_search_with_width_3_step_two_with_residual: .: (0.000145) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000256) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000220) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000257) test_na_self_randomize: .: (0.000202) Bio::TestSequenceDBLink: test_database: .: (0.000335) test_id: .: (0.000110) test_secondary_ids: .: (0.000110) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000281) test_parse_uniprot_DR_line: .: (0.000147) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000865) test_output_width_35: .: (0.000314) test_output_width_nil: .: (0.000321) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000555) test_output_after_adding_sequence: .: (0.000325) test_output_after_truncating_sequence: .: (0.000215) test_output_from_error_probabilities: .: (0.002287) test_output_width45: .: (0.000249) test_output_with_converting_score_phred2solexa: .: (0.000529) test_output_with_converting_score_solexa2phred: .: (0.000349) test_output_with_default_score: .: (0.000246) Bio::TestSequenceMasker: test_mask: .: (0.000282) test_mask_with_enumerator: .: (0.000224) test_mask_with_enumerator_empty_mask_char: .: (0.000204) test_mask_with_enumerator_excess: .: (0.000517) test_mask_with_enumerator_longer_mask_char: .: (0.000167) test_mask_with_enumerator_shorter: .: (0.000203) test_mask_with_error_probability: .: (0.000189) test_mask_with_quality_score: .: (0.000169) Bio::TestSequenceNA: test_at_content: .: (0.000423) test_at_skew: .: (0.000247) test_codon_usage: .: (0.000153) test_complement: .: (0.000130) test_dna: .: (0.000133) test_dna!: .: (0.000152) test_forward_complement: .: (0.000183) test_gc_content: .: (0.000303) test_gc_percent: .: (0.000307) test_gc_skew: .: (0.000327) test_iliegal_bases: .: (0.000127) test_molecular_weight: .: (0.000167) test_names: .: (0.000176) test_reverse_complement: .: (0.000169) test_rna: .: (0.000134) test_rna!: .: (0.000130) test_splicing: .: (0.000187) test_to_re: .: (0.000217) test_to_s: .: (0.000275) Bio::TestSequenceNACommon: test_composition: .: (0.000223) test_concat: .: (0.000123) test_push: .: (0.000125) test_seq: .: (0.000125) test_splicing: .: (0.000189) test_sum: .: (0.000129) test_to_s: .: (0.000116) test_to_str: .: (0.000119) test_total: .: (0.000134) test_window_search: .: (0.000309) Bio::TestSequenceNANew: test_new: .: (0.000218) test_new_n: .: (0.000328) test_new_r: .: (0.000114) test_new_t: .: (0.000115) Bio::TestSequenceNATranslation: test_translate: .: (0.000401) test_translate_0: .: (0.000582) test_translate_1: .: (0.000230) test_translate_2: .: (0.000218) test_translate_3: .: (0.000220) test_translate_4: .: (0.000272) test_translate_5: .: (0.000379) test_translate_6: .: (0.000243) test_translate_7: .: (0.000429) test_translate_given_codon_table: .: (0.032348) test_translate_n1: .: (0.000426) test_translate_n2: .: (0.000498) test_translate_n3: .: (0.000345) test_translate_unknown_o: .: (0.000205) test_translate_unknown_x: .: (0.000202) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000196) test_convert_scores_from_phred_to_solexa: .: (0.000345) test_convert_scores_from_solexa_to_phred: .: (0.000156) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000172) test_convert_scores_from_phred: .: (0.000103) test_convert_scores_from_phred_to_solexa: .: (0.000417) test_convert_scores_from_solexa: .: (0.000172) test_convert_scores_from_solexa_to_phred: .: (0.000152) test_convert_scores_to_phred: .: (0.000087) test_convert_scores_to_solexa: .: (0.000315) test_p2q: .: (0.000140) test_phred_p2q: .: (0.000134) test_phred_q2p: .: (0.003065) test_q2p: .: (0.003011) test_quality_score_type: .: (0.000095) test_self_convert_scores_to_solexa: .: (0.000292) test_self_p2q: .: (0.000154) test_self_q2p: .: (0.002922) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000241) test_convert_scores_from_phred: .: (0.000386) test_convert_scores_from_phred_to_solexa: .: (0.000320) test_convert_scores_from_solexa: .: (0.000086) test_convert_scores_from_solexa_to_phred: .: (0.000151) test_convert_scores_to_phred: .: (0.000161) test_convert_scores_to_solexa: .: (0.000092) test_p2q: .: (0.000209) test_q2p: .: (0.005759) test_quality_score_type: .: (0.000100) test_self_convert_scores_to_phred: .: (0.000165) test_self_p2q: .: (0.000205) test_self_q2p: .: (0.003755) test_solexa_p2q: .: (0.000528) test_solexa_q2p: .: (0.003382) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000219) test_center: .: (0.000138) test_chomp: .: (0.000146) test_chop: .: (0.000157) test_delete: .: (0.000121) test_delete_prefix: .: (0.000115) test_delete_suffix: .: (0.000226) test_downcase: .: (0.000106) test_each_char: .: (0.000147) test_each_char_enum: .: (0.000146) test_each_grapheme_cluster: .: (0.000307) test_each_grapheme_cluster_enum: .: (0.000252) test_each_line: .: (0.000139) test_each_line_enum: .: (0.000124) test_gsub: .: (0.000123) test_gsub_with_block: .: (0.000351) test_ljust: .: (0.000106) test_lstrip: .: (0.000102) test_multiply: .: (0.000106) test_next: .: (0.000119) test_reverse: .: (0.000135) test_rjust: .: (0.000117) test_rstrip: .: (0.000275) test_slice: .: (0.000138) test_slice2: .: (0.000100) test_split: .: (0.000131) test_squeeze: .: (0.000119) test_strip: .: (0.000117) test_sub: .: (0.000127) test_sub_with_block: .: (0.000233) test_succ: .: (0.000103) test_swapcase: .: (0.000102) test_tr: .: (0.000109) test_tr_s: .: (0.000118) test_upcase: .: (0.000119) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000421) test_partition_nomatch: .: (0.000127) test_partition_sep_TSeq: .: (0.000120) test_partition_sep_regexp: .: (0.000129) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000228) test_rpartition_nomatch: .: (0.000151) test_rpartition_sep_TSeq: .: (0.000146) test_rpartition_sep_regexp: .: (0.000152) Bio::TestShRNA: test_blocK_it: .: (0.015526) test_blocK_it_: .: (0.042193) test_blocK_it_BLOCK_IT: .: (0.040420) test_blocK_it_BLOCK_iT: .: (0.015682) test_blocK_it_piGene: .: (0.015877) test_bottom_strand: .: (0.015912) test_bottom_strand_class: .: (0.015846) test_bottom_strand_nil: .: (0.015014) test_design: .: (0.016272) test_design_BLOCK_IT: .: (0.016946) test_report: .: (0.015113) test_report_before_design: .: (0.014770) test_top_strand: .: (0.016695) test_top_strand_class: .: (0.015956) test_top_strand_nil: .: (0.014682) Bio::TestShRNANew: test_new: .: (0.000416) Bio::TestSiRNA: test_antisense_size: .: (0.000196) test_design: .: (0.016256) test_design_reynolds: .: (0.019277) test_design_uitei: .: (0.014768) test_max_gc_percent: .: (0.000119) test_min_gc_percent: .: (0.000100) test_reynolds: .: (0.020118) test_reynolds?: .: (0.000146) test_uitei: .: (0.015693) test_uitei?: .: (0.000133) Bio::TestSiRNANew: test_new: .: (0.000360) Bio::TestSiRNAPair: test_antisense: .: (0.014833) test_gc_percent: .: (0.016447) test_report: .: (0.015628) test_rule: .: (0.014958) test_sense: .: (0.015687) test_start: .: (0.015706) test_stop: .: (0.014865) test_target: .: (0.014472) Bio::TestSiRNAPairNew: test_new: .: (0.000554) Bio::TestSim4Report: test_all_hits: .: (0.000417) test_each: .: (0.000226) test_each_hit: .: (0.000213) test_hits: .: (0.000217) test_num_hits: .: (0.000201) test_query_def: .: (0.000211) test_query_id: .: (0.000224) test_query_len: .: (0.000223) test_seq1: .: (0.000374) Bio::TestSim4Report2: test_all_hits: .: (0.000351) test_each: .: (0.000244) test_each_hit: .: (0.000208) test_hits: .: (0.000226) test_num_hits: .: (0.000195) test_query_def: .: (0.000204) test_query_id: .: (0.000214) test_query_len: .: (0.000213) test_seq1: .: (0.000261) Bio::TestSim4Report4: test_all_hits: .: (0.000430) test_each: .: (0.000224) test_each_hit: .: (0.000217) test_hits: .: (0.000220) test_num_hits: .: (0.000202) test_query_def: .: (0.000210) test_query_id: .: (0.000293) test_query_len: .: (0.000202) test_seq1: .: (0.000241) Bio::TestSim4ReportHit: test_align: .: (0.000360) test_complement?: .: (0.000195) test_definition: .: (0.000191) test_each: .: (0.000343) test_exons: .: (0.000588) test_hit_id: .: (0.000273) test_hsps: .: (0.000286) test_introns: .: (0.000281) test_len: .: (0.000183) test_query_def: .: (0.000175) test_query_id: .: (0.000192) test_query_len: .: (0.000192) test_segmentpairs: .: (0.000602) test_seq1: .: (0.000228) test_seq2: .: (0.000224) test_target_def: .: (0.000189) test_target_id: .: (0.000223) test_target_len: .: (0.000202) Bio::TestSim4ReportHit2: test_align: .: (0.000395) test_complement?: .: (0.000191) test_definition: .: (0.000377) test_each: .: (0.000285) test_exons: .: (0.000279) test_hit_id: .: (0.000204) test_hsps: .: (0.000276) test_introns: .: (0.000303) test_len: .: (0.000184) test_query_def: .: (0.000352) test_query_id: .: (0.000185) test_query_len: .: (0.000184) test_segmentpairs: .: (0.000286) test_seq1: .: (0.000217) test_seq2: .: (0.000209) test_target_def: .: (0.000182) test_target_id: .: (0.000208) test_target_len: .: (0.000221) Bio::TestSim4ReportHit4: test_align: .: (0.000581) test_complement?: .: (0.000205) test_definition: .: (0.000220) test_each: .: (0.000382) test_exons: .: (0.000378) test_hit_id: .: (0.000212) test_hsps: .: (0.000467) test_introns: .: (0.000372) test_len: .: (0.000207) test_query_def: .: (0.000225) test_query_id: .: (0.000200) test_query_len: .: (0.000208) test_segmentpairs: .: (0.000527) test_seq1: .: (0.000264) test_seq2: .: (0.000232) test_target_def: .: (0.000194) test_target_id: .: (0.000201) test_target_len: .: (0.000215) Bio::TestSim4ReportSegment: test_from: .: (0.000217) test_self_new: .: (0.000144) test_seq: .: (0.000115) test_to: .: (0.000120) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000512) test_direction: .: (0.000257) test_hit_from: .: (0.000271) test_hit_to: .: (0.000254) test_hseq: .: (0.000250) test_midline: .: (0.000256) test_percent_identity: .: (0.000452) test_qseq: .: (0.000251) test_query_from: .: (0.000246) test_query_to: .: (0.000268) test_seq1: .: (0.000288) test_seq2: .: (0.000271) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000518) test_direction: .: (0.000257) test_hit_from: .: (0.000252) test_hit_to: .: (0.000253) test_hseq: .: (0.000283) test_midline: .: (0.000265) test_percent_identity: .: (0.000238) test_qseq: .: (0.000355) test_query_from: .: (0.000268) test_query_to: .: (0.000248) test_seq1: .: (0.000280) test_seq2: .: (0.000267) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000394) test_direction: .: (0.000341) test_hit_from: .: (0.000300) test_hit_to: .: (0.000321) test_hseq: .: (0.000301) test_midline: .: (0.000410) test_percent_identity: .: (0.000332) test_qseq: .: (0.000312) test_query_from: .: (0.000306) test_query_to: .: (0.000283) test_seq1: .: (0.000442) test_seq2: .: (0.000354) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000441) test_direction: .: (0.000303) test_hit_from: .: (0.000402) test_hit_to: .: (0.000323) test_hseq: .: (0.000370) test_midline: .: (0.000323) test_percent_identity: .: (0.000285) test_qseq: .: (0.000414) test_query_from: .: (0.000322) test_query_to: .: (0.000286) test_seq1: .: (0.000308) test_seq2: .: (0.000316) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000575) test_direction: .: (0.000304) test_hit_from: .: (0.000331) test_hit_to: .: (0.000292) test_hseq: .: (0.000288) test_midline: .: (0.000368) test_percent_identity: .: (0.000299) test_qseq: .: (0.000297) test_query_from: .: (0.000290) test_query_to: .: (0.000285) test_seq1: .: (0.000613) test_seq2: .: (0.000348) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000352) test_direction: .: (0.000253) test_hit_from: .: (0.000249) test_hit_to: .: (0.000479) test_hseq: .: (0.000251) test_midline: .: (0.000268) test_percent_identity: .: (0.000254) test_qseq: .: (0.000304) test_query_from: .: (0.000248) test_query_to: .: (0.000502) test_seq1: .: (0.000273) test_seq2: .: (0.000269) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000352) test_direction: .: (0.000251) test_hit_from: .: (0.000272) test_hit_to: .: (0.000450) test_hseq: .: (0.000332) test_midline: .: (0.000250) test_percent_identity: .: (0.000328) test_qseq: .: (0.000258) test_query_from: .: (0.000260) test_query_to: .: (0.000268) test_seq1: .: (0.000486) test_seq2: .: (0.000289) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000238) test_entry_id: .: (0.000130) test_filename: .: (0.000132) test_len: .: (0.000132) test_self_new: .: (0.000150) test_self_parse: .: (0.000171) Bio::TestTMHMMReport: test_entry_id: .: (0.000611) test_exp_aas_in_tmhs: .: (0.000274) test_exp_first_60aa: .: (0.000263) test_helix: .: (0.000305) test_predicted_tmhs: .: (0.000279) test_query_len: .: (0.000428) test_tmhs: .: (0.000264) test_to_s: .: (0.000330) test_total_prob_of_N_in: .: (0.000256) Bio::TestTMHMMReport_reports: test_reports: .: (0.000290) Bio::TestTMHMMTMH: test_entry_id: .: (0.000475) test_pos: .: (0.000265) test_range: .: (0.000284) test_status: .: (0.000266) test_version: .: (0.000260) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000320) test_cutoff: .: (0.000212) test_entry_id: .: (0.000208) test_length: .: (0.000206) test_loc: .: (0.000264) test_name: .: (0.000228) test_networks: .: (0.000256) test_prediction: .: (0.000283) test_query_len: .: (0.000321) test_query_sequences: .: (0.000198) test_rc: .: (0.000204) test_version: .: (0.000206) Bio::TestTargetPReportConst: test_delimiter: .: (0.000199) test_rs: .: (0.000118) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000202) test_togows_access_wait: .: (2.004679) Bio::TestTogoWSREST: test_debug: .: (0.000744) test_debug_default: .: (0.000251) test_internal_http: .: (0.000455) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000264) test_entry: .: (0.000323) test_entry_database_list: .: (0.000126) test_new: .: (0.000477) test_new_with_uri_object: .: (0.000264) test_new_with_uri_string: .: (0.000221) test_retrieve: .: (0.000159) test_search: .: (0.000123) test_search_database_list: .: (0.000125) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000387) test_prepare_return_value: .: (0.000260) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000602) Bio::TestTree: test_get_edge_distance: .: (0.000267) test_get_edge_distance_string: .: (0.000179) test_get_node_name: .: (0.000132) test_initialize: .: (0.000148) test_options: .: (0.000128) test_root: .: (0.000111) test_root=: .: (0.000136) Bio::TestTree2: test_add_edge: .: (0.000375) test_add_node: .: (0.000207) test_adjacency_matrix: .: (0.000274) test_adjacency_matrix_with_block: .: (0.000401) test_adjacent_nodes: .: (0.000225) test_adjacent_nodes_nonexistent: .: (0.000163) test_ancestors: .: (0.000211) test_children: .: (0.000206) test_clear: .: (0.000213) test_clear_node: .: (0.000266) test_clear_node_nonexistent: .: (0.000304) test_collect_edge!: .: (0.000266) test_collect_node!: .: (0.000274) test_concat: .: (0.000377) test_descendents: .: (0.000205) test_distance_matrix: .: (0.000431) test_each_edge: .: (0.000211) test_each_node: .: (0.000204) test_each_out_edge: .: (0.000218) test_each_out_edge_chimpanzee: .: (0.000201) test_each_out_edge_human: .: (0.000211) test_each_out_edge_mammals: .: (0.000258) test_each_out_edge_nonexistent: .: (0.000289) test_each_out_edge_primates: .: (0.000219) test_each_out_edge_rat: .: (0.000184) test_each_out_edge_rodents: .: (0.000223) test_edges: .: (0.000196) test_get_edge: .: (0.000308) test_get_edge_indirect: .: (0.000158) test_get_edge_merged: .: (0.000182) test_get_edge_nonexistent: .: (0.000167) test_get_node_bootstrap: .: (0.000355) test_get_node_bootstrap_string=: .: (0.000210) test_get_node_by_name: .: (0.000263) test_get_node_by_name_noexistent: .: (0.000158) test_include?: .: (0.000197) test_include_nonexistent: .: (0.000170) test_insert_node: .: (0.000245) test_leaves: .: (0.000232) test_leaves_noargs: .: (0.000213) test_lowest_common_ancestor: .: (0.000235) test_nodes: .: (0.000208) test_number_of_edges: .: (0.000191) test_number_of_nodes: .: (0.000332) test_out_degree: .: (0.000222) test_out_degree_nonexistent: .: (0.000171) test_out_edges: .: (0.000206) test_out_edges_mammals: .: (0.000253) test_out_edges_nonexistent: .: (0.000201) test_out_edges_primates: .: (0.000269) test_out_edges_rodents: .: (0.000217) test_parent: .: (0.000195) test_path: .: (0.000441) test_remove_edge: .: (0.000215) test_remove_edge_if: .: (0.000248) test_remove_edge_if_nothing_removed: .: (0.000270) test_remove_edge_nonexistent: .: (0.000390) test_remove_node: .: (0.000214) test_remove_node_if: .: (0.000185) test_remove_node_if_false: .: (0.000198) test_remove_node_nonexistent: .: (0.000225) test_remove_nonsense_nodes: .: (0.000226) test_subtree: .: (0.000278) test_subtree_with_all_paths: .: (0.000504) test_total_distance: .: (0.000179) Bio::TestTreeEdge: test_distance: .: (0.000213) test_distance=: .: (0.000153) test_distance_string: .: (0.000125) test_distance_string=: .: (0.000169) test_initialize: .: (0.000162) test_inspect: .: (0.000126) test_to_s: .: (0.000122) Bio::TestTreeNode: test_bootstrap: .: (0.000213) test_bootstrap=: .: (0.000142) test_bootstrap_string: .: (0.000118) test_bootstrap_string=: .: (0.000181) test_initialize: .: (0.000145) test_inspect: .: (0.000329) test_name: .: (0.000117) test_to_s: .: (0.000112) Bio::TestUniProt: test_gene_name: .: (0.002857) Bio::TestUniProtKB: test_ac: .: (0.002913) test_accession: .: (0.002836) test_cc: .: (0.003730) test_cc_alternative_products: .: (0.003804) test_cc_database: .: (0.003664) test_cc_mass_spectrometry: .: (0.008545) test_de: .: (0.003104) test_dr: .: (0.004830) test_dr_with_key: .: (0.004158) test_dr_with_key_empty: .: (0.004350) test_dt: .: (0.003193) test_dt_annotation: .: (0.002640) test_dt_created: .: (0.002617) test_dt_sequence: .: (0.002698) test_entry: .: (0.002937) test_ft: .: (0.007318) test_gene_name: .: (0.003072) test_gene_names: .: (0.005140) test_gn: .: (0.022061) test_gn_old_parser: .: (0.037398) test_gn_uniprot_parser: .: (0.003412) test_id_line: .: (0.003334) test_id_line_data_class: .: (0.003165) test_id_line_entry_name: .: (0.003016) test_id_line_molecule_type: .: (0.003000) test_id_line_sequence_length: .: (0.003350) test_kw: .: (0.002897) test_molecule: .: (0.002912) test_oc: .: (0.002801) test_og_1: .: (0.003046) test_og_2: .: (0.002684) test_og_3: .: (0.002828) test_og_4: .: (0.004849) test_og_5: .: (0.002971) test_og_6: .: (0.002816) test_os: .: (0.002826) test_os_access: .: (0.002958) test_os_access2: .: (0.004186) test_ox: .: (0.003331) test_protein_name: .: (0.003314) test_ref: .: (0.006923) test_seq: .: (0.003068) test_sequence_length: .: (0.003060) test_sq: .: (0.002712) test_sq_crc64: .: (0.002813) test_sq_len: .: (0.002730) test_sq_mw: .: (0.002869) test_synonyms: .: (0.002692) Bio::TestUniProtKB_CC: test_allergen: .: (0.000337) test_alternative_products_access_as_hash: .: (0.000252) test_alternative_products_ai: .: (0.000463) test_alternative_products_apu: .: (0.000433) test_alternative_products_as: .: (0.000285) test_alternative_products_rf: .: (0.000127) test_biophysicochemical_properties: .: (0.000383) test_biotechnology: .: (0.000234) test_catalytic_activity: .: (0.000208) test_caution: .: (0.000388) test_cofactor: .: (0.000213) test_developmental_stage: .: (0.000226) test_disease: .: (0.000340) test_domain: .: (0.000324) test_enzyme_regulation: .: (0.000211) test_function: .: (0.000233) test_induction: .: (0.000201) test_interaction: .: (0.000270) test_mass_spectrometry: .: (0.000318) test_miscellaneous: .: (0.000215) test_pathway: .: (0.000233) test_pharmaceutical: .: (0.000240) test_polymorphism: .: (0.000300) test_ptm: .: (0.000199) test_rna_editing: .: (0.000255) test_similarity: .: (0.000203) test_subcellular_location: .: (0.000243) test_subunit: .: (0.000361) test_tissue_specificity: .: (0.000252) test_toxic_dose: .: (0.000189) test_web_resource: .: (0.000280) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000350) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000480) test_protein_name: .: (0.000452) test_synonyms: .: (0.000334) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000238) test_entry: .: (0.000143) test_entry_id: .: (0.000145) test_entry_name: .: (0.000147) test_id_line: .: (0.000171) test_molecule: .: (0.000157) test_sequence_length: .: (0.000149) Bio::TestUniProtKB_P03589: test_ac: .: (0.000628) test_accession: .: (0.000349) test_cc: .: (0.000680) test_cc_alternative_products: .: (0.000500) test_cc_database: .: (0.000503) test_cc_mass_spectrometry: .: (0.000658) test_de: .: (0.000475) test_dr: .: (0.000667) test_dr_with_key: .: (0.000565) test_dr_with_key_empty: .: (0.000676) test_dt: .: (0.000401) test_dt_annotation: .: (0.000377) test_dt_created: .: (0.000564) test_dt_sequence: .: (0.000366) test_entry: .: (0.000369) test_ft: .: (0.000726) test_gene_name: .: (0.000403) test_gene_names: .: (0.000384) test_gn: .: (0.000523) test_gn_old_parser: .: (0.000425) test_gn_uniprot_parser: .: (0.000409) test_id_line: .: (0.000496) test_id_line_data_class: .: (0.000351) test_id_line_entry_name: .: (0.000348) test_id_line_sequence_length: .: (0.000352) test_kw: .: (0.000449) test_oc: .: (0.000394) test_oh: .: (0.000766) test_os: .: (0.000413) test_os_access: .: (0.000384) test_os_access2: .: (0.000536) test_ox: .: (0.000422) test_protein_name: .: (0.000405) test_protein_name_after_calling_de: .: (0.000600) test_ref: .: (0.000508) test_seq: .: (0.002330) test_sequence_length: .: (0.000421) test_sq: .: (0.000395) test_sq_crc64: .: (0.000672) test_sq_len: .: (0.000435) test_sq_mw: .: (0.000407) test_synonyms: .: (0.000740) Bio::TestUniProtKB_P28907: test_ac: .: (0.001341) test_accession: .: (0.001266) test_cc: .: (0.001899) test_cc_alternative_products: .: (0.001705) test_cc_database: .: (0.001899) test_cc_mass_spectrometry: .: (0.001774) test_de: .: (0.001440) test_dr: .: (0.002965) test_dr_with_key: .: (0.002971) test_dr_with_key_empty: .: (0.002814) test_dt: .: (0.001463) test_dt_annotation: .: (0.001231) test_dt_created: .: (0.001101) test_dt_sequence: .: (0.001146) test_entry: .: (0.001086) test_ft: .: (0.002245) test_gene_name: .: (0.001113) test_gene_names: .: (0.001086) test_gn: .: (0.001114) test_gn_old_parser: .: (0.001141) test_gn_uniprot_parser: .: (0.001132) test_id_line: .: (0.001093) test_id_line_data_class: .: (0.001167) test_id_line_entry_name: .: (0.001075) test_id_line_sequence_length: .: (0.001084) test_kw: .: (0.001172) test_oc: .: (0.001115) test_os: .: (0.001301) test_os_access: .: (0.001238) test_os_access2: .: (0.001218) test_ox: .: (0.001165) test_protein_name: .: (0.001340) test_protein_name_after_calling_de: .: (0.001165) test_ref: .: (0.001865) test_seq: .: (0.001228) test_sequence_length: .: (0.001051) test_sq: .: (0.001204) test_sq_crc64: .: (0.001135) test_sq_len: .: (0.001118) test_sq_mw: .: (0.001135) test_synonyms: .: (0.002923) test_synonyms_after_calling_de: .: (0.001367) Bio::TestUniProtKB_P49144: test_ac: .: (0.000980) test_accession: .: (0.000529) test_cc: .: (0.001107) test_cc_alternative_products: .: (0.001004) test_cc_database: .: (0.001005) test_cc_mass_spectrometry: .: (0.000835) test_de: .: (0.000859) test_dr: .: (0.001165) test_dr_with_key: .: (0.001128) test_dr_with_key_empty: .: (0.001115) test_dt: .: (0.000555) test_dt_annotation: .: (0.000792) test_dt_created: .: (0.000520) test_dt_sequence: .: (0.000657) test_entry: .: (0.000725) test_ft: .: (0.001456) test_gene_name: .: (0.000629) test_gene_names: .: (0.000765) test_gn: .: (0.000563) test_gn_old_parser: .: (0.000820) test_gn_uniprot_parser: .: (0.000782) test_id_line: .: (0.000587) test_id_line_data_class: .: (0.000774) test_id_line_entry_name: .: (0.000599) test_id_line_sequence_length: .: (0.000660) test_kw: .: (0.000566) test_oc: .: (0.000880) test_os: .: (0.000502) test_os_access: .: (0.000811) test_os_access2: .: (0.000539) test_ox: .: (0.000741) test_protein_name: .: (0.000759) test_protein_name_after_calling_de: .: (0.000669) test_ref: .: (0.000858) test_seq: .: (0.000737) test_sequence_length: .: (0.000531) test_sq: .: (0.000652) test_sq_crc64: .: (0.000561) test_sq_len: .: (0.000669) test_sq_mw: .: (0.000583) test_synonyms: .: (0.000780) test_synonyms_after_calling_de: .: (0.000592) Bio::TestUniProtKB_Ref: test_RA: .: (0.000456) test_RC: .: (0.000248) test_RG: .: (0.000241) test_RL: .: (0.000246) test_RN: .: (0.000259) test_RP: .: (0.000387) test_RT: .: (0.000275) test_RX: .: (0.000318) test_ref: .: (0.000252) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000255) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000618) test_alternative_products_with_ft: .: (0.000566) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000311) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000273) test_RL_lines: .: (0.000274) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000462) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000244) test_RG_line: .: (0.000196) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000448) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000441) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000212) test_RL_line: .: (0.000162) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000574) test_RP_line: .: (0.000253) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000156) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000338) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000221) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000213) test_CC_interaction_isoform: .: (0.000206) test_CC_interaction_no_gene_name: .: (0.000212) test_CC_interaction_self_association: .: (0.000249) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000289) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000274) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000414) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000287) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000273) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000274) test_DT_line: .: (0.000207) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.002971) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000510) test_CC_web_resource: .: (0.000059) test_FT_VER_SEQ: .: (0.000130) test_OH_line_exception: .: (0.000340) test_OH_lines: .: (0.000255) Bio::TestUtils: test_centreOfGravity: .: (0.000488) test_dihedral_angle: .: (0.000345) test_distance: .: (0.000533) test_geometricCentre: .: (0.000273) test_rad2deg: .: (0.000196) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000293) test_dijkstra_on_weighted_graph: .: (0.000162) Finished in 12.284954179 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 320.80 tests/s, 1758.33 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.5-1_amd64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/761875/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/761875/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/761875 and its subdirectories I: Current time: Sun Jul 6 12:17:46 +14 2025 I: pbuilder-time-stamp: 1751753866