I: pbuilder: network access will be disabled during build I: Current time: Mon May 6 17:58:49 +14 2024 I: pbuilder-time-stamp: 1714967929 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/2994611/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 6 03:58 /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/2994611/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2994611/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=b82866c8cfbf462a8dd7680217eb0f90 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2994611 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.KWyqNNtr/pbuilderrc_0ZGt --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.KWyqNNtr/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2994611/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libb-hooks-op-check-perl{a} libbsd0{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap-2.5-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-override-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc strace unzip wget zip 0 packages upgraded, 135 newly installed, 0 to remove and 0 not upgraded. Need to get 47.7 MB of archives. After unpacking 182 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1+b1 [48.0 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.40-3 [558 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.6-1 [122 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.6-3.1 [17.8 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.40-3 [771 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 gnupg-utils arm64 2.2.40-3 [883 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.40-3 [903 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.2.1-3+b2 [75.9 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.40-3 [675 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 gpg-wks-client arm64 2.2.40-3 [533 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 gpg-wks-server arm64 2.2.40-3 [525 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.40-3 [650 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.40-3 [847 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 65 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 68 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b1 [34.0 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b3 [35.2 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b1 [10.6 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1 [16.0 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b3 [22.3 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.82-1 [96.9 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libclone-perl arm64 0.46-1+b2 [13.6 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 96 http://deb.debian.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1+b1 [328 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 wdiff arm64 1.2.2-6 [118 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 devscripts all 2.23.7 [1068 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libosp5 arm64 1.5.2-15 [917 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 opensp arm64 1.5.2-15 [444 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 docbook-to-man arm64 1:2.0.0-46 [70.8 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian unstable/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libruby3.1t64 arm64 3.1.2-8.3 [5254 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 ruby3.1 arm64 3.1.2-8.3 [664 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libruby arm64 1:3.1+nmu1 [4664 B] Get: 124 http://deb.debian.org/debian unstable/main arm64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 ruby arm64 1:3.1+nmu1 [5584 B] Get: 126 http://deb.debian.org/debian unstable/main arm64 rake all 13.2.1-1 [65.2 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 gem2deb-test-runner arm64 2.2.3 [17.8 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b1 [619 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 ruby3.1-dev arm64 3.1.2-8.3 [1005 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 ruby-all-dev arm64 1:3.1+nmu1 [5680 B] Get: 132 http://deb.debian.org/debian unstable/main arm64 gem2deb arm64 2.2.3 [47.8 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 ruby-libxml arm64 3.2.4-2+b2 [75.7 kB] Fetched 47.7 MB in 0s (132 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 21052 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... 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Preparing to unpack .../072-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../073-liburi-perl_5.28-1_all.deb ... Unpacking liburi-perl (5.28-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../074-libhtml-parser-perl_3.82-1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.82-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../075-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../076-libclone-perl_0.46-1+b2_arm64.deb ... Unpacking libclone-perl:arm64 (0.46-1+b2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../077-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../078-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../079-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../080-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../081-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../082-perl-openssl-defaults_7+b2_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../083-libnet-ssleay-perl_1.94-1+b1_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-1+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../084-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 .../085-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 .../086-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../087-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../088-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../089-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../090-patchutils_0.4.2-1_arm64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../091-wdiff_1.2.2-6_arm64.deb ... Unpacking wdiff (1.2.2-6) ... Selecting previously unselected package devscripts. Preparing to unpack .../092-devscripts_2.23.7_all.deb ... Unpacking devscripts (2.23.7) ... Selecting previously unselected package xml-core. Preparing to unpack .../093-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../094-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../095-docbook_4.5-10_all.deb ... Unpacking docbook (4.5-10) ... Selecting previously unselected package libosp5. Preparing to unpack .../096-libosp5_1.5.2-15_arm64.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../097-opensp_1.5.2-15_arm64.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../098-docbook-to-man_1%3a2.0.0-46_arm64.deb ... Unpacking docbook-to-man (1:2.0.0-46) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../099-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../100-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 .../101-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../102-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../103-ruby-sdbm_1.0.0-5+b4_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../104-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../105-libedit2_3.1-20230828-1+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20230828-1+b1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../106-libncurses6_6.4+20240414-1_arm64.deb ... Unpacking libncurses6:arm64 (6.4+20240414-1) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../107-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:arm64. Preparing to unpack .../108-libruby3.1t64_3.1.2-8.3_arm64.deb ... Unpacking libruby3.1t64:arm64 (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../109-ruby3.1_3.1.2-8.3_arm64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../110-libruby_1%3a3.1+nmu1_arm64.deb ... Unpacking libruby:arm64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../111-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../112-ruby_1%3a3.1+nmu1_arm64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../113-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../114-gem2deb-test-runner_2.2.3_arm64.deb ... Unpacking gem2deb-test-runner (2.2.3) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../115-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../116-libgmp-dev_2%3a6.3.0+dfsg-2+b1_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package ruby3.1-dev:arm64. Preparing to unpack .../117-ruby3.1-dev_3.1.2-8.3_arm64.deb ... Unpacking ruby3.1-dev:arm64 (3.1.2-8.3) ... Selecting previously unselected package ruby-all-dev:arm64. Preparing to unpack .../118-ruby-all-dev_1%3a3.1+nmu1_arm64.deb ... Unpacking ruby-all-dev:arm64 (1:3.1+nmu1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../119-gem2deb_2.2.3_arm64.deb ... Unpacking gem2deb (2.2.3) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../120-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 .../121-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:arm64. Preparing to unpack .../122-ruby-libxml_3.2.4-2+b2_arm64.deb ... Unpacking ruby-libxml:arm64 (3.2.4-2+b2) ... Setting up libksba8:arm64 (1.6.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:arm64 (1.6-3.1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... 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:arm64 (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (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:arm64 (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:arm64 (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:arm64 (2.5.6-1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (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: Mon May 6 03:59:10 UTC 2024. Universal Time is now: Mon May 6 03:59:10 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up libncurses6:arm64 (6.4+20240414-1) ... 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:arm64 (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:arm64 (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:arm64 (0.0.8-1+b1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... 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:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:arm64 (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 (1.13.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgmp-dev:arm64 (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:arm64 (3.1-20230828-1+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1) ... Setting up libldap-2.5-0:arm64 (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:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... 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:arm64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gpg-wks-server (2.2.40-3) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up gnupg (2.2.40-3) ... Setting up libruby:arm64 (1:3.1+nmu1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.2.1-1) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:arm64 (3.1.2-8.3) ... Setting up ruby3.1-dev:arm64 (3.1.2-8.3) ... Setting up ruby-libxml:arm64 (3.2.4-2+b2) ... Setting up gem2deb-test-runner (2.2.3) ... Setting up ruby-all-dev:arm64 (1:3.1+nmu1) ... Setting up gem2deb (2.2.3) ... Processing triggers for libc-bin (2.38-7) ... 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 (4.5-10) ... 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/2994611/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2994611/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lucas Nussbaum dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_clean dh_ruby --clean W: XS-Ruby-Versions is deprecated, and will be ignored rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_autoreconf_clean -O--buildsystem=ruby dh_clean -O--buildsystem=ruby debian/rules binary dh binary --buildsystem=ruby --with ruby dh_update_autotools_config -O--buildsystem=ruby dh_autoreconf -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby dh_ruby --configure dh_auto_build -O--buildsystem=ruby dh_ruby --build dh_auto_test -O--buildsystem=ruby dh_ruby --test create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.5' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 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/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/aarch64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000450) test_dbs: .: (0.000147) test_go_ids: .: (0.000138) test_go_terms: .: (0.000542) test_parser: .: (0.000363) test_set_date: .: (0.000145) test_set_desc: .: (0.000124) test_to_str: .: (0.000142) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000527) test_mktmpdir_without_block: .: (0.000339) test_remove_entry_secure: .: (0.000257) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.004637) test_call_command_fork: .: (0.000122) test_call_command_open3: .: (0.004466) test_call_command_popen: .: (0.004426) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.004537) test_call_command_fork: .: (0.000121) test_call_command_open3: .: (0.004250) test_call_command_popen: .: (0.004313) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.005031) test_call_command_fork: .: (0.000139) test_call_command_open3: .: (0.004554) test_call_command_popen: .: (0.004998) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.002603) test_call_command_fork_chdir: .: (0.000291) test_call_command_popen_chdir: .: (0.002212) test_query_command_chdir: .: (0.002353) test_query_command_fork_chdir: .: (0.000284) test_query_command_popen_chdir: .: (0.002268) Bio::FuncTestCommandQuery: test_query_command: .: (0.011495) test_query_command_fork: .: (0.003242) test_query_command_open3: .: (0.011745) test_query_command_popen: .: (0.011977) Bio::FuncTestCommandTmpdir: test_close!: .: (0.001144) test_initialize: .: (0.000525) test_path: .: (0.000342) test_path_after_close: .: (0.000598) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.018899) test_output_fasta: .: (0.059615) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000342) test_accession: .: (0.000134) test_accessions: .: (0.000141) test_comment: .: (0.000109) test_common_name: .: (0.000424) test_definition: .: (0.000152) test_features: .: (0.000582) test_gi: .: (0.000136) test_keywords: .: (0.000107) test_locus: .: (0.000072) test_nid: .: (0.000124) test_organism: .: (0.000135) test_origin: .: (0.000092) test_references: .: (0.001172) test_segment: .: (0.000143) test_source: .: (0.000209) test_taxonomy: .: (0.000130) test_version: .: (0.000122) test_versions: .: (0.000110) Bio::TestAA: test_13: .: (0.000198) test_1n: .: (0.000063) test_name2one: .: (0.000105) test_name2three: .: (0.000093) test_one2name: .: (0.000066) test_one2three: .: (0.000333) test_three2name: .: (0.000062) test_three2one: .: (0.000130) test_to_1_1: .: (0.000057) test_to_1_3: .: (0.000063) test_to_1_name: .: (0.000063) test_to_3_1: .: (0.000057) test_to_3_3: .: (0.000073) test_to_3_name: .: (0.000075) test_to_re: .: (0.000094) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000181) Bio::TestAAindex: test_api: .: (0.000109) test_auto_aax1: .: (0.000229) test_auto_aax2: .: (0.000163) Bio::TestAAindex1: test_author: .: (0.000584) test_comment: .: (0.000261) test_correlation_coefficient: .: (0.000558) test_dblinks: .: (0.000188) test_definition: .: (0.000173) test_entry_id: .: (0.000166) test_index: .: (0.000222) test_journal: .: (0.000179) test_title: .: (0.000167) Bio::TestAAindex2: test_access_A_R: .: (0.000747) test_access_R_A: .: (0.000480) test_author: .: (0.000185) test_cols: .: (0.000153) test_comment: .: (0.000761) test_dblinks: .: (0.000168) test_definition: .: (0.000147) test_entry_id: .: (0.000159) test_journal: .: (0.000187) test_matrix: .: (0.000492) test_matrix_1_2: .: (0.000646) test_matrix_2_2: .: (0.000475) test_matrix_A_R: .: (0.000461) test_matrix_R_A: .: (0.000869) test_matrix_determinant: .: (0.002359) test_matrix_rank: .: (0.002763) test_matrix_transpose: .: (0.000683) test_rows: .: (0.000172) test_title: .: (0.000167) Bio::TestAAindexConstant: test_delimiter: .: (0.000183) test_tagsize: .: (0.000058) Bio::TestAbif: test_complement: .: (0.006417) test_seq: .: (0.005970) test_to_biosequence: .: (0.006560) Bio::TestActsLikeMap: test_mixin: .: (0.000303) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000268) Bio::TestActsLikeMarker: test_mixin: .: (0.000181) Bio::TestAlignment: test_add_seq_no_key: .: (0.000272) test_add_seq_using_seq_with_aaseq_method: .: (0.000109) test_add_seq_using_seq_with_definition_method: .: (0.000075) test_add_seq_using_seq_with_entry_id_method: .: (0.000116) test_add_seq_using_seq_with_naseq_method: .: (0.000102) test_add_seq_using_seq_with_seq_method: .: (0.000097) test_consensus_iupac_gap_modes: .: (0.000364) test_consensus_iupac_missing_char: .: (0.000123) test_consensus_iupac_missing_char_option: .: (0.000161) test_consensus_iupac_no_gaps: .: (0.000205) test_consensus_iupac_of_ambiguous_bases: .: (0.000255) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002688) test_consensus_opt_gap_mode: .: (0.000409) test_consensus_opt_missing_char: .: (0.000172) test_consensus_string_no_gaps: .: (0.000168) test_consensus_threshold_four_sequences: .: (0.000268) test_consensus_threshold_two_sequences: .: (0.000253) test_convert_match: .: (0.000169) test_convert_unmatch: .: (0.000107) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000130) test_convert_unmatch_different_match_char: .: (0.000107) test_convert_unmatch_multiple_sequences: .: (0.000149) test_default_gap_char: .: (0.000051) test_default_gap_regexp_matches_default_gap_char: .: (0.000058) test_default_missing_char: .: (0.000042) test_each_site_equal_length: .: (0.000125) test_each_site_unequal_length: .: (0.000098) test_equals: .: (0.000129) test_match_line_protein: .: (0.000354) test_normalizebang_extends_sequences_with_gaps: .: (0.000118) test_seq_length_is_max_seq_length: .: (0.000075) test_seq_length_when_one_sequence: .: (0.000059) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000068) test_seqclass_when_seqclass_set: .: (0.000061) test_seqclass_when_sequence_used: .: (0.000070) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000088) test_set_and_get_gap_char: .: (0.000063) test_store_cannot_override_key: .: (0.000065) test_store_with_default_keys_and_user_defined_keys: .: (0.000101) test_store_with_nil_key_uses_next_number_for_key: .: (0.000059) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000228) test_alignment_concat: .: (0.000125) test_alignment_length: .: (0.000062) test_alignment_lstrip!: .: (0.000163) test_alignment_lstrip_nil: .: (0.000079) test_alignment_normalize!: .: (0.000083) test_alignment_rstrip!: .: (0.000104) test_alignment_rstrip_nil: .: (0.000058) test_alignment_site: .: (0.000078) test_alignment_slice: .: (0.000054) test_alignment_strip!: .: (0.000136) test_alignment_strip_nil: .: (0.000078) test_alignment_subseq: .: (0.000086) test_alignment_window: .: (0.000061) test_collect_each_site: .: (0.000087) test_consensus_each_site_default: .: (0.000129) test_consensus_each_site_gap_mode_1: .: (0.000083) test_consensus_each_site_gap_mode_minus1: .: (0.000106) test_consensus_iupac: .: (0.000240) test_consensus_string_default: .: (0.000101) test_consensus_string_half: .: (0.000120) test_convert_match: .: (0.000085) test_convert_unmatch: .: (0.000077) test_each_seq: .: (0.000074) test_each_site: .: (0.000123) test_each_site_step: .: (0.000094) test_each_window: .: (0.000104) test_match_line: .: (0.000554) test_match_line_amino: .: (0.000911) test_match_line_nuc: .: (0.000167) test_private_alignment_site: .: (0.000080) test_remove_all_gaps!: .: (0.000117) test_seqclass: .: (0.000060) test_seqclass=: .: (0.000074) test_seqclass_default: .: (0.000061) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.002511) test_determine_seq_method: .: (0.001249) test_entries: .: (0.000291) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000291) test_avoid_same_name_numbering: .: (0.000121) test_clustal_have_same_name_true: .: (0.000070) test_have_same_name_false: .: (0.000070) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000168) test_gap_char_default: .: (0.000073) test_gap_char_never_nil: .: (0.000065) test_gap_regexp: .: (0.000069) test_gap_regexp=: .: (0.000101) test_gap_regexp_never_nil: .: (0.000053) test_get_all_property_default: .: (0.000055) test_get_all_property_nodefault: .: (0.000083) test_is_gap_default_false: .: (0.000057) test_is_gap_default_true: .: (0.000052) test_is_gap_nodefault_false: .: (0.000072) test_is_gap_nodefault_true: .: (0.000052) test_missing_char=: .: (0.000051) test_missing_char_default: .: (0.000067) test_missing_char_never_nil: .: (0.000058) test_seqclass=: .: (0.000086) test_seqclass_default: .: (0.000065) test_seqclass_never_nil: .: (0.000056) test_set_all_property: .: (0.000087) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000436) test_consensus_string_50percent: .: (0.000076) test_consensus_string_50percent_nil: .: (0.000066) test_consensus_string_default: .: (0.000073) test_consensus_string_default_nil: .: (0.000050) test_has_gap_false: .: (0.000057) test_has_gap_true: .: (0.000070) test_match_line_amino_100percent: .: (0.000083) test_match_line_amino_missing: .: (0.000099) test_match_line_amino_strong: .: (0.000069) test_match_line_amino_weak: .: (0.000079) test_match_line_nuc_100percent: .: (0.000065) test_match_line_nuc_missing: .: (0.000056) test_remove_gaps!: .: (0.000074) test_remove_gaps_bang_not_removed: .: (0.000043) Bio::TestAtomFinder: test_atoms: .: (0.012770) test_each_atom: .: (0.000202) test_find_atom: .: (0.000150) Bio::TestBioFastaDefline: test_acc_version: .: (0.000443) test_accession: .: (0.000352) test_accessions: .: (0.006476) test_description: .: (0.000292) test_descriptions: .: (0.000224) test_entry_id: .: (0.000250) test_get: .: (0.000280) test_get_all_by_type: .: (0.000576) test_get_by_type: .: (0.000231) test_gi: .: (0.000208) test_id_strings: .: (0.000781) test_locus: .: (0.000368) test_method_missing: .: (0.000261) test_to_s: .: (0.000243) test_words: .: (0.000729) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000729) test_goid2term: .: (0.000304) test_parse_goids: .: (0.000275) Bio::TestBioGenBank: test_basecount: .: (0.000585) test_circular: .: (0.000239) test_classification: .: (0.000301) test_date: .: (0.000205) test_date_modified: .: (0.000585) test_division: .: (0.000279) test_each_cds_feature: .: (0.000841) test_each_cds_qualifiers: .: (0.000589) test_each_gene: .: (0.000891) test_entry_id: .: (0.000203) test_length: .: (0.000197) test_locus_circular: .: (0.000227) test_locus_class: .: (0.000240) test_locus_date: .: (0.000225) test_locus_division: .: (0.000262) test_locus_entry_id: .: (0.000228) test_locus_length: .: (0.000214) test_locus_natype: .: (0.000520) test_locus_strand: .: (0.000202) test_natype: .: (0.000191) test_seq: .: (0.000244) test_seq_len: .: (0.000236) test_strand: .: (0.000203) test_strandedness: .: (0.000209) test_to_biosequence: .: (0.001861) Bio::TestBioGenPept: test_circular: .: (0.000533) test_date: .: (0.000142) test_dbsource: .: (0.000137) test_division: .: (0.000141) test_entry_id: .: (0.000140) test_length: .: (0.000134) test_locus: .: (0.000130) test_seq: .: (0.000155) test_seq_len: .: (0.000144) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000603) test_aaseq: .: (0.000206) test_chromosome: .: (0.000178) test_codon_usage: .: (0.000292) test_cu_list: .: (0.000160) test_dblinks_as_hash: .: (0.000205) test_dblinks_as_strings: .: (0.000165) test_definition: .: (0.000175) test_division: .: (0.000247) test_eclinks: .: (0.000168) test_entry: .: (0.000124) test_entry_id: .: (0.000110) test_gbposition: .: (0.000124) test_gene: .: (0.000130) test_genes: .: (0.000127) test_keggclass: .: (0.000142) test_keggclasses: .: (0.000165) test_locations: .: (0.000372) test_motifs_as_hash: .: (0.000199) test_motifs_as_strings: .: (0.000120) test_name: .: (0.000126) test_names_as_array: .: (0.000134) test_new: .: (0.000145) test_ntlen: .: (0.000215) test_ntseq: .: (0.000232) test_organism: .: (0.000133) test_orthologs_as_hash: .: (0.000172) test_orthologs_as_strings: .: (0.000124) test_pathway: .: (0.000139) test_pathway_after_pathways_as_strings: .: (0.000167) test_pathway_before_pathways_as_strings: .: (0.000160) test_pathways_as_hash: .: (0.000141) test_pathways_as_strings: .: (0.000119) test_position: .: (0.000122) test_structure: .: (0.000213) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000841) test_comment: .: (0.000314) test_data_source: .: (0.000246) test_definition: .: (0.000252) test_disease: .: (0.000249) test_entry_id: .: (0.000240) test_lineage: .: (0.000311) test_nalen: .: (0.000254) test_name: .: (0.000240) test_new: .: (0.000238) test_num_gene: .: (0.000224) test_num_rna: .: (0.000219) test_original_databases: .: (0.000311) test_original_db: .: (0.000306) test_plasmids: .: (0.000282) test_references: .: (0.001712) test_statistics: .: (0.000334) test_taxid: .: (0.000302) test_taxonomy: .: (0.000307) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000383) test_comment: .: (0.000298) test_data_source: .: (0.000179) test_definition: .: (0.000160) test_disease: .: (0.000160) test_entry_id: .: (0.000155) test_lineage: .: (0.000178) test_nalen: .: (0.000196) test_name: .: (0.000170) test_new: .: (0.000159) test_num_gene: .: (0.000250) test_num_rna: .: (0.000174) test_original_databases: .: (0.000156) test_original_db: .: (0.000139) test_plasmids: .: (0.000221) test_references: .: (0.000276) test_statistics: .: (0.000159) test_taxid: .: (0.000233) test_taxonomy: .: (0.000193) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000339) test_compounds_as_strings: .: (0.000160) test_dblinks_as_hash: .: (0.000134) test_dblinks_as_strings: .: (0.000113) test_description: .: (0.000132) test_diseases_as_hash: .: (0.000123) test_diseases_as_strings: .: (0.000107) test_entry_id: .: (0.000157) test_enzymes_as_strings: .: (0.000247) test_genes_as_hash: .: (0.000153) test_genes_as_strings: .: (0.000131) test_keggclass: .: (0.000142) test_ko_pathway: .: (0.000148) test_modules_as_hash: .: (0.000133) test_modules_as_strings: .: (0.000122) test_name: .: (0.000155) test_new: .: (0.000158) test_organism: .: (0.000140) test_orthologs_as_hash: .: (0.000131) test_orthologs_as_strings: .: (0.000127) test_pathways_as_hash: .: (0.000284) test_pathways_as_strings: .: (0.000148) test_reactions_as_hash: .: (0.000126) test_reactions_as_strings: .: (0.000113) test_references: .: (0.000119) test_rel_pathways_as_hash: .: (0.000136) test_rel_pathways_as_strings: .: (0.000117) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000436) test_compounds_as_strings: .: (0.000402) test_dblinks_as_hash: .: (0.000190) test_dblinks_as_strings: .: (0.000131) test_description: .: (0.000150) test_diseases_as_hash: .: (0.000153) test_diseases_as_strings: .: (0.000149) test_entry_id: .: (0.000164) test_enzymes_as_strings: .: (0.000143) test_genes_as_hash: .: (0.000196) test_genes_as_strings: .: (0.000210) test_keggclass: .: (0.000173) test_ko_pathway: .: (0.000138) test_modules_as_hash: .: (0.000138) test_modules_as_strings: .: (0.000119) test_name: .: (0.000144) test_new: .: (0.000145) test_organism: .: (0.000139) test_orthologs_as_hash: .: (0.000121) test_orthologs_as_strings: .: (0.000211) test_pathways_as_hash: .: (0.000179) test_pathways_as_strings: .: (0.000128) test_reactions_as_hash: .: (0.000123) test_reactions_as_strings: .: (0.000116) test_references: .: (0.000116) test_rel_pathways_as_hash: .: (0.000143) test_rel_pathways_as_strings: .: (0.000125) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000286) test_compounds_as_strings: .: (0.000179) test_dblinks_as_hash: .: (0.000119) test_dblinks_as_strings: .: (0.000097) test_description: .: (0.000116) test_diseases_as_hash: .: (0.000094) test_diseases_as_strings: .: (0.000093) test_entry_id: .: (0.000118) test_enzymes_as_strings: .: (0.000118) test_genes_as_hash: .: (0.000117) test_genes_as_strings: .: (0.000106) test_keggclass: .: (0.000116) test_ko_pathway: .: (0.000114) test_modules_as_hash: .: (0.000207) test_modules_as_strings: .: (0.000112) test_name: .: (0.000114) test_new: .: (0.000119) test_organism: .: (0.000110) test_orthologs_as_hash: .: (0.000187) test_orthologs_as_strings: .: (0.000129) test_pathways_as_hash: .: (0.000115) test_pathways_as_strings: .: (0.000127) test_reactions_as_hash: .: (0.000128) test_reactions_as_strings: .: (0.000101) test_references: .: (0.000098) test_rel_pathways_as_hash: .: (0.000300) test_rel_pathways_as_strings: .: (0.000150) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000272) test_compounds_as_strings: .: (0.000132) test_dblinks_as_hash: .: (0.000141) test_dblinks_as_strings: .: (0.000123) test_description: .: (0.000248) test_diseases_as_hash: .: (0.000170) test_diseases_as_strings: .: (0.000161) test_entry_id: .: (0.000355) test_enzymes_as_strings: .: (0.000172) test_genes_as_hash: .: (0.000139) test_genes_as_strings: .: (0.000126) test_keggclass: .: (0.000166) test_ko_pathway: .: (0.000157) test_modules_as_hash: .: (0.000198) test_modules_as_strings: .: (0.000151) test_name: .: (0.000395) test_new: .: (0.000228) test_organism: .: (0.000162) test_orthologs_as_hash: .: (0.000147) test_orthologs_as_strings: .: (0.000154) test_pathways_as_hash: .: (0.000185) test_pathways_as_strings: .: (0.000187) test_reactions_as_hash: .: (0.000173) test_reactions_as_strings: .: (0.000150) test_references: .: (0.000607) test_rel_pathways_as_hash: .: (0.000207) test_rel_pathways_as_strings: .: (0.000181) Bio::TestBioKeggDRUG: test_activity: .: (0.000348) test_comment: .: (0.000186) test_dblinks_as_hash: .: (0.000244) test_dblinks_as_strings: .: (0.004290) test_entry_id: .: (0.000260) test_formula: .: (0.000201) test_kcf: .: (0.000178) test_mass: .: (0.000212) test_name: .: (0.000226) test_names: .: (0.000227) test_pathways_as_hash: .: (0.000243) test_pathways_as_strings: .: (0.000185) test_products: .: (0.000262) test_remark: .: (0.000259) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000363) test_composition: .: (0.000227) test_compounds: .: (0.000178) test_dblinks_as_hash: .: (0.000336) test_dblinks_as_strings: .: (0.000254) test_entry_id: .: (0.000187) test_enzymes: .: (0.000175) test_kcf: .: (0.000192) test_keggclass: .: (0.000182) test_mass: .: (0.000189) test_name: .: (0.000154) test_orthologs_as_hash: .: (0.000223) test_orthologs_as_strings: .: (0.000261) test_pathways_as_hash: .: (0.000173) test_pathways_as_strings: .: (0.000145) test_reactions: .: (0.000151) test_references: .: (0.000191) test_remark: .: (0.000153) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000273) test_composition: .: (0.000391) test_compounds: .: (0.000197) test_dblinks_as_hash: .: (0.000161) test_dblinks_as_strings: .: (0.000116) test_entry_id: .: (0.000135) test_enzymes: .: (0.000143) test_kcf: .: (0.000115) test_keggclass: .: (0.000122) test_mass: .: (0.000124) test_name: .: (0.000130) test_orthologs_as_hash: .: (0.000377) test_orthologs_as_strings: .: (0.000166) test_pathways_as_hash: .: (0.000157) test_pathways_as_strings: .: (0.000119) test_reactions: .: (0.000123) test_references: .: (0.000113) test_remark: .: (0.000120) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000450) test_compounds_as_strings: .: (0.000470) test_dblinks_as_hash: .: (0.000223) test_dblinks_as_strings: .: (0.000140) test_description: .: (0.000161) test_diseases_as_hash: .: (0.000154) test_diseases_as_strings: .: (0.000157) test_entry_id: .: (0.000180) test_enzymes_as_strings: .: (0.000169) test_genes_as_hash: .: (0.000172) test_genes_as_strings: .: (0.000148) test_keggclass: .: (0.000236) test_ko_pathway: .: (0.000171) test_modules_as_hash: .: (0.000246) test_modules_as_strings: .: (0.000188) test_name: .: (0.000177) test_new: .: (0.000168) test_organism: .: (0.000162) test_orthologs_as_hash: .: (0.000149) test_orthologs_as_strings: .: (0.000438) test_pathways_as_hash: .: (0.000173) test_pathways_as_strings: .: (0.000155) test_reactions_as_hash: .: (0.000379) test_reactions_as_strings: .: (0.000272) test_references: .: (0.000528) test_rel_pathways_as_hash: .: (0.000299) test_rel_pathways_as_strings: .: (0.000214) Bio::TestBioLITDB: test_author: .: (0.000307) test_entry_id: .: (0.000143) test_field: .: (0.000135) test_journal: .: (0.000125) test_keyword: .: (0.000336) test_reference: .: (0.000249) test_title: .: (0.000149) test_volume: .: (0.000127) Bio::TestBioNBRF: test_aalen: .: (0.000291) test_aaseq: .: (0.000125) test_entry: .: (0.000103) test_length: .: (0.000103) test_nalen: .: (0.000172) test_naseq: .: (0.000126) test_seq: .: (0.000115) test_seq_class: .: (0.000248) test_to_nbrf: .: (0.000155) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000260) test_to_newick_format_leaf: .: (0.000185) test_to_newick_format_leaf_NHX: .: (0.000140) Bio::TestBl2seqReport: test_db_len: .: (0.000533) test_db_num: .: (0.000335) test_new: .: (0.000417) test_undefed_methods: .: (0.000766) test_undefed_methods_for_iteration: .: (0.000658) Bio::TestBl2seqReportConstants: test_rs: .: (0.000210) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000290) test_hits: .: (0.000189) Bio::TestBlast: test_blast_reports_format0: .: (0.004583) test_blast_reports_format0_with_block: .: (0.000634) test_blast_reports_format7: .: (0.009301) test_blast_reports_format7_with_block: .: (0.026176) test_blast_reports_format7_with_parser: .: (0.039702) test_blast_reports_format7_with_parser_with_block: .: (0.010723) test_blast_reports_format8: .: (0.000693) test_blast_reports_format8_with_block: .: (0.000663) test_blast_reports_format8_with_parser: .: (0.000319) test_blast_reports_format8_with_parser_with_block: .: (0.000199) test_blast_reports_xml: .: (0.009118) test_blast_reports_xml_with_block: .: (0.008681) test_blastll: .: (0.000181) test_db: .: (0.000098) test_exec_genomenet: .: (0.000100) test_exec_local: .: (0.000084) test_exec_ncbi: .: (0.000096) test_filter: .: (0.000106) test_format: .: (0.000108) test_make_command_line: .: (0.000697) test_make_command_line_2: .: (0.000260) test_matrix: .: (0.000104) test_new: .: (0.000164) test_new_opt_string: .: (0.000193) test_option: .: (0.000125) test_option_set: .: (0.000311) test_option_set_m0: .: (0.000142) test_options: .: (0.000089) test_output: .: (0.000080) test_parse_result: .: (0.010080) test_parser: .: (0.000197) test_program: .: (0.000344) test_query: .: (0.000104) test_self_local: .: (0.000230) test_self_remote: .: (0.001488) test_server: .: (0.000181) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000488) test_delete: .: (0.000268) test_equal_equal: .: (0.000238) test_get: .: (0.000225) test_make_command_line_options: .: (0.000345) test_normalize!: .: (0.000151) test_parse: .: (0.000174) test_set: .: (0.000296) Bio::TestBlastReport: test_db: .: (0.009280) test_db_len: .: (0.008700) test_db_num: .: (0.008502) test_each_hit: .: (0.008616) test_each_iteration: .: (0.011274) test_eff_space: .: (0.009093) test_entrez_query: .: (0.008563) test_entropy: .: (0.008377) test_expect: .: (0.008573) test_filter: .: (0.009783) test_gap_extend: .: (0.008801) test_gap_open: .: (0.008807) test_hits: .: (0.008349) test_hsp_len: .: (0.008505) test_inclusion: .: (0.010265) test_iterations: .: (0.008754) test_kappa: .: (0.008640) test_lambda: .: (0.008406) test_matrix: .: (0.008464) test_message: .: (0.010076) test_parameters: .: (0.009065) test_pattern: .: (0.008698) test_program: .: (0.008544) test_query_def: .: (0.009541) test_query_id: .: (0.009289) test_query_len: .: (0.008705) test_reference: .: (0.008623) test_sc_match: .: (0.008358) test_sc_mismatch: .: (0.009799) test_statistics: .: (0.009145) test_version: .: (0.008728) Bio::TestBlastReportDefault: test_db: .: (0.000720) test_db_len: .: (0.000396) test_db_num: .: (0.000517) test_each_hit: .: (0.000397) test_each_iteration: .: (0.000295) test_eff_space: .: (0.000380) test_entropy: .: (0.000349) test_expect: .: (0.000349) test_gap_extend: .: (0.000321) test_gap_open: .: (0.000308) test_gapped_entropy: .: (0.000428) test_gapped_kappa: .: (0.000303) test_gapped_lambda: .: (0.000291) test_hits: .: (0.000294) test_iterations: .: (0.000247) test_kappa: .: (0.000285) test_lambda: .: (0.000273) test_matrix: .: (0.000328) test_message: .: (0.000381) test_pattern: .: (0.000248) test_program: .: (0.000257) test_query_def: .: (0.000278) test_query_len: .: (0.000256) test_reference: .: (0.000315) test_sc_match: .: (0.000329) test_sc_mismatch: .: (0.000401) test_version: .: (0.000287) Bio::TestBlastReportHit: test_Hit_accession: .: (0.008519) test_Hit_bit_score: .: (0.008683) test_Hit_definition: .: (0.010719) test_Hit_evalue: .: (0.008808) test_Hit_hit_id: .: (0.009173) test_Hit_hsps: .: (0.008736) test_Hit_identity: .: (0.009639) test_Hit_lap_at: .: (0.009386) test_Hit_len: .: (0.008771) test_Hit_midline: .: (0.008981) test_Hit_num: .: (0.008474) test_Hit_overlap: .: (0.010201) test_Hit_query_def: .: (0.009148) test_Hit_query_end: .: (0.008723) test_Hit_query_id: .: (0.008776) test_Hit_query_len: .: (0.008736) test_Hit_query_seq: .: (0.010299) test_Hit_query_start: .: (0.008864) test_Hit_taeget_def: .: (0.008630) test_Hit_target_end: .: (0.008684) test_Hit_target_id: .: (0.010035) test_Hit_target_len: .: (0.009498) test_Hit_target_seq: .: (0.008827) test_Hit_target_start: .: (0.008647) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000783) test_Hit_definition: .: (0.000545) test_Hit_evalue: .: (0.000384) test_Hit_hsps: .: (0.000336) test_Hit_identity: .: (0.000353) test_Hit_lap_at: .: (0.000472) test_Hit_len: .: (0.000343) test_Hit_midline: .: (0.000442) test_Hit_overlap: .: (0.000413) test_Hit_query_end: .: (0.000440) test_Hit_query_seq: .: (0.000407) test_Hit_query_start: .: (0.000364) test_Hit_taeget_def: .: (0.000286) test_Hit_target_end: .: (0.000396) test_Hit_target_id: .: (0.000387) test_Hit_target_len: .: (0.000292) test_Hit_target_seq: .: (0.000368) test_Hit_target_start: .: (0.000355) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.026465) test_Hit_bit_score: .: (0.026836) test_Hit_definition: .: (0.024166) test_Hit_evalue: .: (0.027066) test_Hit_hit_id: .: (0.026479) test_Hit_hsps: .: (0.024057) test_Hit_identity: .: (0.026494) test_Hit_lap_at: .: (0.026364) test_Hit_len: .: (0.023817) test_Hit_midline: .: (0.026225) test_Hit_num: .: (0.026719) test_Hit_overlap: .: (0.023988) test_Hit_query_def: .: (0.025806) test_Hit_query_end: .: (0.026702) test_Hit_query_id: .: (0.025369) test_Hit_query_len: .: (0.024771) test_Hit_query_seq: .: (0.026722) test_Hit_query_start: .: (0.026437) test_Hit_taeget_def: .: (0.024176) test_Hit_target_end: .: (0.026372) test_Hit_target_id: .: (0.026971) test_Hit_target_len: .: (0.024009) test_Hit_target_seq: .: (0.026145) test_Hit_target_start: .: (0.026818) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.024427) test_Hit_bit_score: .: (0.025999) test_Hit_definition: .: (0.026706) test_Hit_evalue: .: (0.025199) test_Hit_hit_id: .: (0.025024) test_Hit_hsps: .: (0.026890) test_Hit_identity: .: (0.025573) test_Hit_lap_at: .: (0.024150) test_Hit_len: .: (0.026076) test_Hit_midline: .: (0.026501) test_Hit_num: .: (0.024020) test_Hit_overlap: .: (0.026250) test_Hit_query_def: .: (0.026627) test_Hit_query_end: .: (0.023990) test_Hit_query_id: .: (0.025803) test_Hit_query_len: .: (0.026415) test_Hit_query_seq: .: (0.025276) test_Hit_query_start: .: (0.025080) test_Hit_taeget_def: .: (0.026688) test_Hit_target_end: .: (0.026056) test_Hit_target_id: .: (0.024093) test_Hit_target_len: .: (0.026404) test_Hit_target_seq: .: (0.026768) test_Hit_target_start: .: (0.023811) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.010543) test_Hit_bit_score: .: (0.009220) test_Hit_definition: .: (0.008811) test_Hit_evalue: .: (0.008710) test_Hit_hit_id: .: (0.009756) test_Hit_hsps: .: (0.009473) test_Hit_identity: .: (0.009121) test_Hit_lap_at: .: (0.008908) test_Hit_len: .: (0.008587) test_Hit_midline: .: (0.010372) test_Hit_num: .: (0.009036) test_Hit_overlap: .: (0.008968) test_Hit_query_def: .: (0.008826) test_Hit_query_end: .: (0.009686) test_Hit_query_id: .: (0.009395) test_Hit_query_len: .: (0.008776) test_Hit_query_seq: .: (0.008772) test_Hit_query_start: .: (0.008615) test_Hit_taeget_def: .: (0.010419) test_Hit_target_end: .: (0.008852) test_Hit_target_id: .: (0.008735) test_Hit_target_len: .: (0.008771) test_Hit_target_seq: .: (0.008771) test_Hit_target_start: .: (0.010202) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000432) test_Hit_bit_score: .: (0.000122) test_Hit_definition: .: (0.000096) test_Hit_evalue: .: (0.000095) test_Hit_hit_id: .: (0.000098) test_Hit_hsps: .: (0.000093) test_Hit_identity: .: (0.000084) test_Hit_lap_at: .: (0.000215) test_Hit_len: .: (0.000122) test_Hit_midline: .: (0.000111) test_Hit_num: .: (0.000120) test_Hit_overlap: .: (0.000106) test_Hit_query_def: .: (0.000102) test_Hit_query_end: .: (0.000091) test_Hit_query_id: .: (0.000087) test_Hit_query_len: .: (0.000086) test_Hit_query_seq: .: (0.000082) test_Hit_query_start: .: (0.000090) test_Hit_taeget_def: .: (0.000085) test_Hit_target_end: .: (0.000080) test_Hit_target_id: .: (0.000077) test_Hit_target_len: .: (0.000255) test_Hit_target_seq: .: (0.000098) test_Hit_target_start: .: (0.000098) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.008596) test_Hsp_bit_score: .: (0.008746) test_Hsp_density: .: (0.008793) test_Hsp_evalue: .: (0.010654) test_Hsp_gaps: .: (0.008985) test_Hsp_hit_frame: .: (0.008557) test_Hsp_hit_from: .: (0.008694) test_Hsp_hit_to: .: (0.010069) test_Hsp_hseq: .: (0.009136) test_Hsp_identity: .: (0.008793) test_Hsp_midline: .: (0.008727) test_Hsp_mismatch_count: .: (0.008819) test_Hsp_num: .: (0.010573) test_Hsp_pattern_from: .: (0.008952) test_Hsp_pattern_to: .: (0.008645) test_Hsp_percent_identity: .: (0.008671) test_Hsp_positive: .: (0.010321) test_Hsp_qseq: .: (0.009246) test_Hsp_query_frame: .: (0.008938) test_Hsp_query_from: .: (0.008602) test_Hsp_query_to: .: (0.008835) test_Hsp_score: .: (0.010472) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000928) test_Hsp_bit_score: .: (0.000370) test_Hsp_evalue: .: (0.000339) test_Hsp_gaps: .: (0.000337) test_Hsp_hit_frame: .: (0.000335) test_Hsp_hit_from: .: (0.000448) test_Hsp_hit_to: .: (0.000417) test_Hsp_hseq: .: (0.000537) test_Hsp_identity: .: (0.000364) test_Hsp_midline: .: (0.000438) test_Hsp_percent_identity: .: (0.000311) test_Hsp_positive: .: (0.000292) test_Hsp_qseq: .: (0.000395) test_Hsp_query_frame: .: (0.000511) test_Hsp_query_from: .: (0.000441) test_Hsp_query_to: .: (0.000389) test_Hsp_score: .: (0.000298) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.042181) test_Hsp_bit_score: .: (0.058288) test_Hsp_density: .: (0.026780) test_Hsp_evalue: .: (0.024612) test_Hsp_gaps: .: (0.026098) test_Hsp_hit_frame: .: (0.027021) test_Hsp_hit_from: .: (0.024155) test_Hsp_hit_to: .: (0.026088) test_Hsp_hseq: .: (0.025719) test_Hsp_identity: .: (0.024480) test_Hsp_midline: .: (0.026583) test_Hsp_mismatch_count: .: (0.024315) test_Hsp_num: .: (0.025653) test_Hsp_pattern_from: .: (0.026777) test_Hsp_pattern_to: .: (0.024040) test_Hsp_percent_identity: .: (0.026142) test_Hsp_positive: .: (0.025959) test_Hsp_qseq: .: (0.024217) test_Hsp_query_frame: .: (0.026240) test_Hsp_query_from: .: (0.024228) test_Hsp_query_to: .: (0.026006) test_Hsp_score: .: (0.026714) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.024254) test_Hsp_bit_score: .: (0.026089) test_Hsp_density: .: (0.026603) test_Hsp_evalue: .: (0.024172) test_Hsp_gaps: .: (0.026310) test_Hsp_hit_frame: .: (0.026099) test_Hsp_hit_from: .: (0.024657) test_Hsp_hit_to: .: (0.027167) test_Hsp_hseq: .: (0.025931) test_Hsp_identity: .: (0.024728) test_Hsp_midline: .: (0.026750) test_Hsp_mismatch_count: .: (0.025406) test_Hsp_num: .: (0.024936) test_Hsp_pattern_from: .: (0.026880) test_Hsp_pattern_to: .: (0.024152) test_Hsp_percent_identity: .: (0.025754) test_Hsp_positive: .: (0.026591) test_Hsp_qseq: .: (0.023925) test_Hsp_query_frame: .: (0.025745) test_Hsp_query_from: .: (0.026533) test_Hsp_query_to: .: (0.024059) test_Hsp_score: .: (0.026036) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.009214) test_Hsp_bit_score: .: (0.009011) test_Hsp_density: .: (0.010414) test_Hsp_evalue: .: (0.008782) test_Hsp_gaps: .: (0.008494) test_Hsp_hit_frame: .: (0.008805) test_Hsp_hit_from: .: (0.008664) test_Hsp_hit_to: .: (0.010341) test_Hsp_hseq: .: (0.008935) test_Hsp_identity: .: (0.008599) test_Hsp_midline: .: (0.008629) test_Hsp_mismatch_count: .: (0.009599) test_Hsp_num: .: (0.009751) test_Hsp_pattern_from: .: (0.008924) test_Hsp_pattern_to: .: (0.008737) test_Hsp_percent_identity: .: (0.008763) test_Hsp_positive: .: (0.010234) test_Hsp_qseq: .: (0.009163) test_Hsp_query_frame: .: (0.008858) test_Hsp_query_from: .: (0.008598) test_Hsp_query_to: .: (0.008803) test_Hsp_score: .: (0.010401) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000511) test_Hsp_bit_score: .: (0.000134) test_Hsp_density: .: (0.000107) test_Hsp_evalue: .: (0.000105) test_Hsp_gaps: .: (0.000097) test_Hsp_hit_frame: .: (0.000093) test_Hsp_hit_from: .: (0.000088) test_Hsp_hit_to: .: (0.000083) test_Hsp_hseq: .: (0.000088) test_Hsp_identity: .: (0.000084) test_Hsp_midline: .: (0.000085) test_Hsp_mismatch_count: .: (0.000246) test_Hsp_num: .: (0.000138) test_Hsp_pattern_from: .: (0.000102) test_Hsp_pattern_to: .: (0.000088) test_Hsp_percent_identity: .: (0.000084) test_Hsp_positive: .: (0.000090) test_Hsp_qseq: .: (0.000087) test_Hsp_query_frame: .: (0.000085) test_Hsp_query_from: .: (0.000088) test_Hsp_query_to: .: (0.000086) test_Hsp_score: .: (0.000083) Bio::TestBlastReportIteration: test_hits: .: (0.009092) test_message: .: (0.008792) test_num: .: (0.008733) test_statistics: .: (0.009968) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000698) test_message: .: (0.000364) test_num: .: (0.000364) Bio::TestBlastReportIterationMulti: test_each: .: (0.025353) test_hits: .: (0.027377) test_message: .: (0.024240) test_num: .: (0.026263) test_query_def: .: (0.026773) test_query_id: .: (0.024472) test_query_len: .: (0.025945) test_statistics: .: (0.026828) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.024620) test_hits: .: (0.026007) test_message: .: (0.026599) test_num: .: (0.024142) test_query_def: .: (0.026012) test_query_id: .: (0.026845) test_query_len: .: (0.024341) test_statistics: .: (0.026130) Bio::TestBlastReportIterationREXML: test_hits: .: (0.008969) test_message: .: (0.010466) test_num: .: (0.009477) test_statistics: .: (0.008741) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000413) test_message: .: (0.000136) test_num: .: (0.000118) test_statistics: .: (0.000123) Bio::TestBlastReportMulti: test_db: .: (0.026292) test_db_len: .: (0.024595) test_db_num: .: (0.026560) test_each_hit: .: (0.026886) test_each_iteration: .: (0.024287) test_eff_space: .: (0.027003) test_entropy: .: (0.027320) test_expect: .: (0.024403) test_filter: .: (0.026345) test_gap_extend: .: (0.027240) test_gap_open: .: (0.024381) test_hits: .: (0.026389) test_hsp_len: .: (0.026955) test_iterations: .: (0.026005) test_kappa: .: (0.025215) test_lambda: .: (0.027225) test_matrix: .: (0.025986) test_message: .: (0.024531) test_parameters: .: (0.026725) test_pattern: .: (0.027095) test_program: .: (0.024401) test_query_def: .: (0.026521) test_query_id: .: (0.026552) test_query_len: .: (0.023934) test_reference: .: (0.026086) test_reports: .: (0.026663) test_statistics: .: (0.025394) test_version: .: (0.024579) Bio::TestBlastReportMultiREXML: test_db: .: (0.026534) test_db_len: .: (0.026619) test_db_num: .: (0.024003) test_each_hit: .: (0.026121) test_each_iteration: .: (0.026604) test_eff_space: .: (0.025559) test_entropy: .: (0.024665) test_expect: .: (0.026471) test_filter: .: (0.026505) test_gap_extend: .: (0.023999) test_gap_open: .: (0.026194) test_hits: .: (0.026722) test_hsp_len: .: (0.025962) test_iterations: .: (0.024912) test_kappa: .: (0.026590) test_lambda: .: (0.026706) test_matrix: .: (0.024173) test_message: .: (0.026053) test_parameters: .: (0.026633) test_pattern: .: (0.026460) test_program: .: (0.024482) test_query_def: .: (0.026338) test_query_id: .: (0.026710) test_query_len: .: (0.026442) test_reference: .: (0.024420) test_reports: .: (0.026304) test_statistics: .: (0.026209) test_version: .: (0.025408) Bio::TestBlastReportREXML: test_db: .: (0.009110) test_db_len: .: (0.008916) test_db_num: .: (0.008704) test_each_hit: .: (0.010260) test_each_iteration: .: (0.009013) test_eff_space: .: (0.008824) test_entrez_query: .: (0.008708) test_entropy: .: (0.009614) test_expect: .: (0.009228) test_filter: .: (0.008671) test_gap_extend: .: (0.008595) test_gap_open: .: (0.008826) test_hits: .: (0.010324) test_hsp_len: .: (0.008829) test_inclusion: .: (0.008677) test_iterations: .: (0.008885) test_kappa: .: (0.010252) test_lambda: .: (0.008859) test_matrix: .: (0.008616) test_message: .: (0.008653) test_parameters: .: (0.010152) test_pattern: .: (0.008959) test_program: .: (0.008571) test_query_def: .: (0.008644) test_query_id: .: (0.009983) test_query_len: .: (0.009052) test_reference: .: (0.008679) test_sc_match: .: (0.008419) test_sc_mismatch: .: (0.009772) test_statistics: .: (0.009539) test_version: .: (0.008692) Bio::TestBlastReportTabular: test_db: .: (0.000391) test_db_len: .: (0.000131) test_db_num: .: (0.000107) test_each_hit: .: (0.000121) test_each_iteration: .: (0.000116) test_eff_space: .: (0.000107) test_entrez_query: .: (0.000113) test_entropy: .: (0.000260) test_expect: .: (0.000141) test_filter: .: (0.000098) test_gap_extend: .: (0.000098) test_gap_open: .: (0.000102) test_hits: .: (0.000117) test_hsp_len: .: (0.000104) test_inclusion: .: (0.000101) test_iterations: .: (0.000098) test_kappa: .: (0.000092) test_lambda: .: (0.000104) test_matrix: .: (0.000096) test_message: .: (0.000106) test_parameters: .: (0.000081) test_pattern: .: (0.000105) test_program: .: (0.000161) test_query_def: .: (0.000110) test_query_id: .: (0.000102) test_query_len: .: (0.000098) test_reference: .: (0.000122) test_sc_match: .: (0.000107) test_sc_mismatch: .: (0.000100) test_statistics: .: (0.000116) test_version: .: (0.000103) Bio::TestChain: test_aaseq: .: (0.000325) test_addLigand: .: (0.000076) test_addResidue: .: (0.000064) test_atom_seq: .: (0.000262) test_comp: .: (0.000111) test_each: .: (0.000082) test_each_heterogen: .: (0.000080) test_each_residue: .: (0.000073) test_get_heterogen_by_id: .: (0.000059) test_get_residue_by_id: .: (0.000070) test_inspect: .: (0.000107) test_rehash: .: (0.000075) test_rehash_heterogens: .: (0.000051) test_rehash_residues: .: (0.000072) test_square_brace: .: (0.000078) test_to_s: .: (0.000097) Bio::TestChainFinder: test_chains: .: (0.000362) test_each_chain: .: (0.000089) test_find_chain: .: (0.000073) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.005525) test_header: .: (0.000566) test_match_line: .: (0.000422) test_sequence0: .: (0.000643) test_sequence1: .: (0.000463) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.005734) test_header: .: (0.000671) test_match_line: .: (0.000567) test_sequence0: .: (0.002524) test_sequence1: .: (0.000677) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.007799) test_header: .: (0.000770) test_match_line: .: (0.000480) test_sequence0: .: (0.000448) test_sequence1: .: (0.000599) Bio::TestCodonTable: test_Tables: .: (0.000210) test_accessor: .: (0.000075) test_definition: .: (0.000047) test_each: .: (0.000063) test_revtrans: .: (0.000112) test_self_accessor: .: (0.000049) test_self_copy: .: (0.000563) test_set_accessor: .: (0.105215) test_start: .: (0.000100) test_start_codon?: .: (0.000065) test_stop: .: (0.000043) test_stop_codon?: .: (0.000047) test_table: .: (0.000042) Bio::TestCodonTableConstants: test_Definitions: .: (0.000207) test_Starts: .: (0.000073) test_Tables: .: (0.000052) test_stops: .: (0.000073) Bio::TestColorScheme: test_buried: .: (0.000836) Bio::TestCommand: test_command_constants: .: (0.000381) test_escape_shell: .: (0.000110) test_escape_shell_unix: .: (0.000068) test_escape_shell_windows: .: (0.000068) test_make_cgi_params_by_array_of_array: .: (0.000238) test_make_cgi_params_by_array_of_hash: .: (0.000196) test_make_cgi_params_by_array_of_string: .: (0.000108) test_make_cgi_params_by_hash_in_string: .: (0.000461) test_make_cgi_params_by_hash_in_symbol: .: (0.000294) test_make_cgi_params_by_string: .: (0.000155) test_make_command_line: .: (0.000091) test_make_command_line_unix: .: (0.000071) test_make_command_line_windows: .: (0.000073) test_safe_command_line_array: .: (0.000083) test_safe_command_line_array_passthrough: .: (0.000099) Bio::TestContingencyTable: test_lite_example: .: (0.103031) Bio::TestDB: test_entry_id: .: (0.000281) test_exists: .: (0.000067) test_fetch: .: (0.000112) test_get: .: (0.000058) test_open: .: (0.000075) test_tags: .: (0.000065) Bio::TestDataType: test_const_like_method: .: (0.000641) test_pdb_achar: .: (0.000200) test_pdb_atom: .: (0.000147) test_pdb_character: .: (0.000131) test_pdb_date: .: (0.000142) test_pdb_idcode: .: (0.000139) test_pdb_integer: .: (0.000066) test_pdb_list: .: (0.000072) test_pdb_lstring: .: (0.000132) test_pdb_real: .: (0.000104) test_pdb_resudue_name: .: (0.000130) test_pdb_slist: .: (0.000080) test_pdb_string: .: (0.000139) test_pdb_stringrj: .: (0.000064) test_pdb_symop: .: (0.000123) test_specification_list: .: (0.000207) Bio::TestEMBL: test_ac: .: (0.000471) test_accession: .: (0.000283) test_cc: .: (0.000228) test_de: .: (0.000253) test_division: .: (0.000281) test_dr: .: (0.000233) test_dt: .: (0.000252) test_dt_created: .: (0.000226) test_dt_iterator: .: (0.000311) test_dt_updated: .: (0.000231) test_each_cds: .: (0.000382) test_each_gene: .: (0.000349) test_entry: .: (0.000391) test_fh: .: (0.000259) test_ft: .: (0.000364) test_ft_accessor: .: (0.000328) test_ft_iterator: .: (0.000459) test_id_line: .: (0.000256) test_id_line_data_class: .: (0.000228) test_id_line_division: .: (0.000217) test_id_line_entry_name: .: (0.000326) test_id_line_iterator: .: (0.000236) test_id_line_molecule_type: .: (0.000238) test_id_line_sequence_length: .: (0.000226) test_kw: .: (0.000350) test_molecule: .: (0.000257) test_oc: .: (0.000295) test_og: .: (0.000232) test_os: .: (0.000257) test_ref: .: (0.000398) test_references: .: (0.000428) test_seq: .: (0.000414) test_sequence_length: .: (0.000343) test_sq: .: (0.000258) test_sq_get: .: (0.000220) test_sv: .: (0.000203) test_version: .: (0.000290) Bio::TestEMBL89: test_ac: .: (0.000387) test_accession: .: (0.000229) test_cc: .: (0.000197) test_de: .: (0.000228) test_division: .: (0.000367) test_dr: .: (0.000210) test_dt: .: (0.000225) test_dt_created: .: (0.000220) test_dt_iterator: .: (0.000350) test_dt_updated: .: (0.000220) test_each_cds: .: (0.000346) test_each_gene: .: (0.000303) test_entry: .: (0.000290) test_fh: .: (0.002567) test_ft: .: (0.000452) test_ft_accessor: .: (0.000369) test_ft_iterator: .: (0.000399) test_id_line: .: (0.000434) test_id_line_data_class: .: (0.000251) test_id_line_division: .: (0.000235) test_id_line_entry_name: .: (0.000238) test_id_line_iterator: .: (0.000366) test_id_line_molecule_type: .: (0.000236) test_id_line_sequence_length: .: (0.000218) test_id_line_sequence_version: .: (0.000228) test_kw: .: (0.000280) test_molecule: .: (0.000219) test_oc: .: (0.000261) test_og: .: (0.000187) test_os: .: (0.000294) test_ref: .: (0.000273) test_references: .: (0.000408) test_seq: .: (0.000452) test_sequence_length: .: (0.000233) test_sq: .: (0.000215) test_sq_get: .: (0.000202) test_sv: .: (0.000290) test_version: .: (0.000224) Bio::TestEMBLAPI: test_ac: .: (0.000243) test_accessions: .: (0.000089) Bio::TestEMBLCommon: test_ac: .: (0.000166) test_accession: .: (0.000059) test_accessions: .: (0.000050) test_de: .: (0.000044) test_definition: .: (0.000043) test_description: .: (0.000051) test_dr: .: (0.000042) test_keywords: .: (0.000044) test_kw: .: (0.000040) test_oc: .: (0.000042) test_og: .: (0.000042) test_os: .: (0.000040) test_ref: .: (0.000042) test_references: .: (0.000042) Bio::TestEMBLDB: test_fetch: .: (0.000211) test_p_entry2hash: .: (0.000047) Bio::TestEMBLToBioSequence: test_classification: .: (0.002296) test_date_created: .: (0.000530) test_date_modified: .: (0.000325) test_definition: .: (0.000278) test_division: .: (0.000275) test_entry_id: .: (0.000354) test_entry_version: .: (0.000279) test_features: .: (0.000368) test_keywords: .: (0.000307) test_molecule_type: .: (0.000255) test_primary_accession: .: (0.000239) test_references: .: (0.000474) test_release_created: .: (0.000284) test_release_modified: .: (0.000253) test_secondary_accessions: .: (0.000251) test_sequence_version: .: (0.000271) test_species: .: (0.000231) test_topology: .: (0.000266) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.002191) test_date_created: .: (0.002068) test_date_modified: .: (0.002085) test_definition: .: (0.002353) test_division: .: (0.002488) test_entry_id: .: (0.002266) test_entry_version: .: (0.002501) test_features: .: (0.002702) test_keywords: .: (0.002415) test_molecule_type: .: (0.002269) test_primary_accession: .: (0.002295) test_references: .: (0.005640) test_release_created: .: (0.002554) test_release_modified: .: (0.002418) test_secondary_accessions: .: (0.002283) test_sequence_version: .: (0.002406) test_species: .: (0.002095) test_topology: .: (0.002177) Bio::TestFasta: test_db: .: (0.000229) test_format: .: (0.000060) test_format_arg_integer: .: (0.000085) test_format_arg_str: .: (0.000064) test_ktup: .: (0.000060) test_matrix: .: (0.000048) test_option: .: (0.000096) test_options: .: (0.000071) test_output: .: (0.000056) test_program: .: (0.000063) test_server: .: (0.000058) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000214) test_accession: .: (0.000075) test_accessions: .: (0.000083) test_description: .: (0.000077) test_descriptions: .: (0.000192) test_entry_id: .: (0.000067) test_get_all_by_type: .: (0.000059) test_gi: .: (0.000068) test_id_strings: .: (0.000106) test_list_ids: .: (0.000063) test_locus: .: (0.000073) test_words: .: (0.000093) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000191) test_accession: .: (0.000078) test_accessions: .: (0.000091) test_description: .: (0.000075) test_descriptions: .: (0.000083) test_emb: .: (0.000092) test_entry_id: .: (0.000180) test_get_all_by_type: .: (0.000082) test_get_emb: .: (0.000082) test_gi: .: (0.000073) test_id_strings: .: (0.000106) test_list_ids: .: (0.000062) test_locus: .: (0.000062) test_words: .: (0.000085) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000165) test_accession: .: (0.000068) test_accessions: .: (0.000059) test_description: .: (0.000052) test_descriptions: .: (0.000184) test_entry_id: .: (0.000050) test_get_all_by_type: .: (0.000050) test_gi: .: (0.000059) test_id_strings: .: (0.000085) test_list_ids: .: (0.000053) test_locus: .: (0.000058) test_sp: .: (0.000068) test_words: .: (0.000077) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000187) test_accession: .: (0.000109) test_accessions: .: (0.000108) test_description: .: (0.000184) test_descriptions: .: (0.000098) test_entry_id: .: (0.000087) test_get_all_by_type: .: (0.000087) test_gi: .: (0.000099) test_id_strings: .: (0.000172) test_list_ids: .: (0.000097) test_locus: .: (0.000094) test_words: .: (0.000180) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000405) test_accession: .: (0.000095) test_accessions: .: (0.000086) test_description: .: (0.000081) test_descriptions: .: (0.000089) test_entry_id: .: (0.000097) test_get_all_by_type: .: (0.000085) test_gi: .: (0.000082) test_id_strings: .: (0.000162) test_list_ids: .: (0.000082) test_locus: .: (0.000075) test_words: .: (0.000146) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000230) test_accession: .: (0.000076) test_accessions: .: (0.000070) test_description: .: (0.000062) test_descriptions: .: (0.000057) test_entry_id: .: (0.000050) test_get_all_by_type: .: (0.000049) test_gi: .: (0.000064) test_id_strings: .: (0.000087) test_list_ids: .: (0.000069) test_locus: .: (0.000074) test_words: .: (0.000081) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000162) test_accession: .: (0.000083) test_accessions: .: (0.000071) test_description: .: (0.000362) test_descriptions: .: (0.000077) test_entry_id: .: (0.000068) test_get: .: (0.000076) test_get_all_by_type: .: (0.000056) test_id_strings: .: (0.000109) test_list_ids: .: (0.000068) test_locus: .: (0.000059) test_sp: .: (0.000078) test_words: .: (0.000118) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000188) test_accession: .: (0.000080) test_accessions: .: (0.000081) test_description: .: (0.000286) test_descriptions: .: (0.000073) test_entry_id: .: (0.000066) test_get: .: (0.000074) test_get_all_by_type: .: (0.000055) test_id_strings: .: (0.000132) test_list_ids: .: (0.000065) test_locus: .: (0.000060) test_tr: .: (0.000081) test_words: .: (0.000127) Bio::TestFastaFirstName: test_first_name1: .: (0.000192) test_first_name_multi_identifier: .: (0.000075) test_first_name_single_worded_defintion: .: (0.000065) test_no_definition: .: (0.000064) test_space_before_first_name: .: (0.000324) test_tabbed_defintion: .: (0.000077) Bio::TestFastaFormat: test_aalen: .: (0.000213) test_aaseq: .: (0.000090) test_acc_version: .: (0.000121) test_accession: .: (0.000099) test_accessions: .: (0.000102) test_data: .: (0.000070) test_definition: .: (0.000074) test_entry: .: (0.000083) test_entry_id: .: (0.000099) test_entry_overrun: .: (0.000082) test_first_name: .: (0.000079) test_gi: .: (0.000096) test_identifiers: .: (0.000316) test_length: .: (0.000152) test_query: .: (0.000090) test_seq: .: (0.000066) Bio::TestFastaFormatConst: test_delimiter: .: (0.000154) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000198) test_data: .: (0.000076) test_definition: .: (0.000060) test_entry: .: (0.000061) test_entry_id: .: (0.000096) test_first_name: .: (0.000081) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000186) test_naseq: .: (0.000074) test_naseq_class: .: (0.000306) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000167) Bio::TestFastaInitialize: test_new_1: .: (0.000348) test_option: .: (0.000060) test_option_backward_compatibility: .: (0.000099) Bio::TestFastaNumericFormat: test_arg: .: (0.000182) test_data: .: (0.000086) test_definition: .: (0.000051) test_each: .: (0.000082) test_entry: .: (0.000051) test_entry_id: .: (0.000277) test_length: .: (0.000069) test_to_biosequence: .: (0.000705) Bio::TestFastaQuery: test_query: .: (0.000126) test_self_local: .: (0.000038) test_self_parser: .: (0.000036) test_self_remote: .: (0.000039) Bio::TestFastacmd: test_database: .: (0.000129) test_fastacmd: .: (0.000045) test_methods: .: (0.000079) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000729) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000377) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000348) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000323) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000643) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000358) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000326) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000521) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000382) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000308) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000337) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000524) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000369) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000835) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000729) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000594) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000419) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000339) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.007763) test_error_probabilities_as_sanger: .: (0.003478) test_error_probabilities_as_solexa: .: (0.003511) test_quality_scores_as_illumina: .: (0.000545) test_quality_scores_as_sanger: .: (0.000264) test_quality_scores_as_solexa: .: (0.000255) test_validate_format: .: (0.000381) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000809) test_entry_id: .: (0.000781) test_error_probabilities: .: (0.128488) test_nalen: .: (0.001097) test_naseq: .: (0.000978) test_quality_scores: .: (0.001320) test_quality_string: .: (0.000776) test_roundtrip: .: (0.087430) test_seq: .: (0.000768) test_sequence_string: .: (0.000711) test_to_biosequence: .: (0.081308) test_to_biosequence_and_output: .: (0.003676) test_to_s: .: (0.000897) test_validate_format: .: (0.000634) test_validate_format_with_array: .: (0.000777) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000531) test_mask_20_with_empty_string: .: (0.000287) test_mask_20_with_longer_string: .: (0.000261) test_mask_20_with_x: .: (0.000376) test_mask_60: .: (0.000367) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.004325) test_error_probabilities_as_sanger: .: (0.004204) test_error_probabilities_as_solexa: .: (0.004257) test_quality_scores_as_illumina: .: (0.000419) test_quality_scores_as_sanger: .: (0.000377) test_quality_scores_as_solexa: .: (0.000340) test_validate_format: .: (0.000406) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.004754) test_error_probabilities_as_sanger: .: (0.003277) test_error_probabilities_as_solexa: .: (0.003752) test_quality_scores_as_illumina: .: (0.000679) test_quality_scores_as_sanger: .: (0.000314) test_quality_scores_as_solexa: .: (0.000216) test_validate_format: .: (0.000424) Bio::TestFeature: test_append: .: (0.000259) test_append_nil: .: (0.000057) test_assoc: .: (0.000086) test_each: .: (0.000049) test_feature: .: (0.000043) test_locations: .: (0.000111) test_new: .: (0.000045) test_position: .: (0.000040) test_qualifiers: .: (0.000044) Bio::TestFeatures: test_append: .: (0.000207) test_arg: .: (0.000060) test_each: .: (0.000050) test_features: .: (0.000056) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000914) test_aaindex2: .: (0.000195) test_blast: .: (0.000164) test_blastxml: .: (0.000591) test_embl: .: (0.000229) test_embl_oldrelease: .: (0.000186) test_fastaformat: .: (0.000312) test_fastanumericformat: .: (0.000135) test_fastq: .: (0.000152) test_genbank: .: (0.000163) test_genpept: .: (0.000312) test_hmmer: .: (0.000240) test_maxml_cluster: .: (0.002226) test_maxml_sequence: .: (0.000099) test_medline: .: (0.000115) test_prosite: .: (0.003464) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002881) test_transfac: .: (0.001344) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000280) test_auto_1arg_filename: .: (0.000405) test_auto_1arg_io: .: (0.000381) test_auto_1arg_io_with_block: .: (0.000544) test_auto_1arg_with_block: .: (0.000436) test_auto_2arg_filename_mode: .: (0.000250) test_auto_2arg_filename_mode_with_block: .: (0.000522) test_auto_3arg: .: (0.000292) test_auto_3arg_with_block: .: (0.000398) test_foreach: .: (0.000347) test_new_2arg_class: .: (0.000131) test_new_2arg_nil: .: (0.000241) test_open_0arg: .: (0.000114) test_open_1arg_class: .: (0.000119) test_open_1arg_filename: .: (0.000239) test_open_1arg_io: .: (0.000226) test_open_1arg_io_with_block: .: (0.000440) test_open_1arg_nil: .: (0.000106) test_open_1arg_with_block: .: (0.000557) test_open_2arg_autodetect: .: (0.000290) test_open_2arg_autodetect_io: .: (0.000218) test_open_2arg_autodetect_io_with_block: .: (0.000403) test_open_2arg_autodetect_with_block: .: (0.000385) test_open_2arg_class: .: (0.000113) test_open_2arg_class_io: .: (0.000240) test_open_2arg_class_io_with_block: .: (0.000337) test_open_2arg_class_with_block: .: (0.000280) test_open_2arg_filename_mode: .: (0.000225) test_open_2arg_filename_mode_with_block: .: (0.000354) test_open_3arg: .: (0.000419) test_open_3arg_with_block: .: (0.000889) test_open_4arg: .: (0.000785) test_to_a: .: (0.000364) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000485) test_close: .: (0.000103) test_dbclass: .: (0.000075) test_dbclass_eq: .: (0.000101) test_dbclass_nil: .: (0.000149) test_each: .: (0.000201) test_each_entry: .: (0.000258) test_ended_pos: .: (0.000160) test_entry_pos_flag: .: (0.000099) test_entry_raw: .: (0.000339) test_eof?: .: (0.000235) test_next_entry: .: (0.000244) test_path: .: (0.000112) test_pos: .: (0.000159) test_raw: .: (0.000196) test_rewind: .: (0.000159) test_start_pos: .: (0.000184) test_start_pos_ended_pos_not_recorded: .: (0.000181) test_to_io: .: (0.000246) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000266) test_simpleformat2: .: (0.000146) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000169) test_eof_false_after_prefetch: .: (0.000148) test_eof_false_first: .: (0.000076) test_eof_true: .: (0.000124) test_getc: .: (0.000085) test_getc_after_prefetch: .: (0.000073) test_gets: .: (0.000070) test_gets_equal_prefetch_gets: .: (0.000075) test_gets_paragraph_mode: .: (0.000117) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000211) test_gets_paragraph_mode_within_buffer: .: (0.000378) test_gets_rs: .: (0.000092) test_gets_rs_equal_prefetch_gets: .: (0.000087) test_gets_rs_within_buffer: .: (0.000173) test_pos: .: (0.000074) test_pos=: .: (0.000082) test_prefetch_buffer: .: (0.000070) test_prefetch_gets: .: (0.000078) test_prefetch_gets_with_arg: .: (0.000080) test_rewind: .: (0.000094) test_skip_spaces: .: (0.000086) test_to_io: .: (0.000096) test_ungetc: .: (0.000077) test_ungetc_after_prefetch: .: (0.000071) test_ungets: .: (0.000082) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000245) test_self_open_file: .: (0.000095) test_self_open_file_with_block: .: (0.000115) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000179) test_parse_file_open_arg_int_perm: .: (0.000057) test_parse_file_open_arg_int_perm_opt: .: (0.000060) test_parse_file_open_arg_integer: .: (0.000047) test_parse_file_open_arg_nil: .: (0.000044) test_parse_file_open_arg_opt: .: (0.000081) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000058) test_parse_file_open_arg_str: .: (0.000070) test_parse_file_open_arg_str_opt: .: (0.000068) test_parse_file_open_arg_str_perm: .: (0.000062) test_parse_file_open_arg_str_perm_opt: .: (0.000063) test_parse_file_open_arg_str_with_enc: .: (0.000196) test_parse_file_open_arg_str_with_ext_enc: .: (0.000094) test_parse_file_open_mode_integer: .: (0.000049) test_parse_file_open_mode_nil: .: (0.000053) test_parse_file_open_mode_str: .: (0.000048) test_parse_file_open_mode_str_with_enc: .: (0.000048) test_parse_file_open_mode_str_with_ext_enc: .: (0.000047) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000177) test_entry: .: (0.000066) test_entry_ended_pos: .: (0.000058) test_entry_pos_flag: .: (0.000065) test_entry_start_pos: .: (0.000048) test_get_entry: .: (0.000096) test_rewind: .: (0.000068) test_skip_leader: .: (0.000068) test_stream: .: (0.000045) test_stream_pos: .: (0.000075) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000165) test_delimiter_overrun: .: (0.000049) test_entry: .: (0.000080) test_entry_ended_pos: .: (0.000062) test_entry_ended_pos_default_nil: .: (0.000059) test_entry_start_pos: .: (0.000059) test_entry_start_pos_default_nil: .: (0.000056) test_get_entry: .: (0.000119) test_get_parsed_entry: .: (0.000122) test_header: .: (0.000046) test_skip_leader: .: (0.000076) test_skip_leader_without_header: .: (0.000261) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000249) test_entry_ended_pos: .: (0.000146) test_entry_start_pos: .: (0.000136) test_flag_to_fetch_header: .: (0.000141) test_get_entry: .: (0.000174) test_get_parsed_entry: .: (0.000323) test_rewind: .: (0.000123) test_skip_leader: .: (0.000070) Bio::TestGCGMsf: test_alignment: .: (0.000756) test_checksum: .: (0.000172) test_compcheck: .: (0.003258) test_date: .: (0.000267) test_description: .: (0.000147) test_entry_id: .: (0.000154) test_gap_length_weight: .: (0.000148) test_gap_weight: .: (0.000143) test_heading: .: (0.000141) test_length: .: (0.000372) test_seq_type: .: (0.000142) test_symbol_comparison_table: .: (0.000137) test_validate_checksum: .: (0.001086) Bio::TestGFF: test_record_class: .: (0.000712) test_records: .: (0.000246) Bio::TestGFF2: test_const_version: .: (0.000465) test_gff_version: .: (0.000467) test_metadata: .: (0.000254) test_metadata_size: .: (0.000232) test_records_size: .: (0.000228) test_to_s: .: (0.000614) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000206) test_attributes_case2: .: (0.000113) test_attributes_incompatible_backslash_semicolon: .: (0.000129) Bio::TestGFF2MetaData: test_data: .: (0.000281) test_directive: .: (0.000043) test_parse: .: (0.000055) Bio::TestGFF2Record: test_attribute: .: (0.000325) test_attribute_nonexistent: .: (0.000159) test_attributes: .: (0.000169) test_attributes_to_hash: .: (0.000308) test_comment_only?: .: (0.000151) test_delete_attribute: .: (0.000161) test_delete_attribute_multiple: .: (0.000170) test_delete_attribute_multiple2: .: (0.000173) test_delete_attribute_multiple_nil: .: (0.000153) test_delete_attribute_nil: .: (0.000304) test_delete_attribute_nonexistent: .: (0.000155) test_delete_attributes: .: (0.000151) test_delete_attributes_multiple: .: (0.000167) test_delete_attributes_nonexistent: .: (0.000152) test_end: .: (0.000194) test_eqeq: .: (0.000571) test_eqeq_false: .: (0.000368) test_feature: .: (0.000153) test_frame: .: (0.000302) test_get_attribute: .: (0.000204) test_get_attribute_nonexistent: .: (0.000143) test_get_attributes: .: (0.000203) test_get_attributes_nonexistent: .: (0.000144) test_replace_attributes: .: (0.000168) test_replace_attributes_multiple_multiple_over: .: (0.000310) test_replace_attributes_multiple_multiple_same: .: (0.000166) test_replace_attributes_multiple_multiple_two: .: (0.000163) test_replace_attributes_multiple_single: .: (0.000155) test_replace_attributes_nonexistent: .: (0.000177) test_replace_attributes_nonexistent_multiple: .: (0.000317) test_replace_attributes_single_multiple: .: (0.000164) test_score: .: (0.000129) test_self_parse: .: (0.000374) test_seqname: .: (0.000142) test_set_attribute: .: (0.000491) test_set_attribute_multiple: .: (0.000180) test_set_attribute_nonexistent: .: (0.000232) test_sort_attributes_by_tag!: .: (0.000282) test_sort_attributes_by_tag_bang_test2: .: (0.000216) test_sort_attributes_by_tag_bang_with_block: .: (0.000379) test_source: .: (0.000141) test_start: .: (0.000125) test_strand: .: (0.000124) test_to_s: .: (0.000253) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000186) test_comment_eq: .: (0.000053) test_comment_only?: .: (0.000063) test_comment_only_false: .: (0.000047) test_to_s: .: (0.000052) test_to_s_not_empty: .: (0.000096) Bio::TestGFF3: test_const_version: .: (0.000527) test_gff_version: .: (0.000575) test_records: .: (0.000416) test_sequence_regions: .: (0.000591) test_sequences: .: (0.000374) test_to_s: .: (0.000923) Bio::TestGFF3MetaData: test_data: .: (0.000172) test_directive: .: (0.000052) test_parse: .: (0.000071) Bio::TestGFF3Record: test_attributes: .: (0.000283) test_end: .: (0.000326) test_feature: .: (0.000136) test_frame: .: (0.000124) test_id: .: (0.000133) test_score: .: (0.000141) test_seqname: .: (0.000293) test_source: .: (0.000113) test_start: .: (0.000108) test_strand: .: (0.000121) test_to_s: .: (0.000258) test_to_s_attr_order_changed: .: (0.000408) Bio::TestGFF3RecordEscape: test_escape: .: (0.000215) test_escape_attribute: .: (0.000083) test_escape_seqid: .: (0.000084) test_unescape: .: (0.000079) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000255) test_eqeq: .: (0.000332) test_new_from_sequences_na: .: (0.000164) test_new_from_sequences_na_aa: .: (0.000207) test_new_from_sequences_na_aa_boundary_gap: .: (0.000295) test_new_from_sequences_na_aa_example: .: (0.000239) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000211) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000182) test_process_sequences_na: .: (0.000425) test_process_sequences_na_aa: .: (0.000141) test_process_sequences_na_aa_reverse_frameshift: .: (0.000135) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000128) test_process_sequences_na_aa_tooshort: .: (0.000247) test_process_sequences_na_tooshort: .: (0.000173) test_to_s: .: (0.000312) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000221) test_attributes_one: .: (0.000069) test_attributes_with_escaping: .: (0.000080) test_id_multiple: .: (0.000160) test_id_multiple2: .: (0.000156) test_id_replace: .: (0.000096) test_id_set: .: (0.000097) test_initialize_9: .: (0.000050) test_phase: .: (0.000243) test_score: .: (0.000071) test_to_s_void: .: (0.000069) Bio::TestGFF3RecordTarget: test_end: .: (0.000170) test_parse: .: (0.000112) test_start: .: (0.000054) test_strand: .: (0.000054) test_target_id: .: (0.000054) test_to_s: .: (0.000107) Bio::TestGFF3SequenceRegion: test_end: .: (0.000143) test_parse: .: (0.000297) test_seqid: .: (0.000057) test_start: .: (0.000050) test_to_s: .: (0.000093) Bio::TestGFFRecord: test_attributes: .: (0.000199) test_comment: .: (0.000077) test_end: .: (0.000075) test_feature: .: (0.000079) test_frame: .: (0.000069) test_score: .: (0.000061) test_seqname: .: (0.000072) test_source: .: (0.000077) test_start: .: (0.000242) test_strand: .: (0.000078) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000166) Bio::TestGeneAssociation: test_aspect: .: (0.000140) test_assigned_by: .: (0.000067) test_date: .: (0.000061) test_db: .: (0.000060) test_db_object_id: .: (0.000056) test_db_object_name: .: (0.000058) test_db_object_symbol: .: (0.000059) test_db_object_synonym: .: (0.000065) test_db_object_type: .: (0.000057) test_db_reference: .: (0.000060) test_evidence: .: (0.000061) test_goid: .: (0.000266) test_parser: .: (0.000369) test_qualifier: .: (0.000066) test_taxon: .: (0.000058) test_to_str: .: (0.000066) test_with: .: (0.000061) Bio::TestGenscanReport: test_date_run: .: (0.000906) test_gccontent: .: (0.000497) test_genscan_version: .: (0.000500) test_isochore: .: (0.000598) test_length: .: (0.000464) test_matrix: .: (0.000751) test_predictions_size: .: (0.000487) test_query_name: .: (0.000478) test_time: .: (0.000565) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.004719) test_donor_score: .: (0.000611) test_exon_type: .: (0.000855) test_exon_type_long: .: (0.000566) test_first: .: (0.000492) test_initiation_score: .: (0.000697) test_last: .: (0.000475) test_number: .: (0.000666) test_p_value: .: (0.000468) test_phase: .: (0.000616) test_range: .: (0.000504) test_score: .: (0.000449) test_strand: .: (0.000586) test_t_score: .: (0.000439) test_termination_score: .: (0.000568) Bio::TestGenscanReportGene: test_aaseq: .: (0.000644) test_naseq: .: (0.000678) test_number: .: (0.000445) test_polyA: .: (0.000565) test_promoter: .: (0.000496) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000700) test_reports_ary_contents: .: (0.000598) Bio::TestHMMERReportConstants: test_rs: .: (0.000160) Bio::TestHMMERReportHit: test_accession: .: (0.000571) test_append_hsp: .: (0.000458) test_bit_score: .: (0.000577) test_definition: .: (0.000479) test_description: .: (0.000440) test_each: .: (0.000463) test_each_hsp: .: (0.000604) test_entry_id: .: (0.000458) test_evalue: .: (0.000446) test_hit: .: (0.000433) test_hit_id: .: (0.000601) test_hsps: .: (0.000449) test_num: .: (0.000427) test_score: .: (0.000420) test_target_def: .: (0.000443) test_target_id: .: (0.000415) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000560) test_each: .: (0.000602) test_each_hit: .: (0.000487) test_histogram: .: (0.000434) test_hits: .: (0.000428) test_hsps: .: (0.000652) test_parameter: .: (0.000469) test_program: .: (0.000486) test_query_info: .: (0.000675) test_statistical_detail: .: (0.000512) test_total_seq_searched: .: (0.000438) test_whole_seq_top_hits: .: (0.000430) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000906) test_histogram: .: (0.000604) test_statistical_detail: .: (0.000554) test_total_seq_searched: .: (0.000774) test_whole_seq_top_hit: .: (0.000633) Bio::TestHMMERReportHsp: test_accession: .: (0.000577) test_bit_score: .: (0.000604) test_csline: .: (0.000513) test_domain: .: (0.000452) test_evalue: .: (0.000438) test_flatseq: .: (0.000627) test_hmm_f: .: (0.000482) test_hmm_t: .: (0.000434) test_hmmseq: .: (0.000438) test_hsp: .: (0.000662) test_midline: .: (0.000537) test_query_frame: .: (0.000443) test_query_from: .: (0.000444) test_query_seq: .: (0.000731) test_query_to: .: (0.000550) test_rfline: .: (0.000455) test_score: .: (0.000435) test_seq_f: .: (0.000681) test_seq_ft: .: (0.000526) test_seq_t: .: (0.000487) test_set_alignment: .: (0.000458) test_targat_to: .: (0.000542) test_target_frame: .: (0.000470) test_target_from: .: (0.000474) test_target_seq: .: (0.000673) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000383) test_find_hetatm: .: (0.000183) test_hetatms: .: (0.004460) Bio::TestHeterogen: test_addAtom: .: (0.005962) test_each: .: (0.005059) test_each_hetatm: .: (0.000154) test_get_residue_id_from_atom: .: (0.005214) test_het_atom: .: (0.000122) test_iCode: .: (0.003653) test_inspect: .: (0.000189) test_resSeq: .: (0.000104) test_sort: .: (0.004586) test_square_bracket: .: (0.000137) test_to_s: .: (0.000321) test_update_resudue_id: .: (0.000122) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000337) test_find_heterogen: .: (0.000089) test_heterogens: .: (0.003105) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.002902) test_match_description: .: (0.000212) test_match_evalue: .: (0.000252) test_match_ipr_description: .: (0.000112) test_match_ipr_id: .: (0.000098) test_match_match_end: .: (0.000115) test_match_match_start: .: (0.000102) test_match_method: .: (0.000092) test_matches_size: .: (0.000089) test_query_id: .: (0.000092) test_query_length: .: (0.000107) Bio::TestIprscanRawReport: test_entry_id: .: (0.002361) test_match_accession: .: (0.001722) test_match_crc64: .: (0.001773) test_match_date: .: (0.001674) test_match_description: .: (0.001678) test_match_evalue: .: (0.001873) test_match_go_terms: .: (0.001711) test_match_ipr_description: .: (0.001711) test_match_ipr_id: .: (0.001927) test_match_match_end: .: (0.001756) test_match_match_start: .: (0.001752) test_match_method: .: (0.001957) test_match_query_id: .: (0.001896) test_match_query_length: .: (0.003442) test_match_status: .: (0.001997) test_obj: .: (0.001584) test_query_id: .: (0.001582) test_query_length: .: (0.001710) test_self_reports_in_raw: .: (0.002917) Bio::TestIprscanReport: test_output_raw: .: (0.000776) test_to_raw: .: (0.000330) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000434) test_match_accession: .: (0.000507) test_match_date: .: (0.000338) test_match_description: .: (0.000305) test_match_evalue: .: (0.000300) test_match_go_terms: .: (0.000459) test_match_ipr_description: .: (0.000319) test_match_ipr_id: .: (0.000300) test_match_match_end: .: (0.000317) test_match_match_start: .: (0.000299) test_match_method: .: (0.000449) test_match_status: .: (0.000289) test_matches_size: .: (0.000340) test_query_id: .: (0.000280) test_query_length: .: (0.000383) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000485) test_to_hash_match?: .: (0.000366) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.001020) Bio::TestKeggCompound: test_comment: .: (0.000397) test_dblinks_as_hash: .: (0.000261) test_dblinks_as_strings: .: (0.000463) test_entry_id: .: (0.000202) test_enzymes: .: (0.000421) test_formula: .: (0.000192) test_kcf: .: (0.000164) test_mass: .: (0.000166) test_name: .: (0.000366) test_names: .: (0.000181) test_pathways_as_hash: .: (0.000306) test_pathways_as_strings: .: (0.000237) test_reactions: .: (0.000616) test_remark: .: (0.000225) test_rpairs: .: (0.000201) Bio::TestKeggEnzyme: test_all_reac: .: (0.000543) test_classes: .: (0.000327) test_cofactors: .: (0.000314) test_comment: .: (0.000480) test_dblinks_as_hash: .: (0.000349) test_dblinks_as_strings: .: (0.000315) test_diseases: .: (0.000302) test_entry: .: (0.000313) test_entry_id: .: (0.000299) test_genes: .: (0.011768) test_genes_as_hash: .: (0.010027) test_genes_as_strings: .: (0.003085) test_inhibitors: .: (0.000697) test_iubmb_reactions: .: (0.000436) test_kegg_reactions: .: (0.000373) test_motifs: .: (0.000341) test_name: .: (0.000389) test_names: .: (0.000389) test_obsolete?: .: (0.000318) test_orthologs_as_hash: .: (0.000491) test_orthologs_as_strings: .: (0.000321) test_pathways_as_hash: .: (0.000395) test_pathways_as_strings: .: (0.000350) test_products: .: (0.000370) test_reaction: .: (0.000707) test_structures: .: (0.000529) test_substrates: .: (0.000395) test_sysname: .: (0.000399) Bio::TestKeggGenesDblinks: test_data: .: (0.000270) test_dblinks_0: .: (0.000108) test_dblinks_1: .: (0.000096) test_dblinks_2: .: (0.000179) Bio::TestKeggGenesStructure: test_data: .: (0.000202) test_ids: .: (0.000129) test_ids_in_array: .: (0.002762) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.006304) test_graphics__size: .: (0.006046) test_id: .: (0.006060) test_link: .: (0.006307) test_name: .: (0.007662) test_reaction: .: (0.005587) test_type: .: (0.005495) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.005250) test_graphics__size: .: (0.005335) test_id: .: (0.055727) test_link: .: (0.005914) test_name: .: (0.005712) test_reaction: .: (0.005286) test_type: .: (0.005616) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.005480) test_category: .: (0.005611) test_entry_id: .: (0.006558) test_fgcolor=: .: (0.005678) test_height=: .: (0.005457) test_label=: .: (0.005388) test_shape=: .: (0.005159) test_width=: .: (0.005286) test_x=: .: (0.005132) test_y=: .: (0.005251) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.006326) test_graphics__size: .: (0.005363) test_id: .: (0.005195) test_link: .: (0.005131) test_name: .: (0.005261) test_reaction: .: (0.005096) test_type: .: (0.005149) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000220) test_graphics=: .: (0.000070) test_id=: .: (0.000082) test_link=: .: (0.000075) test_name=: .: (0.000064) test_reaction=: .: (0.000056) test_type=: .: (0.000056) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000392) test_category=: .: (0.000094) test_entry_id=: .: (0.000083) test_fgcolor=: .: (0.000088) test_height=: .: (0.000081) test_label=: .: (0.000082) test_pathway=: .: (0.000069) test_shape=: .: (0.000099) test_width=: .: (0.000091) test_x=: .: (0.000095) test_y=: .: (0.000154) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.006714) test_coords: .: (0.005194) test_fgcolor: .: (0.005203) test_height: .: (0.005198) test_name: .: (0.005113) test_type: .: (0.005099) test_width: .: (0.005078) test_x: .: (0.006436) test_y: .: (0.005524) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.005294) test_coords: .: (0.005246) test_fgcolor: .: (0.005252) test_height: .: (0.005089) test_name: .: (0.005209) test_type: .: (0.006774) test_width: .: (0.005319) test_x: .: (0.005250) test_y: .: (0.005304) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000396) test_coords=: .: (0.000083) test_fgcolor=: .: (0.000073) test_height=: .: (0.000070) test_name=: .: (0.000069) test_type=: .: (0.000066) test_width=: .: (0.000071) test_x=: .: (0.000071) test_y=: .: (0.000075) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.005270) test_entries__size: .: (0.005210) test_image: .: (0.005112) test_link: .: (0.006704) test_name: .: (0.005341) test_number: .: (0.005094) test_org: .: (0.005156) test_reactions=: .: (0.005267) test_reactions__size: .: (0.004999) test_relations=: .: (0.005076) test_relations__size: .: (0.006561) test_title: .: (0.005376) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.010528) test_name: .: (0.010022) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000234) test_initialize_0: .: (0.000057) test_initialize_1: .: (0.000066) test_initialize_2: .: (0.000063) test_name=: .: (0.000216) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.005232) test_name: .: (0.006479) test_products: .: (0.005341) test_substrates: .: (0.005304) test_type: .: (0.005202) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000261) test_name=: .: (0.000081) test_products=: .: (0.000075) test_substraces=: .: (0.000068) test_type=: .: (0.000238) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000201) test_entry_id=: .: (0.000085) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.005050) test_entry2: .: (0.005125) test_name: .: (0.005234) test_type: .: (0.006537) test_value: .: (0.005339) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000212) test_node1=: .: (0.000089) test_node2=: .: (0.000081) test_rel=: .: (0.000082) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000208) test_entry2=: .: (0.000064) test_name=: .: (0.000064) test_type=: .: (0.000061) test_value=: .: (0.000061) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.010529) test_name: .: (0.009887) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000225) test_initialize_0: .: (0.000056) test_initialize_1: .: (0.000052) test_initialize_2: .: (0.000051) test_name=: .: (0.000062) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000344) test_initialize_0: .: (0.000050) test_initialize_1: .: (0.000049) test_initialize_2: .: (0.000051) test_name=: .: (0.000062) Bio::TestKeggModule: test_compounds: .: (0.000377) test_compounds_as_hash: .: (0.000213) test_compounds_as_strings: .: (0.000170) test_definition: .: (0.000172) test_entry_id: .: (0.000238) test_keggclass: .: (0.000164) test_name: .: (0.000118) test_new: .: (0.000128) test_orthologs: .: (0.000188) test_orthologs_as_array: .: (0.000222) test_orthologs_as_hash: .: (0.000184) test_orthologs_as_strings: .: (0.000149) test_pathways: .: (0.000269) test_pathways_as_hash: .: (0.000119) test_pathways_as_strings: .: (0.000111) test_reactions: .: (0.000177) test_reactions_as_hash: .: (0.000189) test_reactions_as_strings: .: (0.000164) Bio::TestKeggOrthology: test_dblinks: .: (0.000465) test_dblinks_as_hash: .: (0.000507) test_dblinks_as_strings: .: (0.000345) test_definition: .: (0.000329) test_entry_id: .: (0.000304) test_genes_as_hash: .: (0.009530) test_genes_as_strings: .: (0.002953) test_keggclass: .: (0.000459) test_keggclasses: .: (0.000606) test_modules: .: (0.000364) test_modules_as_hash: .: (0.000276) test_modules_as_strings: .: (0.000278) test_name: .: (0.000291) test_names: .: (0.000273) test_pathways_as_strings: .: (0.000271) test_pathways_in_keggclass: .: (0.000348) test_references: .: (0.000525) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000319) test_compounds_as_strings: .: (0.000134) test_dblinks_as_hash: .: (0.000126) test_dblinks_as_strings: .: (0.000170) test_description: .: (0.000147) test_diseases_as_hash: .: (0.000120) test_diseases_as_strings: .: (0.000115) test_entry_id: .: (0.000129) test_enzymes_as_strings: .: (0.000271) test_genes_as_hash: .: (0.000126) test_genes_as_strings: .: (0.000111) test_keggclass: .: (0.000134) test_ko_pathway: .: (0.000134) test_modules_as_hash: .: (0.000178) test_modules_as_strings: .: (0.000136) test_name: .: (0.000134) test_organism: .: (0.000130) test_orthologs_as_hash: .: (0.000300) test_orthologs_as_strings: .: (0.000166) test_pathways_as_hash: .: (0.000141) test_pathways_as_strings: .: (0.000119) test_reactions_as_hash: .: (0.000114) test_reactions_as_strings: .: (0.000111) test_references: .: (0.000115) test_rel_pathways_as_hash: .: (0.000154) test_rel_pathways_as_strings: .: (0.000130) Bio::TestKeggReaction: test_definition: .: (0.000328) test_entry_id: .: (0.000221) test_enzymes: .: (0.000158) test_equation: .: (0.000148) test_name: .: (0.000150) test_orthologs_as_hash: .: (0.000183) test_orthologs_as_strings: .: (0.000156) test_pathways_as_hash: .: (0.000153) test_pathways_as_strings: .: (0.000125) test_rpairs_as_hash: .: (0.000319) test_rpairs_as_strings: .: (0.000137) test_rpairs_as_tokens: .: (0.000189) Bio::TestLasergene: test_methods: .: (0.004442) Bio::TestLocations: test_complement: .: (0.000264) test_hat: .: (0.000097) test_normal: .: (0.000256) test_replace_single_base: .: (0.000082) test_should_not_modify_argument: .: (0.000066) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002197) test_locations_to_s: .: (0.001094) Bio::TestMEDLINE: test_authors: .: (0.000552) test_authors_with_last_name_all_caps: .: (0.000080) test_authors_with_suffix: .: (0.000065) Bio::TestMEDLINE_20146148: test_ab: .: (0.000633) test_ad: .: (0.000246) test_au: .: (0.000227) test_authors: .: (0.000238) test_doi: .: (0.000485) test_dp: .: (0.000300) test_ip: .: (0.000233) test_mh: .: (0.000228) test_pages: .: (0.000220) test_pg: .: (0.000683) test_pii: .: (0.000276) test_pmid: .: (0.000253) test_pt: .: (0.000258) test_reference: .: (0.000740) test_self_new: .: (0.000291) test_so: .: (0.000269) test_ta: .: (0.000378) test_ti: .: (0.002927) test_ui: .: (0.000443) test_vi: .: (0.000267) test_year: .: (0.000283) Bio::TestMapSimple: test_attributes: .: (0.000271) Bio::TestMapping: test_add_mapping_as_map: .: (0.000620) test_add_mapping_as_marker: .: (0.000127) test_contains_marker?: .: (0.000091) test_mapped_to?: .: (0.000070) test_mapping_location_comparison: .: (0.000226) test_mappings_as_map_each: .: (0.000085) test_mappings_as_marker_each: .: (0.000121) test_mappings_on: .: (0.000113) test_multiple_mappings_between_same_marker_and_map: .: (0.000449) test_positions_on: .: (0.000142) test_raise_error_kind_of: .: (0.000289) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000312) test_check_options_with_invalid_opts: .: (0.000125) test_check_options_with_valid_opts: .: (0.000107) test_command_to_be_run: .: (0.000115) test_config_defaults: .: (0.000081) test_minimal_config: .: (0.000088) test_more_config: .: (0.000083) test_run: .: (0.000240) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000381) test_report_has_motifs: .: (0.000182) Bio::TestModel: test_addChain: .: (0.000155) test_comp: .: (0.000083) test_each: .: (0.000075) test_each_chain: .: (0.000059) test_inspect: .: (0.000061) test_rehash: .: (0.000049) test_square_brace: .: (0.000055) test_to_s: .: (0.000255) Bio::TestModelFinder: test_find_model: .: (0.000170) Bio::TestMotif: test_creation_and_attributes: .: (0.000164) test_length: .: (0.000051) Bio::TestMyGraph: test_cliquishness: .: (0.000361) Bio::TestNA: test_accessor: .: (0.000131) test_na: .: (0.000055) test_name: .: (0.000047) test_names: .: (0.000044) test_to_re: .: (0.000300) test_weight: .: (0.000059) test_weight_rna: .: (0.000047) Bio::TestNAConstants: test_NAMES: .: (0.000118) test_NAMES_1_to_name: .: (0.000044) test_WEIGHT: .: (0.000051) Bio::TestNATranslate: test_translate: .: (0.000292) test_translate_1: .: (0.000098) test_translate_2: .: (0.000055) test_translate_3: .: (0.000053) test_translate_4: .: (0.000102) test_translate_5: .: (0.000063) test_translate_6: .: (0.000337) Bio::TestNCBIDB: test_fetch: .: (0.000182) test_p_entry2hash: .: (0.000041) test_p_subtag2array: .: (0.000036) test_p_toptag2array: .: (0.000035) Bio::TestNewick: test_reparse: .: (0.000858) test_reparse_before_lazy_parsing: .: (0.000524) test_string_tree: .: (0.000647) Bio::TestNewick2: test_string_tree: .: (0.000511) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000165) test_parse_newick_leaf: .: (0.000143) test_parse_newick_tokenize: .: (0.000502) Bio::TestNexus: test_nexus: .: (0.007692) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000252) test_uncapitalized_letter_Q32725_9POAL: .: (0.000096) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000171) test_load_parameters: .: (0.000084) test_parameters: .: (0.000320) test_set_default_parameters: .: (0.000095) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000520) test_expected_parameters_set_in_control_file: .: (0.000401) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000186) test_new_with_parameters: .: (0.000117) test_new_with_two_argument: .: (0.000088) test_new_without_argument: .: (0.000068) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.001110) test_rates_hundred_and_fiftieth_position: .: (0.001019) test_rates_last_position: .: (0.000993) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.005621) test_tree: .: (0.005315) test_tree_length: .: (0.005706) test_tree_log_likelihood: .: (0.005357) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000412) test_parameters_should_be_loaded_from_control: .: (0.000216) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001155) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000290) test_dN_dS: .: (0.000131) test_kappa: .: (0.000120) test_lnL: .: (0.000119) test_m3_classes: .: (0.000199) test_m3_lnL: .: (0.000116) test_m3_to_s: .: (0.000112) test_m3_tree: .: (0.000411) test_omega: .: (0.000119) test_to_s: .: (0.000121) test_tree: .: (0.000359) test_tree_length: .: (0.000130) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000593) test_p: .: (0.000270) test_position: .: (0.000262) test_probability: .: (0.000411) test_w: .: (0.000259) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000438) test_graph_omega: .: (0.000613) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000247) test_footer: .: (0.000118) test_header: .: (0.000115) test_initialize: .: (0.000126) test_models: .: (0.000121) test_nb_sites: .: (0.000673) test_num_codons: .: (0.000156) test_num_sequences: .: (0.000162) test_significant: .: (0.000139) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000266) test_nb_sites: .: (0.000203) test_significant: .: (0.000137) test_sites: .: (0.001010) Bio::TestPDB: test_accession: .: (0.001267) test_addModel: .: (0.000620) test_authors: .: (0.000692) test_bracket: .: (0.005640) test_classification: .: (0.000728) test_dbref: .: (0.001038) test_definition: .: (0.000606) test_each: .: (0.000613) test_each_model: .: (0.000554) test_entry_id: .: (0.000604) test_helix: .: (0.000983) test_inspect: .: (0.000568) test_jrnl: .: (0.000721) test_keywords: .: (0.000561) test_record: .: (0.000802) test_remark: .: (0.000731) test_seqres: .: (0.001009) test_sheet: .: (0.001032) test_ssbond: .: (0.000646) test_to_s: .: (0.000990) test_turn: .: (0.000548) test_version: .: (0.000517) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000259) test_U12: .: (0.000110) test_U13: .: (0.000071) test_U22: .: (0.000068) test_U23: .: (0.000071) test_U33: .: (0.000067) test_altLoc: .: (0.000070) test_chainID: .: (0.000068) test_charge: .: (0.000071) test_element: .: (0.000066) test_iCode: .: (0.000067) test_name: .: (0.000070) test_resName: .: (0.000120) test_resSeq: .: (0.000091) test_segID: .: (0.000083) test_serial: .: (0.000270) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000212) test_anisou: .: (0.000074) test_chainID: .: (0.000066) test_charge: .: (0.000061) test_comparable: .: (0.000097) test_do_parse: .: (0.000072) test_element: .: (0.000078) test_iCode: .: (0.000058) test_name: .: (0.000054) test_occupancy: .: (0.000109) test_original_data: .: (0.000068) test_record_name: .: (0.000058) test_resName: .: (0.000266) test_resSeq: .: (0.000062) test_residue: .: (0.000048) test_segID: .: (0.000047) test_serial: .: (0.000045) test_sigatm: .: (0.000047) test_tempFactor: .: (0.000100) test_ter: .: (0.000063) test_to_a: .: (0.000062) test_to_s: .: (0.000087) test_x: .: (0.000081) test_xyz: .: (0.000108) test_y: .: (0.000091) test_z: .: (0.000084) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000452) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000170) test_idcode: .: (0.000056) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000177) test_chainID2: .: (0.000072) test_icode1: .: (0.000070) test_icode2: .: (0.000064) test_measure: .: (0.000067) test_modNum: .: (0.000066) test_pep1: .: (0.000065) test_pep2: .: (0.000064) test_seqNum1: .: (0.000066) test_seqNum2: .: (0.000079) test_serNum: .: (0.000243) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000190) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000138) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000150) test_alpha: .: (0.000061) test_b: .: (0.000055) test_beta: .: (0.000056) test_c: .: (0.000056) test_gamma: .: (0.000057) test_sGroup: .: (0.000059) test_z: .: (0.000068) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000410) test_database: .: (0.000107) test_dbAccession: .: (0.000076) test_dbIdCode: .: (0.000075) test_dbseqBegin: .: (0.000095) test_dbseqEnd: .: (0.000099) test_idCode: .: (0.000102) test_idbnsBeg: .: (0.000090) test_insertBegin: .: (0.000093) test_insertEnd: .: (0.000097) test_seqBegin: .: (0.000092) test_seqEnd: .: (0.000102) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000415) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000154) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000145) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000144) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000153) test_depDate: .: (0.000076) test_idCode: .: (0.000080) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000176) test_hetID: .: (0.000091) test_iCode: .: (0.000083) test_numHetAtoms: .: (0.000081) test_seqNum: .: (0.000082) test_text: .: (0.000277) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000190) test_anisou: .: (0.000075) test_chainID: .: (0.000073) test_charge: .: (0.000077) test_comparable: .: (0.000080) test_do_parse: .: (0.000067) test_element: .: (0.000058) test_iCode: .: (0.000051) test_name: .: (0.000063) test_occupancy: .: (0.000123) test_original_data: .: (0.000077) test_record_name: .: (0.000068) test_resName: .: (0.000057) test_resSeq: .: (0.000234) test_residue: .: (0.000055) test_segID: .: (0.000061) test_serial: .: (0.000064) test_sigatm: .: (0.000059) test_tempFactor: .: (0.000110) test_ter: .: (0.000071) test_to_a: .: (0.000069) test_to_s: .: (0.000095) test_x: .: (0.000101) test_xyz: .: (0.000101) test_y: .: (0.000087) test_z: .: (0.000081) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000411) test_ChainH: .: (0.000107) test_ICode1: .: (0.000095) test_altLoc1: .: (0.000092) test_altLoc2: .: (0.000087) test_altLocH: .: (0.000122) test_chainID2: .: (0.000103) test_iCode2: .: (0.000091) test_iCodeH: .: (0.000099) test_name1: .: (0.000098) test_name2: .: (0.000106) test_nameH: .: (0.000345) test_resName1: .: (0.000119) test_resName2: .: (0.000116) test_resSeq1: .: (0.000119) test_resSeq2: .: (0.000159) test_resSeqH: .: (0.000099) test_sym1: .: (0.000098) test_sym2: .: (0.000101) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000204) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000185) test_altLoc2: .: (0.000313) test_chainID1: .: (0.000101) test_chainID2: .: (0.000086) test_iCode1: .: (0.000094) test_iCode2: .: (0.000094) test_name1: .: (0.000089) test_name2: .: (0.000103) test_resName1: .: (0.000090) test_resName2: .: (0.000081) test_resSeq1: .: (0.000101) test_resSeq2: .: (0.000089) test_sym1: .: (0.000080) test_sym2: .: (0.000071) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000188) test_numCoord: .: (0.000059) test_numHelix: .: (0.000055) test_numHet: .: (0.000056) test_numRemark: .: (0.000055) test_numSeq: .: (0.000054) test_numSheet: .: (0.000054) test_numSite: .: (0.000171) test_numTer: .: (0.000073) test_numTurn: .: (0.000078) test_numXform: .: (0.000072) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000282) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.007132) test_comment: .: (0.000152) test_iCode: .: (0.000091) test_idCode: .: (0.000081) test_resName: .: (0.007725) test_seqNum: .: (0.000107) test_stdRes: .: (0.000084) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.007935) test_Mn2: .: (0.000083) test_Mn3: .: (0.000073) test_Vn: .: (0.006885) test_iGiven: .: (0.000180) test_serial: .: (0.000085) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.004408) test_Mn2: .: (0.000144) test_Mn3: .: (0.000074) test_Vn: .: (0.000067) test_iGiven: .: (0.000200) test_serial: .: (0.000080) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000229) test_Mn2: .: (0.000079) test_Mn3: .: (0.000068) test_Vn: .: (0.000066) test_iGiven: .: (0.000078) test_serial: .: (0.000087) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000209) test_rIdCode: .: (0.000094) test_repDate: .: (0.000080) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000189) test_On2: .: (0.000082) test_On3: .: (0.000092) test_Tn: .: (0.000054) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000178) test_modId: .: (0.000066) test_modNum: .: (0.000063) test_modType: .: (0.000058) test_record: .: (0.000063) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000150) test_text: .: (0.000060) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000152) test_Sn2: .: (0.000054) test_Sn3: .: (0.000053) test_Un: .: (0.000055) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000505) test_Sn2: .: (0.000067) test_Sn3: .: (0.000067) test_Un: .: (0.000063) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000141) test_Sn2: .: (0.000056) test_Sn3: .: (0.000050) test_Un: .: (0.000050) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000177) test_conflict: .: (0.000079) test_database: .: (0.000077) test_dbIdCode: .: (0.000073) test_dbRes: .: (0.000301) test_dbSeq: .: (0.000085) test_iCode: .: (0.000066) test_idCode: .: (0.000063) test_resName: .: (0.000065) test_seqNum: .: (0.000064) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000165) test_numRes: .: (0.000069) test_resName: .: (0.000073) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000181) test_curChainId: .: (0.000097) test_curICode: .: (0.000341) test_curResName: .: (0.000099) test_curResSeq: .: (0.000080) test_endChainID: .: (0.000081) test_endICode: .: (0.000083) test_endResName: .: (0.000084) test_endSeqNum: .: (0.000083) test_initChainID: .: (0.000085) test_initICode: .: (0.000086) test_initResName: .: (0.000085) test_initSeqNum: .: (0.000296) test_numStrands: .: (0.000103) test_prevAtom: .: (0.000086) test_prevChainId: .: (0.000089) test_prevICode: .: (0.000087) test_prevResName: .: (0.000087) test_prevResSeq: .: (0.000087) test_sense: .: (0.000087) test_sheetID: .: (0.000088) test_strand: .: (0.000087) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000489) test_chainID: .: (0.000099) test_charge: .: (0.000074) test_element: .: (0.000069) test_iCode: .: (0.000065) test_name: .: (0.000069) test_resName: .: (0.000069) test_resSeq: .: (0.000068) test_segID: .: (0.000075) test_serial: .: (0.000087) test_sigOcc: .: (0.000075) test_sigTemp: .: (0.000068) test_sigX: .: (0.000070) test_sigY: .: (0.000071) test_sigZ: .: (0.000069) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000224) test_SigmaU12: .: (0.000073) test_SigmaU13: .: (0.000069) test_SigmaU22: .: (0.000068) test_SigmaU23: .: (0.000070) test_SigmaU33: .: (0.000068) test_altLoc: .: (0.000072) test_chainID: .: (0.000068) test_charge: .: (0.000075) test_element: .: (0.000069) test_iCode: .: (0.000069) test_name: .: (0.000065) test_resName: .: (0.000256) test_resSeq: .: (0.000089) test_segID: .: (0.000068) test_serial: .: (0.000077) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000203) test_chainID2: .: (0.000086) test_chainID3: .: (0.000080) test_chainID4: .: (0.000077) test_iCode1: .: (0.000077) test_iCode2: .: (0.000075) test_iCode3: .: (0.000078) test_iCode4: .: (0.000074) test_numRes: .: (0.000076) test_resName1: .: (0.000084) test_resName2: .: (0.000071) test_resName3: .: (0.000077) test_resName4: .: (0.000074) test_seq1: .: (0.000073) test_seq2: .: (0.000073) test_seq3: .: (0.000090) test_seq4: .: (0.000070) test_seqNum: .: (0.000073) test_siteID: .: (0.000073) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000177) test_altLoc2: .: (0.000078) test_atom1: .: (0.000060) test_atom2: .: (0.000059) test_chainID1: .: (0.000059) test_chainID2: .: (0.000058) test_iCode1: .: (0.000059) test_iCode2: .: (0.000061) test_resName1: .: (0.000059) test_resName2: .: (0.000060) test_resSeq1: .: (0.000060) test_resSeq2: .: (0.000058) test_sym1: .: (0.000061) test_sym2: .: (0.000060) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000447) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000156) test_sIdCode: .: (0.000062) test_sprsdeDate: .: (0.000055) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000142) test_iCode: .: (0.000058) test_resName: .: (0.000056) test_resSeq: .: (0.000057) test_serial: .: (0.000053) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000137) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000150) test_t1: .: (0.000063) test_t2: .: (0.000214) test_t3: .: (0.000072) test_text: .: (0.000064) Bio::TestPROSITE: test_ac: .: (0.001196) test_cc: .: (0.001117) test_de: .: (0.000947) test_division: .: (0.001124) test_dr: .: (0.011381) test_dt: .: (0.001428) test_false_neg: .: (0.001226) test_false_pos: .: (0.001289) test_false_positive_sequences: .: (0.001308) test_list_falsenegative: .: (0.014319) test_list_falsepositive: .: (0.012128) test_list_potentialhit: .: (0.012113) test_list_truepositive: .: (0.016210) test_list_unknown: .: (0.013067) test_list_xref: .: (0.011322) test_ma: .: (0.001136) test_max_repeat: .: (0.001109) test_name: .: (0.001001) test_nr: .: (0.001062) test_pa: .: (0.001141) test_pa2re: .: (0.001184) test_partial: .: (0.001143) test_pdb_xref: .: (0.001144) test_pdoc_xref: .: (0.001104) test_positive: .: (0.001137) test_positive_hits: .: (0.001141) test_positive_sequences: .: (0.001105) test_release: .: (0.001125) test_ru: .: (0.001055) test_self_pa2re: .: (0.001099) test_site: .: (0.001072) test_skip_flag: .: (0.001029) test_swissprot_release_number: .: (0.001067) test_swissprot_release_sequences: .: (0.001081) test_taxon_range: .: (0.001080) test_total: .: (0.001074) test_total_hits: .: (0.001074) test_total_sequences: .: (0.001087) test_unknown: .: (0.001049) test_unknown_hits: .: (0.001056) test_unknown_sequences: .: (0.001070) Bio::TestPROSITEConst: test_delimiter: .: (0.000225) test_tagsize: .: (0.000051) Bio::TestPTS1: test_function_set: .: (0.000210) test_function_set_number_1: .: (0.000064) test_function_set_number_2: .: (0.000053) test_function_set_number_3: .: (0.000049) test_function_show: .: (0.000044) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000157) Bio::TestPTS1New: test_fungi: .: (0.000132) test_general: .: (0.000073) test_metazoa: .: (0.000046) Bio::TestQualifier: test_qualifier: .: (0.000141) test_value: .: (0.000044) Bio::TestREBASE: test_methods: .: (0.000658) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000807) test_bit_score: .: (0.000489) test_evalue: .: (0.000485) test_gaps: .: (0.000462) test_hit_from: .: (0.000468) test_hit_to: .: (0.000472) test_hseq: .: (0.000442) test_identity: .: (0.000430) test_midline: .: (0.000452) test_percent_identity: .: (0.000428) test_positive: .: (0.000439) test_qseq: .: (0.000470) test_query_from: .: (0.000428) test_query_to: .: (0.000427) test_score: .: (0.000425) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000517) test_hits_size: .: (0.000916) test_iterations_size: .: (0.000859) test_program: .: (0.000388) test_query_def: .: (0.004185) test_query_len: .: (0.000981) test_version: .: (0.000457) test_version_date: .: (0.000459) test_version_number: .: (0.000879) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000662) test_definition: .: (0.000491) test_evalue: .: (0.000470) test_hsps_size: .: (0.000807) test_identity: .: (0.000622) test_lap_at: .: (0.000581) test_len: .: (0.000472) test_midline: .: (0.000483) test_overlap: .: (0.000686) test_query_end: .: (0.000562) test_query_seq: .: (0.000466) test_query_start: .: (0.000448) test_target_def: .: (0.000851) test_target_end: .: (0.000609) test_target_len: .: (0.000458) test_target_seq: .: (0.000475) test_target_start: .: (0.000879) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000411) test_get_entry: .: (0.000320) test_rewind: .: (0.000106) test_skip_leader: .: (0.000156) Bio::TestReference: test_abstract: .: (0.000184) test_affiliations: .: (0.000069) test_authors: .: (0.000071) test_format_bibitem: .: (0.000120) test_format_bibtex: .: (0.000199) test_format_bibtex_with_arguments: .: (0.000137) test_format_cell: .: (0.000087) test_format_current: .: (0.000078) test_format_endnote: .: (0.000085) test_format_general: .: (0.000081) test_format_genome_biol: .: (0.000080) test_format_genome_res: .: (0.000076) test_format_nar: .: (0.000073) test_format_nature: .: (0.000090) test_format_rd: .: (0.000503) test_format_science: .: (0.000122) test_format_trends: .: (0.000079) test_issue: .: (0.000056) test_journal: .: (0.000053) test_mesh: .: (0.000055) test_pages: .: (0.000055) test_pubmed: .: (0.000060) test_pubmed_url: .: (0.000064) test_url: .: (0.000049) test_volume: .: (0.000061) test_year: .: (0.000057) Bio::TestReference_noURL: test_format_endnote: .: (0.000233) test_url: .: (0.000308) Bio::TestReferences: test_append: .: (0.000231) test_each: .: (0.000086) Bio::TestRelation: test_comparison_operator: .: (0.000184) test_uniq: .: (0.000093) Bio::TestResidue: test_addAtom: .: (0.000280) test_each: .: (0.000149) test_each_atom: .: (0.000438) test_get_residue_id_from_atom: .: (0.000125) test_het_atom: .: (0.000087) test_iCode: .: (0.000089) test_inspect: .: (0.000213) test_resSeq: .: (0.000094) test_sort: .: (0.000122) test_square_bracket: .: (0.000104) test_to_s: .: (0.000483) test_update_resudue_id: .: (0.000107) Bio::TestResidueFinder: test_each_residue: .: (0.000222) test_find_residue: .: (0.000081) test_residues: .: (0.000096) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.073601) test_cut_from_bio_sequence_na: .: (0.027451) test_cut_without_permutations: .: (0.013744) test_view_ranges: .: (0.013850) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000951) test_cuts_after_remove_incomplete_cuts: .: (0.000399) test_strands_for_display: .: (0.001716) test_strands_for_display_current: .: (0.000492) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000462) test_fragments_for_display_1: .: (0.000529) test_fragments_for_display_10: .: (0.002549) test_fragments_for_display_2: .: (0.000623) test_fragments_for_display_3: .: (0.001054) test_fragments_for_display_4: .: (0.000661) test_fragments_for_display_5: .: (0.000636) test_fragments_for_display_6: .: (0.000408) test_fragments_for_display_7: .: (0.000405) test_fragments_for_display_8: .: (0.000386) test_fragments_for_display_9: .: (0.000570) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000323) test_obj_3: .: (0.000157) test_obj_7: .: (0.000128) test_obj_z: .: (0.000127) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000294) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000201) test_bracket_eq: .: (0.000127) test_concat: .: (0.000086) test_delete: .: (0.000079) test_dup: .: (0.000113) test_each: .: (0.000103) test_eqeq: .: (0.000073) test_eqeq_false: .: (0.000061) test_eqeq_other: .: (0.000208) test_eqeq_self: .: (0.000051) test_include?: .: (0.000056) test_internal_data: .: (0.000057) test_internal_data_eq: .: (0.000061) test_length: .: (0.000055) test_ltlt: .: (0.000060) test_ltlt_larger: .: (0.000060) test_ltlt_middle: .: (0.000060) test_plus: .: (0.000079) test_plus_error: .: (0.000115) test_push: .: (0.000073) test_reverse_each: .: (0.000115) test_self_bracket: .: (0.000058) test_self_new: .: (0.000229) test_size: .: (0.000058) test_sort!: .: (0.000048) test_to_a: .: (0.000051) test_uniq!: .: (0.000047) test_unshift: .: (0.000114) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.003301) test_complement: .: (0.002921) test_complement_with_cut_symbols: .: (0.002963) test_cut_locations: .: (0.002731) test_cut_locations_in_enzyme_notation: .: (0.002640) test_primary: .: (0.002661) test_primary_with_cut_symbols: .: (0.002670) test_to_re: .: (0.002587) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000753) test_align_with_cuts: .: (0.000601) test_argument_error: .: (0.000858) test_ds: .: (0.000540) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000339) test_complement: .: (0.000203) test_contents: .: (0.000114) test_primary: .: (0.000107) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000279) test_complement: .: (0.000121) test_contents: .: (0.000104) test_primary: .: (0.000097) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000268) test_contents: .: (0.000088) test_primary: .: (0.000075) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000172) test_complement_to_array_index: .: (0.000154) test_complement_to_array_index_class: .: (0.000122) test_contents: .: (0.000088) test_primary: .: (0.000082) test_primary_to_array_index: .: (0.000121) test_primary_to_array_index_class: .: (0.000113) test_to_array_index: .: (0.000382) test_to_array_index_class: .: (0.000244) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000323) test_rebase: .: (0.000090) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000711) test_creation_with_no_cuts: .: (0.000295) test_cut_locations: .: (0.000272) test_cut_locations_in_enzyme_notation: .: (0.000280) test_orientation: .: (0.000416) test_pattern: .: (0.000285) test_pattern_palindromic?: .: (0.000328) test_stripped: .: (0.000363) test_to_re: .: (0.000211) test_with_cut_symbols: .: (0.000258) test_with_spaces: .: (0.000310) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000674) test_creation_with_no_cuts: .: (0.000299) test_cut_locations: .: (0.000276) test_cut_locations_in_enzyme_notation: .: (0.000393) test_orientation: .: (0.000307) test_pattern: .: (0.000286) test_pattern_palindromic?: .: (0.000420) test_stripped: .: (0.000259) test_to_re: .: (0.000228) test_with_cut_symbols: .: (0.000275) test_with_spaces: .: (0.000410) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000370) test_initialize_with_pattern: .: (0.000217) test_max: .: (0.000099) test_min: .: (0.000082) test_to_array_index: .: (0.000091) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000195) test_bracket_eq: .: (0.000110) test_concat: .: (0.000062) test_delete: .: (0.000052) test_dup: .: (0.000113) test_each: .: (0.000103) test_eqeq: .: (0.000064) test_eqeq_false: .: (0.000052) test_eqeq_other: .: (0.000049) test_eqeq_self: .: (0.000044) test_include?: .: (0.000050) test_internal_data_hash: .: (0.000050) test_internal_data_hash_eq: .: (0.000061) test_length: .: (0.000045) test_ltlt: .: (0.000127) test_ltlt_noeffect: .: (0.000054) test_plus: .: (0.000053) test_plus_error: .: (0.000097) test_private_push_element: .: (0.000055) test_private_push_element_intermediate: .: (0.000056) test_private_push_element_last: .: (0.000052) test_private_push_element_noeffect: .: (0.000047) test_private_sorted_keys: .: (0.000045) test_private_unshift_element: .: (0.000049) test_private_unshift_element_first: .: (0.000055) test_private_unshift_element_intermediate: .: (0.000052) test_private_unshift_element_noeffect: .: (0.000049) test_push: .: (0.000055) test_reverse_each: .: (0.000085) test_self_bracket: .: (0.000048) test_self_new: .: (0.000064) test_size: .: (0.000043) test_sort!: .: (0.000042) test_to_a: .: (0.000044) test_uniq!: .: (0.000042) test_unshift: .: (0.000070) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000187) test_left_padding: .: (0.000077) test_right_padding: .: (0.000065) test_strip_padding: .: (0.000080) Bio::TestSOFT: test_dataset: .: (0.008758) test_series: .: (0.005234) Bio::TestSOSUIReport: test_entry_id: .: (0.000434) test_prediction: .: (0.000115) test_tmh: .: (0.000096) test_tmhs: .: (0.000120) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000160) test_rs: .: (0.000059) Bio::TestSOSUITMH: test_grade: .: (0.000173) test_range: .: (0.000095) test_sequence: .: (0.000086) Bio::TestSampleGraph: test_bellman_ford: .: (0.000495) test_bfs_shortest_path: .: (0.000122) test_breadth_first_search: .: (0.000133) test_depth_first_search: .: (0.000205) test_dijkstra: .: (0.000160) test_dump_list: .: (0.000160) test_dump_matrix: .: (0.000457) test_extract_subgraph_by_label: .: (0.000145) test_extract_subgraph_by_list: .: (0.000128) test_extract_subgraph_retains_disconnected_nodes: .: (0.000092) test_small_world_aka_node_degree_histogram: .: (0.000096) test_to_matrix: .: (0.000249) test_to_matrix_fixed_index: .: (0.000166) test_undirected_cliquishness: .: (0.000245) Bio::TestScf_version_2: test_complement: .: (0.007538) test_seq: .: (0.006849) test_to_biosequence: .: (0.006850) Bio::TestScf_version_3: test_complement: .: (0.021315) test_seq: .: (0.020469) test_to_biosequence: .: (0.020658) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000220) test_AA_new_sequence_all_legal_symbols: .: (0.000072) test_AA_new_sequence_removes_whitespace: .: (0.000060) test_AA_new_sequence_upcases_symbols: .: (0.000050) test_DNA_new_blank_sequence: .: (0.000048) test_DNA_new_sequence_downcases_symbols: .: (0.000050) test_DNA_new_sequence_removes_whitespace: .: (0.000047) test_NA_randomize_with_counts: .: (0.000637) test_NA_randomize_with_counts_and_block: .: (0.000726) test_RNA_new_sequence: .: (0.000065) test_ambiguous_dna_sequence_complement: .: (0.000068) test_ambiguous_rna_sequence_complement: .: (0.000062) test_amino_acid_codes: .: (0.000100) test_amino_acid_molecular_weight: .: (0.000171) test_amino_acid_names: .: (0.000097) test_amino_acid_randomize_can_be_chained: .: (0.000815) test_amino_acid_randomize_has_same_composition: .: (0.000518) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000470) test_dna_composition: .: (0.000100) test_dna_gc_percent: .: (0.000107) test_dna_molecular_weight: .: (0.000174) test_dna_pikachu: .: (0.000078) test_dna_sequence_complement: .: (0.000075) test_dna_sequence_translate: .: (0.000336) test_dna_to_re: .: (0.000128) test_element_reference_operator_with_one_argument: .: (0.000059) test_element_reference_operator_with_two_arguments: .: (0.000055) test_invalid_nucleic_acid_illegal_bases: .: (0.000087) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000204) test_nucleic_acid_names: .: (0.000071) test_randomize_dna_can_be_chained: .: (0.000208) test_randomize_dna_retains_composition: .: (0.000149) test_randomize_dna_with_block: .: (0.000174) test_rna_composition: .: (0.000189) test_rna_gc_percent: .: (0.000073) test_rna_molecular_weight: .: (0.000117) test_rna_pikachu: .: (0.000053) test_rna_sequence_complement: .: (0.000052) test_rna_sequence_translate: .: (0.000254) test_rna_to_re: .: (0.000119) test_total: .: (0.000073) test_two_consecutive_dna_randomizations_not_equal: .: (0.000150) test_valid_dna_sequence_illegal_bases: .: (0.000061) Bio::TestSequenceAA: test_codes: .: (0.000342) test_molecular_weight: .: (0.000134) test_names: .: (0.000071) test_to_re: .: (0.000097) test_to_s: .: (0.000043) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000185) Bio::TestSequenceAANew: test_new: .: (0.000103) test_new_n: .: (0.000050) test_new_r: .: (0.000041) test_new_t: .: (0.000042) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000148) test_concat: .: (0.000165) test_push: .: (0.000045) test_seq: .: (0.000041) test_splicing: .: (0.000128) test_sum: .: (0.000044) test_to_s: .: (0.000040) test_to_str: .: (0.000043) test_total: .: (0.000052) test_window_search: .: (0.000142) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000120) test_normalize_A: .: (0.000050) test_normalize_a: .: (0.000045) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000731) test_randomize_with_block: .: (0.002418) test_randomize_with_hash: .: (0.000797) test_randomize_with_hash_block: .: (0.007274) 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' =============================================================================== : (0.000828) 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' =============================================================================== : (0.000798) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000252) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000076) test_subseq_returns_subsequence: .: (0.000065) test_to_s_returns_self_as_string: .: (0.000070) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000156) test_window_search_with_width_3_step_two_with_residual: .: (0.000257) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000163) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000107) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000183) test_na_self_randomize: .: (0.000109) Bio::TestSequenceDBLink: test_database: .: (0.000120) test_id: .: (0.000048) test_secondary_ids: .: (0.000049) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000381) test_parse_uniprot_DR_line: .: (0.000097) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000683) test_output_width_35: .: (0.000452) test_output_width_nil: .: (0.000290) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000379) test_output_after_adding_sequence: .: (0.000468) test_output_after_truncating_sequence: .: (0.000194) test_output_from_error_probabilities: .: (0.002259) test_output_width45: .: (0.000190) test_output_with_converting_score_phred2solexa: .: (0.000448) test_output_with_converting_score_solexa2phred: .: (0.000364) test_output_with_default_score: .: (0.000180) Bio::TestSequenceMasker: test_mask: .: (0.000229) test_mask_with_enumerator: .: (0.000118) test_mask_with_enumerator_empty_mask_char: .: (0.000111) test_mask_with_enumerator_excess: .: (0.000351) test_mask_with_enumerator_longer_mask_char: .: (0.000106) test_mask_with_enumerator_shorter: .: (0.000143) test_mask_with_error_probability: .: (0.000100) test_mask_with_quality_score: .: (0.000089) Bio::TestSequenceNA: test_at_content: .: (0.000463) test_at_skew: .: (0.000163) test_codon_usage: .: (0.000089) test_complement: .: (0.000064) test_dna: .: (0.000058) test_dna!: .: (0.000068) test_forward_complement: .: (0.000082) test_gc_content: .: (0.000174) test_gc_percent: .: (0.000236) test_gc_skew: .: (0.000229) test_iliegal_bases: .: (0.000067) test_molecular_weight: .: (0.000093) test_names: .: (0.000109) test_reverse_complement: .: (0.000088) test_rna: .: (0.000053) test_rna!: .: (0.000052) test_splicing: .: (0.000098) test_to_re: .: (0.000103) test_to_s: .: (0.000044) Bio::TestSequenceNACommon: test_composition: .: (0.000335) test_concat: .: (0.000052) test_push: .: (0.000044) test_seq: .: (0.000042) test_splicing: .: (0.000100) test_sum: .: (0.000059) test_to_s: .: (0.000049) test_to_str: .: (0.000056) test_total: .: (0.000069) test_window_search: .: (0.000172) Bio::TestSequenceNANew: test_new: .: (0.000142) test_new_n: .: (0.000052) test_new_r: .: (0.000163) test_new_t: .: (0.000042) Bio::TestSequenceNATranslation: test_translate: .: (0.000303) test_translate_0: .: (0.000474) test_translate_1: .: (0.000141) test_translate_2: .: (0.000121) test_translate_3: .: (0.000119) test_translate_4: .: (0.000134) test_translate_5: .: (0.000307) test_translate_6: .: (0.000124) test_translate_7: .: (0.000278) test_translate_given_codon_table: .: (0.032382) test_translate_n1: .: (0.000730) test_translate_n2: .: (0.000339) test_translate_n3: .: (0.000347) test_translate_unknown_o: .: (0.000213) test_translate_unknown_x: .: (0.000180) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000198) test_convert_scores_from_phred_to_solexa: .: (0.000498) test_convert_scores_from_solexa_to_phred: .: (0.000129) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000164) test_convert_scores_from_phred: .: (0.000057) test_convert_scores_from_phred_to_solexa: .: (0.000262) test_convert_scores_from_solexa: .: (0.000111) test_convert_scores_from_solexa_to_phred: .: (0.000102) test_convert_scores_to_phred: .: (0.000048) test_convert_scores_to_solexa: .: (0.000273) test_p2q: .: (0.000304) test_phred_p2q: .: (0.000104) test_phred_q2p: .: (0.003059) test_q2p: .: (0.003246) test_quality_score_type: .: (0.000088) test_self_convert_scores_to_solexa: .: (0.000282) test_self_p2q: .: (0.000108) test_self_q2p: .: (0.002818) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000454) test_convert_scores_from_phred: .: (0.000277) test_convert_scores_from_phred_to_solexa: .: (0.000238) test_convert_scores_from_solexa: .: (0.000055) test_convert_scores_from_solexa_to_phred: .: (0.000108) test_convert_scores_to_phred: .: (0.000111) test_convert_scores_to_solexa: .: (0.000072) test_p2q: .: (0.000155) test_q2p: .: (0.002931) test_quality_score_type: .: (0.000095) test_self_convert_scores_to_phred: .: (0.000150) test_self_p2q: .: (0.000138) test_self_q2p: .: (0.039749) test_solexa_p2q: .: (0.005396) test_solexa_q2p: .: (0.019086) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000248) test_center: .: (0.000076) test_chomp: .: (0.000096) test_chop: .: (0.000088) test_delete: .: (0.000060) test_delete_prefix: .: (0.000064) test_delete_suffix: .: (0.000150) test_downcase: .: (0.000293) test_each_char: .: (0.000131) test_each_char_enum: .: (0.000119) test_each_grapheme_cluster: .: (0.000484) test_each_grapheme_cluster_enum: .: (0.000118) test_each_line: .: (0.000110) test_each_line_enum: .: (0.000101) test_gsub: .: (0.000086) test_gsub_with_block: .: (0.000428) test_ljust: .: (0.000078) test_lstrip: .: (0.000065) test_multiply: .: (0.000054) test_next: .: (0.000055) test_reverse: .: (0.000067) test_rjust: .: (0.000066) test_rstrip: .: (0.000090) test_slice: .: (0.000104) test_slice2: .: (0.000071) test_split: .: (0.000088) test_squeeze: .: (0.000074) test_strip: .: (0.000063) test_sub: .: (0.000085) test_sub_with_block: .: (0.000389) test_succ: .: (0.000073) test_swapcase: .: (0.000067) test_tr: .: (0.000069) test_tr_s: .: (0.000080) test_upcase: .: (0.000061) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000223) test_partition_nomatch: .: (0.000091) test_partition_sep_TSeq: .: (0.000087) test_partition_sep_regexp: .: (0.000099) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000319) test_rpartition_nomatch: .: (0.000090) test_rpartition_sep_TSeq: .: (0.000081) test_rpartition_sep_regexp: .: (0.000089) Bio::TestShRNA: test_blocK_it: .: (0.016802) test_blocK_it_: .: (0.016163) test_blocK_it_BLOCK_IT: .: (0.018602) test_blocK_it_BLOCK_iT: .: (0.015722) test_blocK_it_piGene: .: (0.015246) test_bottom_strand: .: (0.016812) test_bottom_strand_class: .: (0.015580) test_bottom_strand_nil: .: (0.016055) test_design: .: (0.015730) test_design_BLOCK_IT: .: (0.016626) test_report: .: (0.016633) test_report_before_design: .: (0.015641) test_top_strand: .: (0.015318) test_top_strand_class: .: (0.016473) test_top_strand_nil: .: (0.015236) Bio::TestShRNANew: test_new: .: (0.000376) Bio::TestSiRNA: test_antisense_size: .: (0.000149) test_design: .: (0.016091) test_design_reynolds: .: (0.019480) test_design_uitei: .: (0.015340) test_max_gc_percent: .: (0.000108) test_min_gc_percent: .: (0.000065) test_reynolds: .: (0.020469) test_reynolds?: .: (0.000136) test_uitei: .: (0.015337) test_uitei?: .: (0.000125) Bio::TestSiRNANew: test_new: .: (0.000517) Bio::TestSiRNAPair: test_antisense: .: (0.016596) test_gc_percent: .: (0.015579) test_report: .: (0.015270) test_rule: .: (0.016604) test_sense: .: (0.015087) test_start: .: (0.015047) test_stop: .: (0.016446) test_target: .: (0.015122) Bio::TestSiRNAPairNew: test_new: .: (0.000395) Bio::TestSim4Report: test_all_hits: .: (0.000576) test_each: .: (0.000192) test_each_hit: .: (0.000151) test_hits: .: (0.000152) test_num_hits: .: (0.000133) test_query_def: .: (0.000145) test_query_id: .: (0.000127) test_query_len: .: (0.000148) test_seq1: .: (0.000175) Bio::TestSim4Report2: test_all_hits: .: (0.000290) test_each: .: (0.000225) test_each_hit: .: (0.000135) test_hits: .: (0.000144) test_num_hits: .: (0.000131) test_query_def: .: (0.000131) test_query_id: .: (0.000113) test_query_len: .: (0.000108) test_seq1: .: (0.000168) Bio::TestSim4Report4: test_all_hits: .: (0.000294) test_each: .: (0.000160) test_each_hit: .: (0.000265) test_hits: .: (0.000176) test_num_hits: .: (0.000107) test_query_def: .: (0.000141) test_query_id: .: (0.000138) test_query_len: .: (0.000118) test_seq1: .: (0.000166) Bio::TestSim4ReportHit: test_align: .: (0.000327) test_complement?: .: (0.000127) test_definition: .: (0.000225) test_each: .: (0.000279) test_exons: .: (0.000225) test_hit_id: .: (0.000112) test_hsps: .: (0.000195) test_introns: .: (0.000211) test_len: .: (0.000111) test_query_def: .: (0.000102) test_query_id: .: (0.000092) test_query_len: .: (0.000169) test_segmentpairs: .: (0.000219) test_seq1: .: (0.000142) test_seq2: .: (0.000128) test_target_def: .: (0.000097) test_target_id: .: (0.000110) test_target_len: .: (0.000117) Bio::TestSim4ReportHit2: test_align: .: (0.000305) test_complement?: .: (0.000111) test_definition: .: (0.000233) test_each: .: (0.000264) test_exons: .: (0.000217) test_hit_id: .: (0.000107) test_hsps: .: (0.000173) test_introns: .: (0.000166) test_len: .: (0.000094) test_query_def: .: (0.000095) test_query_id: .: (0.000091) test_query_len: .: (0.000262) test_segmentpairs: .: (0.000289) test_seq1: .: (0.000159) test_seq2: .: (0.000129) test_target_def: .: (0.000102) test_target_id: .: (0.000089) test_target_len: .: (0.000094) Bio::TestSim4ReportHit4: test_align: .: (0.000400) test_complement?: .: (0.000161) test_definition: .: (0.000266) test_each: .: (0.000333) test_exons: .: (0.000308) test_hit_id: .: (0.000141) test_hsps: .: (0.000256) test_introns: .: (0.000383) test_len: .: (0.000172) test_query_def: .: (0.000130) test_query_id: .: (0.000107) test_query_len: .: (0.000107) test_segmentpairs: .: (0.000258) test_seq1: .: (0.000146) test_seq2: .: (0.000252) test_target_def: .: (0.000149) test_target_id: .: (0.000099) test_target_len: .: (0.000114) Bio::TestSim4ReportSegment: test_from: .: (0.000170) test_self_new: .: (0.000069) test_seq: .: (0.000045) test_to: .: (0.000040) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000281) test_direction: .: (0.000174) test_hit_from: .: (0.000279) test_hit_to: .: (0.000197) test_hseq: .: (0.000154) test_midline: .: (0.000151) test_percent_identity: .: (0.000148) test_qseq: .: (0.000149) test_query_from: .: (0.000152) test_query_to: .: (0.000279) test_seq1: .: (0.000244) test_seq2: .: (0.000175) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000278) test_direction: .: (0.000161) test_hit_from: .: (0.000183) test_hit_to: .: (0.000175) test_hseq: .: (0.000302) test_midline: .: (0.000215) test_percent_identity: .: (0.000149) test_qseq: .: (0.000143) test_query_from: .: (0.000144) test_query_to: .: (0.000144) test_seq1: .: (0.000183) test_seq2: .: (0.002183) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000414) test_direction: .: (0.000288) test_hit_from: .: (0.000263) test_hit_to: .: (0.000484) test_hseq: .: (0.000271) test_midline: .: (0.000215) test_percent_identity: .: (0.000207) test_qseq: .: (0.000233) test_query_from: .: (0.000387) test_query_to: .: (0.000220) test_seq1: .: (0.000246) test_seq2: .: (0.000230) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000484) test_direction: .: (0.000230) test_hit_from: .: (0.000205) test_hit_to: .: (0.000197) test_hseq: .: (0.000195) test_midline: .: (0.000314) test_percent_identity: .: (0.000212) test_qseq: .: (0.000189) test_query_from: .: (0.000189) test_query_to: .: (0.000205) test_seq1: .: (0.000433) test_seq2: .: (0.000238) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000333) test_direction: .: (0.000226) test_hit_from: .: (0.000338) test_hit_to: .: (0.000218) test_hseq: .: (0.000187) test_midline: .: (0.000181) test_percent_identity: .: (0.000388) test_qseq: .: (0.000269) test_query_from: .: (0.000201) test_query_to: .: (0.000188) test_seq1: .: (0.000259) test_seq2: .: (0.000443) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000306) test_direction: .: (0.000167) test_hit_from: .: (0.000151) test_hit_to: .: (0.000192) test_hseq: .: (0.000173) test_midline: .: (0.000354) test_percent_identity: .: (0.000165) test_qseq: .: (0.000154) test_query_from: .: (0.000149) test_query_to: .: (0.000241) test_seq1: .: (0.000196) test_seq2: .: (0.000307) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000303) test_direction: .: (0.000186) test_hit_from: .: (0.000165) test_hit_to: .: (0.000157) test_hseq: .: (0.000150) test_midline: .: (0.000284) test_percent_identity: .: (0.000204) test_qseq: .: (0.000168) test_query_from: .: (0.000161) test_query_to: .: (0.000150) test_seq1: .: (0.000180) test_seq2: .: (0.000173) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000306) test_entry_id: .: (0.000059) test_filename: .: (0.000048) test_len: .: (0.000046) test_self_new: .: (0.000061) test_self_parse: .: (0.000067) Bio::TestTMHMMReport: test_entry_id: .: (0.000321) test_exp_aas_in_tmhs: .: (0.000185) test_exp_first_60aa: .: (0.000363) test_helix: .: (0.000215) test_predicted_tmhs: .: (0.000174) test_query_len: .: (0.000172) test_tmhs: .: (0.000179) test_to_s: .: (0.000428) test_total_prob_of_N_in: .: (0.000199) Bio::TestTMHMMReport_reports: test_reports: .: (0.000178) Bio::TestTMHMMTMH: test_entry_id: .: (0.000268) test_pos: .: (0.000342) test_range: .: (0.000173) test_status: .: (0.000166) test_version: .: (0.000174) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000256) test_cutoff: .: (0.000126) test_entry_id: .: (0.000109) test_length: .: (0.000269) test_loc: .: (0.000110) test_name: .: (0.000105) test_networks: .: (0.000101) test_prediction: .: (0.000121) test_query_len: .: (0.000112) test_query_sequences: .: (0.000110) test_rc: .: (0.000108) test_version: .: (0.000111) Bio::TestTargetPReportConst: test_delimiter: .: (0.000291) test_rs: .: (0.000052) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000137) test_togows_access_wait: .: (2.005387) Bio::TestTogoWSREST: test_debug: .: (0.000901) test_debug_default: .: (0.000314) test_internal_http: .: (0.000319) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000349) test_entry: .: (0.000143) test_entry_database_list: .: (0.000128) test_new: .: (0.000540) test_new_with_uri_object: .: (0.000355) test_new_with_uri_string: .: (0.000321) test_retrieve: .: (0.000168) test_search: .: (0.000133) test_search_database_list: .: (0.000112) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000611) test_prepare_return_value: .: (0.000381) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000674) Bio::TestTree: test_get_edge_distance: .: (0.000686) test_get_edge_distance_string: .: (0.000255) test_get_node_name: .: (0.000181) test_initialize: .: (0.000194) test_options: .: (0.000176) test_root: .: (0.000126) test_root=: .: (0.000141) Bio::TestTree2: test_add_edge: .: (0.000592) test_add_node: .: (0.000382) test_adjacency_matrix: .: (0.000406) test_adjacency_matrix_with_block: .: (0.000376) test_adjacent_nodes: .: (0.000643) test_adjacent_nodes_nonexistent: .: (0.000248) test_ancestors: .: (0.000330) test_children: .: (0.000282) test_clear: .: (0.000301) test_clear_node: .: (0.000358) test_clear_node_nonexistent: .: (0.000400) test_collect_edge!: .: (0.000466) test_collect_node!: .: (0.000456) test_concat: .: (0.000708) test_descendents: .: (0.000351) test_distance_matrix: .: (0.000904) test_each_edge: .: (0.000379) test_each_node: .: (0.000345) test_each_out_edge: .: (0.000303) test_each_out_edge_chimpanzee: .: (0.000290) test_each_out_edge_human: .: (0.000316) test_each_out_edge_mammals: .: (0.000593) test_each_out_edge_nonexistent: .: (0.000276) test_each_out_edge_primates: .: (0.000439) test_each_out_edge_rat: .: (0.000301) test_each_out_edge_rodents: .: (0.000390) test_edges: .: (0.000269) test_get_edge: .: (0.000527) test_get_edge_indirect: .: (0.000604) test_get_edge_merged: .: (0.000309) test_get_edge_nonexistent: .: (0.000258) test_get_node_bootstrap: .: (0.000254) test_get_node_bootstrap_string=: .: (0.000271) test_get_node_by_name: .: (0.000362) test_get_node_by_name_noexistent: .: (0.000234) test_include?: .: (0.000310) test_include_nonexistent: .: (0.000211) test_insert_node: .: (0.000386) test_leaves: .: (0.000342) test_leaves_noargs: .: (0.000537) test_lowest_common_ancestor: .: (0.000310) test_nodes: .: (0.000266) test_number_of_edges: .: (0.000267) test_number_of_nodes: .: (0.000242) test_out_degree: .: (0.000324) test_out_degree_nonexistent: .: (0.000237) test_out_edges: .: (0.000297) test_out_edges_mammals: .: (0.000340) test_out_edges_nonexistent: .: (0.000212) test_out_edges_primates: .: (0.000719) test_out_edges_rodents: .: (0.000387) test_parent: .: (0.000340) test_path: .: (0.000314) test_remove_edge: .: (0.000317) test_remove_edge_if: .: (0.000341) test_remove_edge_if_nothing_removed: .: (0.000342) test_remove_edge_nonexistent: .: (0.000699) test_remove_node: .: (0.000424) test_remove_node_if: .: (0.000534) test_remove_node_if_false: .: (0.000332) test_remove_node_nonexistent: .: (0.000445) test_remove_nonsense_nodes: .: (0.000347) test_subtree: .: (0.000403) test_subtree_with_all_paths: .: (0.000569) test_total_distance: .: (0.000273) Bio::TestTreeEdge: test_distance: .: (0.000362) test_distance=: .: (0.000208) test_distance_string: .: (0.000133) test_distance_string=: .: (0.000423) test_initialize: .: (0.000207) test_inspect: .: (0.000125) test_to_s: .: (0.000115) Bio::TestTreeNode: test_bootstrap: .: (0.000315) test_bootstrap=: .: (0.000177) test_bootstrap_string: .: (0.000107) test_bootstrap_string=: .: (0.000193) test_initialize: .: (0.000147) test_inspect: .: (0.000157) test_name: .: (0.000118) test_to_s: .: (0.000107) Bio::TestUniProt: test_gene_name: .: (0.008053) Bio::TestUniProtKB: test_ac: .: (0.007015) test_accession: .: (0.006465) test_cc: .: (0.008612) test_cc_alternative_products: .: (0.007785) test_cc_database: .: (0.006982) test_cc_mass_spectrometry: .: (0.011302) test_de: .: (0.004331) test_dr: .: (0.005860) test_dr_with_key: .: (0.005789) test_dr_with_key_empty: .: (0.005039) test_dt: .: (0.003348) test_dt_annotation: .: (0.003565) test_dt_created: .: (0.003663) test_dt_sequence: .: (0.003749) test_entry: .: (0.004168) test_ft: .: (0.068300) test_gene_name: .: (0.003386) test_gene_names: .: (0.003077) test_gn: .: (0.003276) test_gn_old_parser: .: (0.003303) test_gn_uniprot_parser: .: (0.003057) test_id_line: .: (0.002820) test_id_line_data_class: .: (0.003266) test_id_line_entry_name: .: (0.003000) test_id_line_molecule_type: .: (0.002958) test_id_line_sequence_length: .: (0.003092) test_kw: .: (0.003201) test_molecule: .: (0.003456) test_oc: .: (0.003252) test_og_1: .: (0.004581) test_og_2: .: (0.003181) test_og_3: .: (0.003340) test_og_4: .: (0.003047) test_og_5: .: (0.003193) test_og_6: .: (0.003047) test_os: .: (0.002964) test_os_access: .: (0.002980) test_os_access2: .: (0.003012) test_ox: .: (0.003038) test_protein_name: .: (0.002947) test_ref: .: (0.007331) test_seq: .: (0.003430) test_sequence_length: .: (0.004298) test_sq: .: (0.003125) test_sq_crc64: .: (0.003263) test_sq_len: .: (0.003182) test_sq_mw: .: (0.002966) test_synonyms: .: (0.002943) Bio::TestUniProtKB_CC: test_allergen: .: (0.000292) test_alternative_products_access_as_hash: .: (0.000160) test_alternative_products_ai: .: (0.000203) test_alternative_products_apu: .: (0.000496) test_alternative_products_as: .: (0.000225) test_alternative_products_rf: .: (0.000063) test_biophysicochemical_properties: .: (0.000289) test_biotechnology: .: (0.000166) test_catalytic_activity: .: (0.000126) test_caution: .: (0.000352) test_cofactor: .: (0.000174) test_developmental_stage: .: (0.000165) test_disease: .: (0.000224) test_domain: .: (0.000244) test_enzyme_regulation: .: (0.000138) test_function: .: (0.000165) test_induction: .: (0.000126) test_interaction: .: (0.000348) test_mass_spectrometry: .: (0.000201) test_miscellaneous: .: (0.000129) test_pathway: .: (0.000159) test_pharmaceutical: .: (0.000205) test_polymorphism: .: (0.000210) test_ptm: .: (0.000116) test_rna_editing: .: (0.000151) test_similarity: .: (0.000098) test_subcellular_location: .: (0.000345) test_subunit: .: (0.000094) test_tissue_specificity: .: (0.000165) test_toxic_dose: .: (0.000102) test_web_resource: .: (0.000173) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000294) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000509) test_protein_name: .: (0.000200) test_synonyms: .: (0.000242) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000163) test_entry: .: (0.000063) test_entry_id: .: (0.000055) test_entry_name: .: (0.000056) test_id_line: .: (0.000057) test_molecule: .: (0.000254) test_sequence_length: .: (0.000055) Bio::TestUniProtKB_P03589: test_ac: .: (0.000471) test_accession: .: (0.000311) test_cc: .: (0.000649) test_cc_alternative_products: .: (0.000469) test_cc_database: .: (0.000454) test_cc_mass_spectrometry: .: (0.000590) test_de: .: (0.000345) test_dr: .: (0.000681) test_dr_with_key: .: (0.000508) test_dr_with_key_empty: .: (0.000631) test_dt: .: (0.000305) test_dt_annotation: .: (0.000292) test_dt_created: .: (0.000480) test_dt_sequence: .: (0.000356) test_entry: .: (0.000326) test_ft: .: (0.000652) test_gene_name: .: (0.000360) test_gene_names: .: (0.000552) test_gn: .: (0.000382) test_gn_old_parser: .: (0.000350) test_gn_uniprot_parser: .: (0.000344) test_id_line: .: (0.000482) test_id_line_data_class: .: (0.000296) test_id_line_entry_name: .: (0.000269) test_id_line_sequence_length: .: (0.000519) test_kw: .: (0.000368) test_oc: .: (0.000359) test_oh: .: (0.000791) test_os: .: (0.000348) test_os_access: .: (0.000336) test_os_access2: .: (0.000538) test_ox: .: (0.000386) test_protein_name: .: (0.000352) test_protein_name_after_calling_de: .: (0.000554) test_ref: .: (0.000375) test_seq: .: (0.000765) test_sequence_length: .: (0.000327) test_sq: .: (0.000319) test_sq_crc64: .: (0.000545) test_sq_len: .: (0.000380) test_sq_mw: .: (0.000307) test_synonyms: .: (0.000648) Bio::TestUniProtKB_P28907: test_ac: .: (0.001378) test_accession: .: (0.001181) test_cc: .: (0.002001) test_cc_alternative_products: .: (0.001869) test_cc_database: .: (0.001616) test_cc_mass_spectrometry: .: (0.003737) test_de: .: (0.001609) test_dr: .: (0.002848) test_dr_with_key: .: (0.002973) test_dr_with_key_empty: .: (0.003150) test_dt: .: (0.001229) test_dt_annotation: .: (0.001133) test_dt_created: .: (0.001361) test_dt_sequence: .: (0.001169) test_entry: .: (0.001133) test_ft: .: (0.002116) test_gene_name: .: (0.001127) test_gene_names: .: (0.001375) test_gn: .: (0.001254) test_gn_old_parser: .: (0.001262) test_gn_uniprot_parser: .: (0.001413) test_id_line: .: (0.001150) test_id_line_data_class: .: (0.001157) test_id_line_entry_name: .: (0.001200) test_id_line_sequence_length: .: (0.001126) test_kw: .: (0.001381) test_oc: .: (0.001171) test_os: .: (0.001095) test_os_access: .: (0.001285) test_os_access2: .: (0.001263) test_ox: .: (0.001190) test_protein_name: .: (0.001196) test_protein_name_after_calling_de: .: (0.001446) test_ref: .: (0.001971) test_seq: .: (0.001308) test_sequence_length: .: (0.001178) test_sq: .: (0.001483) test_sq_crc64: .: (0.001487) test_sq_len: .: (0.003245) test_sq_mw: .: (0.001702) test_synonyms: .: (0.001404) test_synonyms_after_calling_de: .: (0.001342) Bio::TestUniProtKB_P49144: test_ac: .: (0.001053) test_accession: .: (0.000736) test_cc: .: (0.000942) test_cc_alternative_products: .: (0.001174) test_cc_database: .: (0.001057) test_cc_mass_spectrometry: .: (0.000813) test_de: .: (0.000895) test_dr: .: (0.001118) test_dr_with_key: .: (0.001100) test_dr_with_key_empty: .: (0.001050) test_dt: .: (0.000681) test_dt_annotation: .: (0.000509) test_dt_created: .: (0.000618) test_dt_sequence: .: (0.000454) test_entry: .: (0.000687) test_ft: .: (0.001336) test_gene_name: .: (0.000697) test_gene_names: .: (0.000531) test_gn: .: (0.000692) test_gn_old_parser: .: (0.000539) test_gn_uniprot_parser: .: (0.000675) test_id_line: .: (0.000460) test_id_line_data_class: .: (0.000624) test_id_line_entry_name: .: (0.000446) test_id_line_sequence_length: .: (0.000637) test_kw: .: (0.000731) test_oc: .: (0.000575) test_os: .: (0.000744) test_os_access: .: (0.000548) test_os_access2: .: (0.000695) test_ox: .: (0.000533) test_protein_name: .: (0.000777) test_protein_name_after_calling_de: .: (0.000565) test_ref: .: (0.000794) test_seq: .: (0.000807) test_sequence_length: .: (0.000483) test_sq: .: (0.000686) test_sq_crc64: .: (0.000499) test_sq_len: .: (0.000681) test_sq_mw: .: (0.000688) test_synonyms: .: (0.000688) test_synonyms_after_calling_de: .: (0.000773) Bio::TestUniProtKB_Ref: test_RA: .: (0.000333) test_RC: .: (0.000183) test_RG: .: (0.000169) test_RL: .: (0.000177) test_RN: .: (0.000160) test_RP: .: (0.000171) test_RT: .: (0.000178) test_RX: .: (0.000318) test_ref: .: (0.000189) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000241) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000387) test_alternative_products_with_ft: .: (0.000700) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000265) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000223) test_RL_lines: .: (0.000099) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000539) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000185) test_RG_line: .: (0.000108) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000370) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000231) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000366) test_RL_line: .: (0.000117) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000532) test_RP_line: .: (0.000181) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000109) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000199) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000336) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000113) test_CC_interaction_isoform: .: (0.000101) test_CC_interaction_no_gene_name: .: (0.000100) test_CC_interaction_self_association: .: (0.000124) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000187) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000196) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000428) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000215) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000186) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000162) test_DT_line: .: (0.000097) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.003053) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000563) test_CC_web_resource: .: (0.000055) test_FT_VER_SEQ: .: (0.000118) test_OH_line_exception: .: (0.000211) test_OH_lines: .: (0.000432) Bio::TestUtils: test_centreOfGravity: .: (0.000412) test_dihedral_angle: .: (0.000361) test_distance: .: (0.000252) test_geometricCentre: .: (0.000407) test_rad2deg: .: (0.000106) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000247) test_dijkstra_on_weighted_graph: .: (0.000088) Finished in 11.678078404 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 337.47 tests/s, 1849.70 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ └──────────────────────────────────────────────────────────────────────────────┘ for FILE in `ls debian/ruby-bio/usr/bin/*rb`; do \ BINNAME=$(echo $FILE | sed 's/\.rb$//'); \ mv $FILE $BINNAME; \ done ls: cannot access 'debian/ruby-bio/usr/bin/*rb': No such file or directory make[1]: Leaving directory '/build/reproducible-path/ruby-bio-2.0.5' dh_installdocs -O--buildsystem=ruby dh_ruby_fixdocs -O--buildsystem=ruby dh_installchangelogs -O--buildsystem=ruby dh_installexamples -O--buildsystem=ruby dh_installsystemduser -O--buildsystem=ruby dh_perl -O--buildsystem=ruby dh_link -O--buildsystem=ruby dh_strip_nondeterminism -O--buildsystem=ruby dh_compress -X.rb -O--buildsystem=ruby dh_fixperms -O--buildsystem=ruby dh_missing -O--buildsystem=ruby dh_ruby_fixdepends -O--buildsystem=ruby dh_installdeb -O--buildsystem=ruby dh_gencontrol -O--buildsystem=ruby dpkg-gencontrol: warning: Depends field of package ruby-bio: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package ruby-bio: substitution variable ${ruby:Versions} used, but is not defined dh_md5sums -O--buildsystem=ruby dh_builddeb -O--buildsystem=ruby dpkg-deb: building package 'ruby-bio' in '../ruby-bio_2.0.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.5-1_arm64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2994611/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2994611/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/2994611 and its subdirectories I: Current time: Mon May 6 17:59:49 +14 2024 I: pbuilder-time-stamp: 1714967989