I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 22 06:26:48 +14 2024 I: pbuilder-time-stamp: 1711038408 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job 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/48915/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. 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 Mar 21 16:27 /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/48915/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/48915/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]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=d0a4d76a977e48c6985d4d0ec0ba74b3 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=48915 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.hT6CnQeU/pbuilderrc_EpDf --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hT6CnQeU/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 19 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/48915/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: i386 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 ... 19816 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} libelf1{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} libmagic1{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librole-tiny-perl{a} libruby{a} libruby3.1{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 49.4 MB of archives. After unpacking 172 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 openssl i386 3.1.5-1 [1246 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 debhelper all 13.14.1 [890 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libassuan0 i386 2.5.6-1 [51.9 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 gpgconf i386 2.2.40-1.1+b1 [572 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libksba8 i386 1.6.6-1 [138 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libnpth0 i386 1.6-3+b1 [18.1 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 dirmngr i386 2.2.40-1.1+b1 [820 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 gnupg-utils i386 2.2.40-1.1+b1 [973 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 gpg i386 2.2.40-1.1+b1 [991 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 pinentry-curses i386 1.2.1-3 [79.4 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 gpg-agent i386 2.2.40-1.1+b1 [716 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 gpg-wks-client i386 2.2.40-1.1+b1 [551 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 gpg-wks-server i386 2.2.40-1.1+b1 [541 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 gpgsm i386 2.2.40-1.1+b1 [691 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 gnupg all 2.2.40-1.1 [846 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 65 http://deb.debian.org/debian trixie/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libfile-touch-perl all 0.12-2 [8816 B] Get: 68 http://deb.debian.org/debian trixie/main i386 libio-pty-perl i386 1:1.20-1 [35.7 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libipc-run-perl all 20231003.0-1 [102 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libclass-xsaccessor-perl i386 1.19-4+b2 [37.7 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libb-hooks-op-check-perl i386 0.22-2+b2 [10.7 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libdevel-callchecker-perl i386 0.008-2+b1 [15.1 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libparams-classify-perl i386 0.015-2+b2 [23.1 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 liburi-perl all 5.27-1 [98.4 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libhtml-parser-perl i386 3.81-1+b1 [100 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libclone-perl i386 0.46-1+b1 [13.9 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 perl-openssl-defaults i386 7+b1 [7920 B] Get: 96 http://deb.debian.org/debian trixie/main i386 libnet-ssleay-perl i386 1.94-1 [339 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libnet-http-perl all 6.23-1 [23.9 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libwww-perl all 6.77-1 [183 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 patchutils i386 0.4.2-1 [79.6 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 wdiff i386 1.2.2-6 [120 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 devscripts all 2.23.7 [1068 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libosp5 i386 1.5.2-15 [1003 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 opensp i386 1.5.2-15 [455 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 docbook-to-man i386 1:2.0.0-46 [76.9 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian trixie/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libruby i386 1:3.1 [4968 B] Get: 117 http://deb.debian.org/debian trixie/main i386 ruby-sdbm i386 1.0.0-5+b2 [16.7 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20230828-1 [97.5 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240113-1 [111 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libruby3.1 i386 3.1.2-8 [5456 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 ruby3.1 i386 3.1.2-8 [663 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 ruby-rubygems all 3.4.20-1 [309 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 ruby i386 1:3.1 [5872 B] Get: 126 http://deb.debian.org/debian trixie/main i386 rake all 13.0.6-3 [83.9 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 gem2deb-test-runner i386 2.2.2 [17.8 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-2+b1 [330 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-2+b1 [659 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 ruby3.1-dev i386 3.1.2-8 [1002 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 ruby-all-dev i386 1:3.1 [5976 B] Get: 132 http://deb.debian.org/debian trixie/main i386 gem2deb i386 2.2.2 [47.8 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 ruby-libxml i386 3.2.4-2 [88.6 kB] Fetched 49.4 MB in 2s (26.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19816 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. 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Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../5-libreadline8_8.2-3+b1_i386.deb ... Unpacking libreadline8:i386 (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... 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 ... 21121 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... 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Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnpth0:i386. Preparing to unpack .../040-libnpth0_1.6-3+b1_i386.deb ... Unpacking libnpth0:i386 (1.6-3+b1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../041-dirmngr_2.2.40-1.1+b1_i386.deb ... Unpacking dirmngr (2.2.40-1.1+b1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../042-gnupg-l10n_2.2.40-1.1_all.deb ... Unpacking gnupg-l10n (2.2.40-1.1) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../043-gnupg-utils_2.2.40-1.1+b1_i386.deb ... Unpacking gnupg-utils (2.2.40-1.1+b1) ... Selecting previously unselected package gpg. Preparing to unpack .../044-gpg_2.2.40-1.1+b1_i386.deb ... Unpacking gpg (2.2.40-1.1+b1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../045-pinentry-curses_1.2.1-3_i386.deb ... Unpacking pinentry-curses (1.2.1-3) ... 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Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../058-libclass-xsaccessor-perl_1.19-4+b2_i386.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:i386. Preparing to unpack .../059-libb-hooks-op-check-perl_0.22-2+b2_i386.deb ... Unpacking libb-hooks-op-check-perl:i386 (0.22-2+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../060-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:i386. Preparing to unpack .../061-libdevel-callchecker-perl_0.008-2+b1_i386.deb ... Unpacking libdevel-callchecker-perl:i386 (0.008-2+b1) ... Selecting previously unselected package libparams-classify-perl:i386. 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Selecting previously unselected package libhtml-parser-perl:i386. Preparing to unpack .../074-libhtml-parser-perl_3.81-1+b1_i386.deb ... Unpacking libhtml-parser-perl:i386 (3.81-1+b1) ... 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:i386. Preparing to unpack .../076-libclone-perl_0.46-1+b1_i386.deb ... Unpacking libclone-perl:i386 (0.46-1+b1) ... 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:i386. Preparing to unpack .../082-perl-openssl-defaults_7+b1_i386.deb ... Unpacking perl-openssl-defaults:i386 (7+b1) ... Selecting previously unselected package libnet-ssleay-perl:i386. Preparing to unpack .../083-libnet-ssleay-perl_1.94-1_i386.deb ... Unpacking libnet-ssleay-perl:i386 (1.94-1) ... 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_i386.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../091-wdiff_1.2.2-6_i386.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_i386.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../097-opensp_1.5.2-15_i386.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_i386.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 libruby:i386. Preparing to unpack .../103-libruby_1%3a3.1_i386.deb ... Unpacking libruby:i386 (1:3.1) ... Selecting previously unselected package ruby-sdbm:i386. Preparing to unpack .../104-ruby-sdbm_1.0.0-5+b2_i386.deb ... Unpacking ruby-sdbm:i386 (1.0.0-5+b2) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../105-libbsd0_0.12.2-1_i386.deb ... Unpacking libbsd0:i386 (0.12.2-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../106-libedit2_3.1-20230828-1_i386.deb ... Unpacking libedit2:i386 (3.1-20230828-1) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../107-libncurses6_6.4+20240113-1_i386.deb ... Unpacking libncurses6:i386 (6.4+20240113-1) ... Selecting previously unselected package libyaml-0-2:i386. Preparing to unpack .../108-libyaml-0-2_0.2.5-1_i386.deb ... Unpacking libyaml-0-2:i386 (0.2.5-1) ... Selecting previously unselected package libruby3.1:i386. Preparing to unpack .../109-libruby3.1_3.1.2-8_i386.deb ... Unpacking libruby3.1:i386 (3.1.2-8) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../110-ruby3.1_3.1.2-8_i386.deb ... Unpacking ruby3.1 (3.1.2-8) ... 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_i386.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package rake. Preparing to unpack .../113-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../114-gem2deb-test-runner_2.2.2_i386.deb ... Unpacking gem2deb-test-runner (2.2.2) ... Selecting previously unselected package libgmpxx4ldbl:i386. Preparing to unpack .../115-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_i386.deb ... Unpacking libgmpxx4ldbl:i386 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:i386. Preparing to unpack .../116-libgmp-dev_2%3a6.3.0+dfsg-2+b1_i386.deb ... Unpacking libgmp-dev:i386 (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package ruby3.1-dev:i386. Preparing to unpack .../117-ruby3.1-dev_3.1.2-8_i386.deb ... Unpacking ruby3.1-dev:i386 (3.1.2-8) ... Selecting previously unselected package ruby-all-dev:i386. Preparing to unpack .../118-ruby-all-dev_1%3a3.1_i386.deb ... Unpacking ruby-all-dev:i386 (1:3.1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../119-gem2deb_2.2.2_i386.deb ... Unpacking gem2deb (2.2.2) ... 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:i386. Preparing to unpack .../122-ruby-libxml_3.2.4-2_i386.deb ... Unpacking ruby-libxml:i386 (3.2.4-2) ... Setting up libksba8:i386 (1.6.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... 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) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libclone-perl:i386 (0.46-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.14.1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up perl-openssl-defaults:i386 (7+b1) ... 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 libnpth0:i386 (1.6-3+b1) ... Setting up file (1:5.45-2+b1) ... Setting up libassuan0:i386 (2.5.6-1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up libosp5 (1.5.2-15) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 21 16:27:26 UTC 2024. Universal Time is now: Thu Mar 21 16:27:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-2+b1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libncurses6:i386 (6.4+20240113-1) ... 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:i386 (0.22-2+b2) ... Setting up libipc-run-perl (20231003.0-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (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+b2) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.1.5-1) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up liburi-perl (5.27-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:i386 (1.94-1) ... 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) ... 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:i386 (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:i386 (3.1-20230828-1) ... Setting up libreadline8:i386 (8.2-3+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:i386 (0.008-2+b1) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... 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 dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:i386 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up gnupg-utils (2.2.40-1.1+b1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-1.1+b1) ... 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:i386 (3.11.8-1) ... Setting up libparams-classify-perl:i386 (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-1.1+b1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.14.1) ... Setting up python3 (3.11.6-1) ... Setting up gnupg (2.2.40-1.1) ... Setting up libruby:i386 (1:3.1) ... Setting up libwww-perl (6.77-1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up devscripts (2.23.7) ... Setting up ruby3.1 (3.1.2-8) ... Setting up ruby-sdbm:i386 (1.0.0-5+b2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up ruby (1:3.1) ... Setting up rake (13.0.6-3) ... Setting up rdtool (0.6.38-4.1) ... Setting up libruby3.1:i386 (3.1.2-8) ... Setting up gem2deb-test-runner (2.2.2) ... Setting up ruby3.1-dev:i386 (3.1.2-8) ... Setting up ruby-libxml:i386 (3.2.4-2) ... Setting up ruby-all-dev:i386 (1:3.1) ... Setting up gem2deb (2.2.2) ... Processing triggers for libc-bin (2.37-15) ... 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/48915/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/48915/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 i386 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/i386-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/i386-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/lib/ruby/gems/3.1.0/gems/rake-13.0.6/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/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.012808) test_dbs: .: (0.000362) test_go_ids: .: (0.000254) test_go_terms: .: (0.000297) test_parser: .: (0.000873) test_set_date: .: (0.000328) test_set_desc: .: (0.000304) test_to_str: .: (0.000349) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.008323) test_mktmpdir_without_block: .: (0.000819) test_remove_entry_secure: .: (0.000500) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.045609) test_call_command_fork: .: (0.000237) test_call_command_open3: .: (0.004145) test_call_command_popen: .: (0.003588) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.004272) test_call_command_fork: .: (0.000274) test_call_command_open3: .: (0.003880) test_call_command_popen: .: (0.004124) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.004301) test_call_command_fork: .: (0.000266) test_call_command_open3: .: (0.005243) test_call_command_popen: .: (0.003661) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.002632) test_call_command_fork_chdir: .: (0.000400) test_call_command_popen_chdir: .: (0.004547) test_query_command_chdir: .: (0.007811) test_query_command_fork_chdir: .: (0.000458) test_query_command_popen_chdir: .: (0.007046) Bio::FuncTestCommandQuery: test_query_command: .: (0.008785) test_query_command_fork: .: (0.002671) test_query_command_open3: .: (0.007988) test_query_command_popen: .: (0.009421) Bio::FuncTestCommandTmpdir: test_close!: .: (0.001538) test_initialize: .: (0.000707) test_path: .: (0.000584) test_path_after_close: .: (0.000752) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.018503) test_output_fasta: .: (0.012767) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000710) test_accession: .: (0.000413) test_accessions: .: (0.000420) test_comment: .: (0.000447) test_common_name: .: (0.000432) test_definition: .: (0.000398) test_features: .: (0.000669) test_gi: .: (0.000369) test_keywords: .: (0.000452) test_locus: .: (0.000323) test_nid: .: (0.000377) test_organism: .: (0.000376) test_origin: .: (0.000372) test_references: .: (0.001026) test_segment: .: (0.000428) test_source: .: (0.000568) test_taxonomy: .: (0.000424) test_version: .: (0.000483) test_versions: .: (0.000434) Bio::TestAA: test_13: .: (0.000478) test_1n: .: (0.000211) test_name2one: .: (0.000343) test_name2three: .: (0.000350) test_one2name: .: (0.000319) test_one2three: .: (0.000265) test_three2name: .: (0.000217) test_three2one: .: (0.000291) test_to_1_1: .: (0.000249) test_to_1_3: .: (0.000321) test_to_1_name: .: (0.000281) test_to_3_1: .: (0.000252) test_to_3_3: .: (0.000223) test_to_3_name: .: (0.000280) test_to_re: .: (0.000310) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000402) Bio::TestAAindex: test_api: .: (0.000364) test_auto_aax1: .: (0.007090) test_auto_aax2: .: (0.018536) Bio::TestAAindex1: test_author: .: (0.000558) test_comment: .: (0.000391) test_correlation_coefficient: .: (0.000664) test_dblinks: .: (0.000413) test_definition: .: (0.000385) test_entry_id: .: (0.000411) test_index: .: (0.000597) test_journal: .: (0.000476) test_title: .: (0.000433) Bio::TestAAindex2: test_access_A_R: .: (0.001158) test_access_R_A: .: (0.000986) test_author: .: (0.000396) test_cols: .: (0.000407) test_comment: .: (0.000440) test_dblinks: .: (0.000392) test_definition: .: (0.000406) test_entry_id: .: (0.000452) test_journal: .: (0.000422) test_matrix: .: (0.001018) test_matrix_1_2: .: (0.001010) test_matrix_2_2: .: (0.001045) test_matrix_A_R: .: (0.000986) test_matrix_R_A: .: (0.001059) test_matrix_determinant: .: (0.005932) test_matrix_rank: .: (0.005462) test_matrix_transpose: .: (0.001476) test_rows: .: (0.000582) test_title: .: (0.013716) Bio::TestAAindexConstant: test_delimiter: .: (0.000468) test_tagsize: .: (0.000301) Bio::TestAbif: test_complement: .: (0.020669) test_seq: .: (0.016331) test_to_biosequence: .: (0.016600) Bio::TestActsLikeMap: test_mixin: .: (0.000830) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000574) Bio::TestActsLikeMarker: test_mixin: .: (0.000436) Bio::TestAlignment: test_add_seq_no_key: .: (0.000533) test_add_seq_using_seq_with_aaseq_method: .: (0.000325) test_add_seq_using_seq_with_definition_method: .: (0.000332) test_add_seq_using_seq_with_entry_id_method: .: (0.000292) test_add_seq_using_seq_with_naseq_method: .: (0.000318) test_add_seq_using_seq_with_seq_method: .: (0.000326) test_consensus_iupac_gap_modes: .: (0.000958) test_consensus_iupac_missing_char: .: (0.000403) test_consensus_iupac_missing_char_option: .: (0.000445) test_consensus_iupac_no_gaps: .: (0.000534) test_consensus_iupac_of_ambiguous_bases: .: (0.000726) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.007415) test_consensus_opt_gap_mode: .: (0.000913) test_consensus_opt_missing_char: .: (0.000476) test_consensus_string_no_gaps: .: (0.000583) test_consensus_threshold_four_sequences: .: (0.001188) test_consensus_threshold_two_sequences: .: (0.000663) test_convert_match: .: (0.000427) test_convert_unmatch: .: (0.000351) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000349) test_convert_unmatch_different_match_char: .: (0.000371) test_convert_unmatch_multiple_sequences: .: (0.000669) test_default_gap_char: .: (0.000298) test_default_gap_regexp_matches_default_gap_char: .: (0.000268) test_default_missing_char: .: (0.000248) test_each_site_equal_length: .: (0.000386) test_each_site_unequal_length: .: (0.000458) test_equals: .: (0.000396) test_match_line_protein: .: (0.000779) test_normalizebang_extends_sequences_with_gaps: .: (0.000423) test_seq_length_is_max_seq_length: .: (0.000327) test_seq_length_when_one_sequence: .: (0.000232) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000244) test_seqclass_when_seqclass_set: .: (0.000277) test_seqclass_when_sequence_used: .: (0.000230) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000268) test_set_and_get_gap_char: .: (0.000255) test_store_cannot_override_key: .: (0.000271) test_store_with_default_keys_and_user_defined_keys: .: (0.000280) test_store_with_nil_key_uses_next_number_for_key: .: (0.000455) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000484) test_alignment_concat: .: (0.000330) test_alignment_length: .: (0.000231) test_alignment_lstrip!: .: (0.000383) test_alignment_lstrip_nil: .: (0.000293) test_alignment_normalize!: .: (0.000254) test_alignment_rstrip!: .: (0.000669) test_alignment_rstrip_nil: .: (0.000318) test_alignment_site: .: (0.000300) test_alignment_slice: .: (0.000299) test_alignment_strip!: .: (0.000456) test_alignment_strip_nil: .: (0.000294) test_alignment_subseq: .: (0.000336) test_alignment_window: .: (0.000306) test_collect_each_site: .: (0.000288) test_consensus_each_site_default: .: (0.000355) test_consensus_each_site_gap_mode_1: .: (0.000363) test_consensus_each_site_gap_mode_minus1: .: (0.000440) test_consensus_iupac: .: (0.000973) test_consensus_string_default: .: (0.000386) test_consensus_string_half: .: (0.000332) test_convert_match: .: (0.000309) test_convert_unmatch: .: (0.000270) test_each_seq: .: (0.000305) test_each_site: .: (0.000416) test_each_site_step: .: (0.000337) test_each_window: .: (0.000366) test_match_line: .: (0.001518) test_match_line_amino: .: (0.002115) test_match_line_nuc: .: (0.000467) test_private_alignment_site: .: (0.000258) test_remove_all_gaps!: .: (0.000285) test_seqclass: .: (0.000248) test_seqclass=: .: (0.000314) test_seqclass_default: .: (0.000252) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.004947) test_determine_seq_method: .: (0.002568) test_entries: .: (0.000572) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000489) test_avoid_same_name_numbering: .: (0.000320) test_clustal_have_same_name_true: .: (0.000281) test_have_same_name_false: .: (0.000277) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000777) test_gap_char_default: .: (0.000246) test_gap_char_never_nil: .: (0.000290) test_gap_regexp: .: (0.000266) test_gap_regexp=: .: (0.000252) test_gap_regexp_never_nil: .: (0.000235) test_get_all_property_default: .: (0.000272) test_get_all_property_nodefault: .: (0.000261) test_is_gap_default_false: .: (0.000261) test_is_gap_default_true: .: (0.000291) test_is_gap_nodefault_false: .: (0.000245) test_is_gap_nodefault_true: .: (0.000292) test_missing_char=: .: (0.000268) test_missing_char_default: .: (0.000251) test_missing_char_never_nil: .: (0.000292) test_seqclass=: .: (0.000557) test_seqclass_default: .: (0.000266) test_seqclass_never_nil: .: (0.000286) test_set_all_property: .: (0.000288) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001138) test_consensus_string_50percent: .: (0.000354) test_consensus_string_50percent_nil: .: (0.000280) test_consensus_string_default: .: (0.000287) test_consensus_string_default_nil: .: (0.000276) test_has_gap_false: .: (0.000287) test_has_gap_true: .: (0.000316) test_match_line_amino_100percent: .: (0.000555) test_match_line_amino_missing: .: (0.000737) test_match_line_amino_strong: .: (0.000317) test_match_line_amino_weak: .: (0.000378) test_match_line_nuc_100percent: .: (0.000276) test_match_line_nuc_missing: .: (0.000260) test_remove_gaps!: .: (0.000261) test_remove_gaps_bang_not_removed: .: (0.000273) Bio::TestAtomFinder: test_atoms: .: (0.027841) test_each_atom: .: (0.000495) test_find_atom: .: (0.000386) Bio::TestBioFastaDefline: test_acc_version: .: (0.000839) test_accession: .: (0.000758) test_accessions: .: (0.000675) test_description: .: (0.000579) test_descriptions: .: (0.000575) test_entry_id: .: (0.000689) test_get: .: (0.000837) test_get_all_by_type: .: (0.000665) test_get_by_type: .: (0.000564) test_gi: .: (0.000602) test_id_strings: .: (0.000938) test_locus: .: (0.000504) test_method_missing: .: (0.000620) test_to_s: .: (0.000622) test_words: .: (0.001106) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.001587) test_goid2term: .: (0.000669) test_parse_goids: .: (0.000623) Bio::TestBioGenBank: test_basecount: .: (0.008858) test_circular: .: (0.000740) test_classification: .: (0.000674) test_date: .: (0.000498) test_date_modified: .: (0.001179) test_division: .: (0.000536) test_each_cds_feature: .: (0.001644) test_each_cds_qualifiers: .: (0.001221) test_each_gene: .: (0.001296) test_entry_id: .: (0.000485) test_length: .: (0.000569) test_locus_circular: .: (0.000573) test_locus_class: .: (0.000581) test_locus_date: .: (0.000555) test_locus_division: .: (0.000501) test_locus_entry_id: .: (0.000507) test_locus_length: .: (0.000523) test_locus_natype: .: (0.000539) test_locus_strand: .: (0.000546) test_natype: .: (0.000448) test_seq: .: (0.000532) test_seq_len: .: (0.000546) test_strand: .: (0.000510) test_strandedness: .: (0.000467) test_to_biosequence: .: (0.003152) Bio::TestBioGenPept: test_circular: .: (0.003445) test_date: .: (0.000382) test_dbsource: .: (0.008143) test_division: .: (0.000488) test_entry_id: .: (0.000525) test_length: .: (0.000458) test_locus: .: (0.000415) test_seq: .: (0.000481) test_seq_len: .: (0.000383) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000933) test_aaseq: .: (0.000699) test_chromosome: .: (0.000406) test_codon_usage: .: (0.000610) test_cu_list: .: (0.000433) test_dblinks_as_hash: .: (0.000491) test_dblinks_as_strings: .: (0.000398) test_definition: .: (0.000472) test_division: .: (0.000479) test_eclinks: .: (0.000646) test_entry: .: (0.000542) test_entry_id: .: (0.000515) test_gbposition: .: (0.000537) test_gene: .: (0.000644) test_genes: .: (0.000459) test_keggclass: .: (0.000500) test_keggclasses: .: (0.000514) test_locations: .: (0.000601) test_motifs_as_hash: .: (0.000478) test_motifs_as_strings: .: (0.000410) test_name: .: (0.000439) test_names_as_array: .: (0.000460) test_new: .: (0.000458) test_ntlen: .: (0.000542) test_ntseq: .: (0.000476) test_organism: .: (0.000363) test_orthologs_as_hash: .: (0.000678) test_orthologs_as_strings: .: (0.000428) test_pathway: .: (0.000427) test_pathway_after_pathways_as_strings: .: (0.001540) test_pathway_before_pathways_as_strings: .: (0.000634) test_pathways_as_hash: .: (0.000569) test_pathways_as_strings: .: (0.000474) test_position: .: (0.000416) test_structure: .: (0.000511) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.002486) test_comment: .: (0.000909) test_data_source: .: (0.000648) test_definition: .: (0.000620) test_disease: .: (0.000593) test_entry_id: .: (0.000737) test_lineage: .: (0.000664) test_nalen: .: (0.000633) test_name: .: (0.000624) test_new: .: (0.000641) test_num_gene: .: (0.000833) test_num_rna: .: (0.000694) test_original_databases: .: (0.000712) test_original_db: .: (0.000763) test_plasmids: .: (0.001019) test_references: .: (0.003890) test_statistics: .: (0.000904) test_taxid: .: (0.000700) test_taxonomy: .: (0.000720) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001598) test_comment: .: (0.000849) test_data_source: .: (0.000531) test_definition: .: (0.000569) test_disease: .: (0.000481) test_entry_id: .: (0.000444) test_lineage: .: (0.000434) test_nalen: .: (0.000407) test_name: .: (0.000494) test_new: .: (0.000510) test_num_gene: .: (0.000803) test_num_rna: .: (0.000594) test_original_databases: .: (0.000449) test_original_db: .: (0.000463) test_plasmids: .: (0.000575) test_references: .: (0.000602) test_statistics: .: (0.000426) test_taxid: .: (0.000634) test_taxonomy: .: (0.000458) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.006505) test_compounds_as_strings: .: (0.000432) test_dblinks_as_hash: .: (0.000353) test_dblinks_as_strings: .: (0.000390) test_description: .: (0.000423) test_diseases_as_hash: .: (0.000346) test_diseases_as_strings: .: (0.000351) test_entry_id: .: (0.000825) test_enzymes_as_strings: .: (0.000540) test_genes_as_hash: .: (0.000397) test_genes_as_strings: .: (0.000395) test_keggclass: .: (0.000491) test_ko_pathway: .: (0.000497) test_modules_as_hash: .: (0.000434) test_modules_as_strings: .: (0.000396) test_name: .: (0.000374) test_new: .: (0.000390) test_organism: .: (0.000401) test_orthologs_as_hash: .: (0.000864) test_orthologs_as_strings: .: (0.000462) test_pathways_as_hash: .: (0.000380) test_pathways_as_strings: .: (0.000378) test_reactions_as_hash: .: (0.000386) test_reactions_as_strings: .: (0.000335) test_references: .: (0.000412) test_rel_pathways_as_hash: .: (0.000376) test_rel_pathways_as_strings: .: (0.000383) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001132) test_compounds_as_strings: .: (0.000664) test_dblinks_as_hash: .: (0.000487) test_dblinks_as_strings: .: (0.000367) test_description: .: (0.000399) test_diseases_as_hash: .: (0.000388) test_diseases_as_strings: .: (0.000692) test_entry_id: .: (0.000429) test_enzymes_as_strings: .: (0.000458) test_genes_as_hash: .: (0.000691) test_genes_as_strings: .: (0.000528) test_keggclass: .: (0.000529) test_ko_pathway: .: (0.000456) test_modules_as_hash: .: (0.000531) test_modules_as_strings: .: (0.000439) test_name: .: (0.000418) test_new: .: (0.000446) test_organism: .: (0.000507) test_orthologs_as_hash: .: (0.000604) test_orthologs_as_strings: .: (0.000419) test_pathways_as_hash: .: (0.000455) test_pathways_as_strings: .: (0.000489) test_reactions_as_hash: .: (0.000392) test_reactions_as_strings: .: (0.000396) test_references: .: (0.000382) test_rel_pathways_as_hash: .: (0.000405) test_rel_pathways_as_strings: .: (0.000430) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.001924) test_compounds_as_strings: .: (0.000532) test_dblinks_as_hash: .: (0.000382) test_dblinks_as_strings: .: (0.000321) test_description: .: (0.000366) test_diseases_as_hash: .: (0.000354) test_diseases_as_strings: .: (0.000401) test_entry_id: .: (0.000424) test_enzymes_as_strings: .: (0.000364) test_genes_as_hash: .: (0.000378) test_genes_as_strings: .: (0.000371) test_keggclass: .: (0.000442) test_ko_pathway: .: (0.000375) test_modules_as_hash: .: (0.000371) test_modules_as_strings: .: (0.000809) test_name: .: (0.000478) test_new: .: (0.000399) test_organism: .: (0.000512) test_orthologs_as_hash: .: (0.000370) test_orthologs_as_strings: .: (0.000325) test_pathways_as_hash: .: (0.000316) test_pathways_as_strings: .: (0.000313) test_reactions_as_hash: .: (0.000327) test_reactions_as_strings: .: (0.000317) test_references: .: (0.000612) test_rel_pathways_as_hash: .: (0.000387) test_rel_pathways_as_strings: .: (0.000343) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000841) test_compounds_as_strings: .: (0.000324) test_dblinks_as_hash: .: (0.000391) test_dblinks_as_strings: .: (0.000377) test_description: .: (0.000669) test_diseases_as_hash: .: (0.000354) test_diseases_as_strings: .: (0.000594) test_entry_id: .: (0.000415) test_enzymes_as_strings: .: (0.000335) test_genes_as_hash: .: (0.000335) test_genes_as_strings: .: (0.000359) test_keggclass: .: (0.000375) test_ko_pathway: .: (0.000380) test_modules_as_hash: .: (0.000505) test_modules_as_strings: .: (0.000564) test_name: .: (0.000418) test_new: .: (0.000382) test_organism: .: (0.000390) test_orthologs_as_hash: .: (0.000344) test_orthologs_as_strings: .: (0.000407) test_pathways_as_hash: .: (0.000347) test_pathways_as_strings: .: (0.000356) test_reactions_as_hash: .: (0.000349) test_reactions_as_strings: .: (0.000462) test_references: .: (0.001081) test_rel_pathways_as_hash: .: (0.000448) test_rel_pathways_as_strings: .: (0.000363) Bio::TestBioKeggDRUG: test_activity: .: (0.002161) test_comment: .: (0.000504) test_dblinks_as_hash: .: (0.000478) test_dblinks_as_strings: .: (0.000393) test_entry_id: .: (0.000374) test_formula: .: (0.000399) test_kcf: .: (0.000371) test_mass: .: (0.000410) test_name: .: (0.000440) test_names: .: (0.000588) test_pathways_as_hash: .: (0.000486) test_pathways_as_strings: .: (0.000371) test_products: .: (0.000421) test_remark: .: (0.000417) Bio::TestBioKeggGLYCAN: test_comment: .: (0.007029) test_composition: .: (0.000421) test_compounds: .: (0.000406) test_dblinks_as_hash: .: (0.000710) test_dblinks_as_strings: .: (0.000390) test_entry_id: .: (0.000428) test_enzymes: .: (0.000410) test_kcf: .: (0.000341) test_keggclass: .: (0.000379) test_mass: .: (0.000395) test_name: .: (0.000373) test_orthologs_as_hash: .: (0.000629) test_orthologs_as_strings: .: (0.000393) test_pathways_as_hash: .: (0.000465) test_pathways_as_strings: .: (0.000376) test_reactions: .: (0.000416) test_references: .: (0.000431) test_remark: .: (0.000360) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.013645) test_composition: .: (0.000417) test_compounds: .: (0.000277) test_dblinks_as_hash: .: (0.000379) test_dblinks_as_strings: .: (0.000326) test_entry_id: .: (0.000317) test_enzymes: .: (0.000265) test_kcf: .: (0.000346) test_keggclass: .: (0.000412) test_mass: .: (0.000356) test_name: .: (0.000293) test_orthologs_as_hash: .: (0.000653) test_orthologs_as_strings: .: (0.000345) test_pathways_as_hash: .: (0.000318) test_pathways_as_strings: .: (0.000316) test_reactions: .: (0.000326) test_references: .: (0.000415) test_remark: .: (0.000365) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.001239) test_compounds_as_strings: .: (0.000543) test_dblinks_as_hash: .: (0.000705) test_dblinks_as_strings: .: (0.000394) test_description: .: (0.000460) test_diseases_as_hash: .: (0.000469) test_diseases_as_strings: .: (0.000474) test_entry_id: .: (0.000436) test_enzymes_as_strings: .: (0.000374) test_genes_as_hash: .: (0.000358) test_genes_as_strings: .: (0.000372) test_keggclass: .: (0.000359) test_ko_pathway: .: (0.000579) test_modules_as_hash: .: (0.000470) test_modules_as_strings: .: (0.000427) test_name: .: (0.000374) test_new: .: (0.000377) test_organism: .: (0.000366) test_orthologs_as_hash: .: (0.000438) test_orthologs_as_strings: .: (0.000431) test_pathways_as_hash: .: (0.000456) test_pathways_as_strings: .: (0.000343) test_reactions_as_hash: .: (0.000686) test_reactions_as_strings: .: (0.000496) test_references: .: (0.004550) test_rel_pathways_as_hash: .: (0.000587) test_rel_pathways_as_strings: .: (0.000520) Bio::TestBioLITDB: test_author: .: (0.000924) test_entry_id: .: (0.000313) test_field: .: (0.000317) test_journal: .: (0.000391) test_keyword: .: (0.000701) test_reference: .: (0.000560) test_title: .: (0.000355) test_volume: .: (0.000315) Bio::TestBioNBRF: test_aalen: .: (0.003313) test_aaseq: .: (0.000274) test_entry: .: (0.000280) test_length: .: (0.000236) test_nalen: .: (0.000335) test_naseq: .: (0.000602) test_seq: .: (0.000312) test_seq_class: .: (0.000286) test_to_nbrf: .: (0.000318) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000543) test_to_newick_format_leaf: .: (0.000486) test_to_newick_format_leaf_NHX: .: (0.000305) Bio::TestBl2seqReport: test_db_len: .: (0.002493) test_db_num: .: (0.001031) test_new: .: (0.000498) test_undefed_methods: .: (0.001521) test_undefed_methods_for_iteration: .: (0.001476) Bio::TestBl2seqReportConstants: test_rs: .: (0.000436) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000806) test_hits: .: (0.000456) Bio::TestBlast: test_blast_reports_format0: .: (0.007853) test_blast_reports_format0_with_block: .: (0.000917) test_blast_reports_format7: .: (0.027381) test_blast_reports_format7_with_block: .: (0.021564) test_blast_reports_format7_with_parser: .: (0.023838) test_blast_reports_format7_with_parser_with_block: .: (0.028431) test_blast_reports_format8: .: (0.001721) test_blast_reports_format8_with_block: .: (0.000911) test_blast_reports_format8_with_parser: .: (0.000521) test_blast_reports_format8_with_parser_with_block: .: (0.000369) test_blast_reports_xml: .: (0.023239) test_blast_reports_xml_with_block: .: (0.018913) test_blastll: .: (0.000275) test_db: .: (0.000337) test_exec_genomenet: .: (0.000215) test_exec_local: .: (0.000415) test_exec_ncbi: .: (0.000272) test_filter: .: (0.000319) test_format: .: (0.000364) test_make_command_line: .: (0.000908) test_make_command_line_2: .: (0.000861) test_matrix: .: (0.000387) test_new: .: (0.000876) test_new_opt_string: .: (0.000562) test_option: .: (0.000305) test_option_set: .: (0.000383) test_option_set_m0: .: (0.000353) test_options: .: (0.000252) test_output: .: (0.000246) test_parse_result: .: (0.039287) test_parser: .: (0.000334) test_program: .: (0.000318) test_query: .: (0.004217) test_self_local: .: (0.000424) test_self_remote: .: (0.004847) test_server: .: (0.000281) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000646) test_delete: .: (0.006625) test_equal_equal: .: (0.000875) test_get: .: (0.007114) test_make_command_line_options: .: (0.000735) test_normalize!: .: (0.007541) test_parse: .: (0.000688) test_set: .: (0.004753) Bio::TestBlastReport: test_db: .: (0.037536) test_db_len: .: (0.022270) test_db_num: .: (0.022038) test_each_hit: .: (0.020969) test_each_iteration: .: (0.022766) test_eff_space: .: (0.021223) test_entrez_query: .: (0.021841) test_entropy: .: (0.021205) test_expect: .: (0.020757) test_filter: .: (0.022345) test_gap_extend: .: (0.022268) test_gap_open: .: (0.021873) test_hits: .: (0.021490) test_hsp_len: .: (0.024428) test_inclusion: .: (0.021696) test_iterations: .: (0.019758) test_kappa: .: (0.021234) test_lambda: .: (0.020585) test_matrix: .: (0.019891) test_message: .: (0.023994) test_parameters: .: (0.022568) test_pattern: .: (0.022125) test_program: .: (0.022051) test_query_def: .: (0.021704) test_query_id: .: (0.022850) test_query_len: .: (0.023202) test_reference: .: (0.021774) test_sc_match: .: (0.022437) test_sc_mismatch: .: (0.021623) test_statistics: .: (0.021878) test_version: .: (0.023898) Bio::TestBlastReportDefault: test_db: .: (0.001395) test_db_len: .: (0.000805) test_db_num: .: (0.000740) test_each_hit: .: (0.000788) test_each_iteration: .: (0.000792) test_eff_space: .: (0.000887) test_entropy: .: (0.000790) test_expect: .: (0.001096) test_gap_extend: .: (0.000946) test_gap_open: .: (0.000867) test_gapped_entropy: .: (0.000937) test_gapped_kappa: .: (0.000758) test_gapped_lambda: .: (0.000820) test_hits: .: (0.000751) test_iterations: .: (0.000891) test_kappa: .: (0.000779) test_lambda: .: (0.000800) test_matrix: .: (0.000916) test_message: .: (0.000708) test_pattern: .: (0.000767) test_program: .: (0.000858) test_query_def: .: (0.000796) test_query_len: .: (0.000935) test_reference: .: (0.000815) test_sc_match: .: (0.000962) test_sc_mismatch: .: (0.000956) test_version: .: (0.000797) Bio::TestBlastReportHit: test_Hit_accession: .: (0.025282) test_Hit_bit_score: .: (0.025488) test_Hit_definition: .: (0.027871) test_Hit_evalue: .: (0.021394) test_Hit_hit_id: .: (0.023857) test_Hit_hsps: .: (0.021399) test_Hit_identity: .: (0.021559) test_Hit_lap_at: .: (0.023318) test_Hit_len: .: (0.021327) test_Hit_midline: .: (0.020950) test_Hit_num: .: (0.021677) test_Hit_overlap: .: (0.021224) test_Hit_query_def: .: (0.022054) test_Hit_query_end: .: (0.020989) test_Hit_query_id: .: (0.021290) test_Hit_query_len: .: (0.021614) test_Hit_query_seq: .: (0.023167) test_Hit_query_start: .: (0.019685) test_Hit_taeget_def: .: (0.021395) test_Hit_target_end: .: (0.020249) test_Hit_target_id: .: (0.019502) test_Hit_target_len: .: (0.021008) test_Hit_target_seq: .: (0.032463) test_Hit_target_start: .: (0.035020) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001336) test_Hit_definition: .: (0.000677) test_Hit_evalue: .: (0.000948) test_Hit_hsps: .: (0.000780) test_Hit_identity: .: (0.000997) test_Hit_lap_at: .: (0.001391) test_Hit_len: .: (0.001284) test_Hit_midline: .: (0.001081) test_Hit_overlap: .: (0.000724) test_Hit_query_end: .: (0.001421) test_Hit_query_seq: .: (0.001308) test_Hit_query_start: .: (0.001033) test_Hit_taeget_def: .: (0.000585) test_Hit_target_end: .: (0.001165) test_Hit_target_id: .: (0.000981) test_Hit_target_len: .: (0.000635) test_Hit_target_seq: .: (0.001271) test_Hit_target_start: .: (0.001333) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.080376) test_Hit_bit_score: .: (0.099544) test_Hit_definition: .: (0.083739) test_Hit_evalue: .: (0.097299) test_Hit_hit_id: .: (0.091054) test_Hit_hsps: .: (0.079320) test_Hit_identity: .: (0.093112) test_Hit_lap_at: .: (0.098065) test_Hit_len: .: (0.099346) test_Hit_midline: .: (0.101134) test_Hit_num: .: (0.091509) test_Hit_overlap: .: (0.076589) test_Hit_query_def: .: (0.066986) test_Hit_query_end: .: (0.058842) test_Hit_query_id: .: (0.057234) test_Hit_query_len: .: (0.059186) test_Hit_query_seq: .: (0.059362) test_Hit_query_start: .: (0.066507) test_Hit_taeget_def: .: (0.062250) test_Hit_target_end: .: (0.061058) test_Hit_target_id: .: (0.062554) test_Hit_target_len: .: (0.067654) test_Hit_target_seq: .: (0.063896) test_Hit_target_start: .: (0.063333) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.059220) test_Hit_bit_score: .: (0.057842) test_Hit_definition: .: (0.066059) test_Hit_evalue: .: (0.059828) test_Hit_hit_id: .: (0.057993) test_Hit_hsps: .: (0.058700) test_Hit_identity: .: (0.061527) test_Hit_lap_at: .: (0.073919) test_Hit_len: .: (0.074723) test_Hit_midline: .: (0.075444) test_Hit_num: .: (0.058014) test_Hit_overlap: .: (0.055833) test_Hit_query_def: .: (0.058732) test_Hit_query_end: .: (0.071193) test_Hit_query_id: .: (0.062170) test_Hit_query_len: .: (0.059119) test_Hit_query_seq: .: (0.057350) test_Hit_query_start: .: (0.070055) test_Hit_taeget_def: .: (0.060009) test_Hit_target_end: .: (0.059882) test_Hit_target_id: .: (0.066018) test_Hit_target_len: .: (0.060953) test_Hit_target_seq: .: (0.061680) test_Hit_target_start: .: (0.070562) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.017852) test_Hit_bit_score: .: (0.018113) test_Hit_definition: .: (0.018947) test_Hit_evalue: .: (0.017391) test_Hit_hit_id: .: (0.017529) test_Hit_hsps: .: (0.017594) test_Hit_identity: .: (0.017791) test_Hit_lap_at: .: (0.018630) test_Hit_len: .: (0.018156) test_Hit_midline: .: (0.018251) test_Hit_num: .: (0.018628) test_Hit_overlap: .: (0.021172) test_Hit_query_def: .: (0.020867) test_Hit_query_end: .: (0.019221) test_Hit_query_id: .: (0.019489) test_Hit_query_len: .: (0.018965) test_Hit_query_seq: .: (0.019695) test_Hit_query_start: .: (0.017855) test_Hit_taeget_def: .: (0.018027) test_Hit_target_end: .: (0.018060) test_Hit_target_id: .: (0.020496) test_Hit_target_len: .: (0.018550) test_Hit_target_seq: .: (0.018423) test_Hit_target_start: .: (0.018773) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000528) test_Hit_bit_score: .: (0.000263) test_Hit_definition: .: (0.000286) test_Hit_evalue: .: (0.000289) test_Hit_hit_id: .: (0.000256) test_Hit_hsps: .: (0.000405) test_Hit_identity: .: (0.000300) test_Hit_lap_at: .: (0.000258) test_Hit_len: .: (0.000241) test_Hit_midline: .: (0.000256) test_Hit_num: .: (0.000263) test_Hit_overlap: .: (0.000242) test_Hit_query_def: .: (0.000276) test_Hit_query_end: .: (0.000230) test_Hit_query_id: .: (0.000229) test_Hit_query_len: .: (0.000230) test_Hit_query_seq: .: (0.000301) test_Hit_query_start: .: (0.000258) test_Hit_taeget_def: .: (0.000381) test_Hit_target_end: .: (0.000284) test_Hit_target_id: .: (0.000228) test_Hit_target_len: .: (0.000247) test_Hit_target_seq: .: (0.000244) test_Hit_target_start: .: (0.000242) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.019709) test_Hsp_bit_score: .: (0.018072) test_Hsp_density: .: (0.019122) test_Hsp_evalue: .: (0.018868) test_Hsp_gaps: .: (0.019709) test_Hsp_hit_frame: .: (0.019690) test_Hsp_hit_from: .: (0.019345) test_Hsp_hit_to: .: (0.019223) test_Hsp_hseq: .: (0.019600) test_Hsp_identity: .: (0.019766) test_Hsp_midline: .: (0.018707) test_Hsp_mismatch_count: .: (0.020548) test_Hsp_num: .: (0.021046) test_Hsp_pattern_from: .: (0.019095) test_Hsp_pattern_to: .: (0.018263) test_Hsp_percent_identity: .: (0.017871) test_Hsp_positive: .: (0.018555) test_Hsp_qseq: .: (0.022891) test_Hsp_query_frame: .: (0.026411) test_Hsp_query_from: .: (0.024094) test_Hsp_query_to: .: (0.023352) test_Hsp_score: .: (0.019336) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.001110) test_Hsp_bit_score: .: (0.000824) test_Hsp_evalue: .: (0.000705) test_Hsp_gaps: .: (0.000632) test_Hsp_hit_frame: .: (0.000706) test_Hsp_hit_from: .: (0.000806) test_Hsp_hit_to: .: (0.000807) test_Hsp_hseq: .: (0.000835) test_Hsp_identity: .: (0.000852) test_Hsp_midline: .: (0.000940) test_Hsp_percent_identity: .: (0.000762) test_Hsp_positive: .: (0.000624) test_Hsp_qseq: .: (0.000927) test_Hsp_query_frame: .: (0.000838) test_Hsp_query_from: .: (0.001056) test_Hsp_query_to: .: (0.000807) test_Hsp_score: .: (0.000872) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.058808) test_Hsp_bit_score: .: (0.059095) test_Hsp_density: .: (0.058268) test_Hsp_evalue: .: (0.061435) test_Hsp_gaps: .: (0.072444) test_Hsp_hit_frame: .: (0.060790) test_Hsp_hit_from: .: (0.061741) test_Hsp_hit_to: .: (0.059888) test_Hsp_hseq: .: (0.061392) test_Hsp_identity: .: (0.060802) test_Hsp_midline: .: (0.060480) test_Hsp_mismatch_count: .: (0.058394) test_Hsp_num: .: (0.060233) test_Hsp_pattern_from: .: (0.059310) test_Hsp_pattern_to: .: (0.061758) test_Hsp_percent_identity: .: (0.060169) test_Hsp_positive: .: (0.059924) test_Hsp_qseq: .: (0.065184) test_Hsp_query_frame: .: (0.058507) test_Hsp_query_from: .: (0.062717) test_Hsp_query_to: .: (0.062088) test_Hsp_score: .: (0.059614) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.060571) test_Hsp_bit_score: .: (0.068919) test_Hsp_density: .: (0.067765) test_Hsp_evalue: .: (0.068633) test_Hsp_gaps: .: (0.067814) test_Hsp_hit_frame: .: (0.068387) test_Hsp_hit_from: .: (0.067238) test_Hsp_hit_to: .: (0.066269) test_Hsp_hseq: .: (0.066278) test_Hsp_identity: .: (0.066888) test_Hsp_midline: .: (0.067700) test_Hsp_mismatch_count: .: (0.066859) test_Hsp_num: .: (0.058275) test_Hsp_pattern_from: .: (0.058735) test_Hsp_pattern_to: .: (0.058682) test_Hsp_percent_identity: .: (0.060423) test_Hsp_positive: .: (0.056632) test_Hsp_qseq: .: (0.058504) test_Hsp_query_frame: .: (0.060576) test_Hsp_query_from: .: (0.059754) test_Hsp_query_to: .: (0.083928) test_Hsp_score: .: (0.106256) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.025684) test_Hsp_bit_score: .: (0.020914) test_Hsp_density: .: (0.021156) test_Hsp_evalue: .: (0.024865) test_Hsp_gaps: .: (0.022465) test_Hsp_hit_frame: .: (0.019406) test_Hsp_hit_from: .: (0.019770) test_Hsp_hit_to: .: (0.019913) test_Hsp_hseq: .: (0.019515) test_Hsp_identity: .: (0.018258) test_Hsp_midline: .: (0.018771) test_Hsp_mismatch_count: .: (0.020292) test_Hsp_num: .: (0.018431) test_Hsp_pattern_from: .: (0.017927) test_Hsp_pattern_to: .: (0.018055) test_Hsp_percent_identity: .: (0.019545) test_Hsp_positive: .: (0.027062) test_Hsp_qseq: .: (0.027467) test_Hsp_query_frame: .: (0.028083) test_Hsp_query_from: .: (0.028668) test_Hsp_query_to: .: (0.027631) test_Hsp_score: .: (0.027081) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000789) test_Hsp_bit_score: .: (0.000388) test_Hsp_density: .: (0.000405) test_Hsp_evalue: .: (0.000365) test_Hsp_gaps: .: (0.000364) test_Hsp_hit_frame: .: (0.000353) test_Hsp_hit_from: .: (0.000368) test_Hsp_hit_to: .: (0.000372) test_Hsp_hseq: .: (0.000400) test_Hsp_identity: .: (0.000365) test_Hsp_midline: .: (0.000368) test_Hsp_mismatch_count: .: (0.000359) test_Hsp_num: .: (0.000612) test_Hsp_pattern_from: .: (0.000482) test_Hsp_pattern_to: .: (0.000435) test_Hsp_percent_identity: .: (0.000402) test_Hsp_positive: .: (0.000420) test_Hsp_qseq: .: (0.000363) test_Hsp_query_frame: .: (0.000353) test_Hsp_query_from: .: (0.000380) test_Hsp_query_to: .: (0.000553) test_Hsp_score: .: (0.000378) Bio::TestBlastReportIteration: test_hits: .: (0.026217) test_message: .: (0.026522) test_num: .: (0.025654) test_statistics: .: (0.025958) Bio::TestBlastReportIterationDefault: test_hits: .: (0.001420) test_message: .: (0.000793) test_num: .: (0.000770) Bio::TestBlastReportIterationMulti: test_each: .: (0.076522) test_hits: .: (0.078519) test_message: .: (0.065001) test_num: .: (0.073471) test_query_def: .: (0.062337) test_query_id: .: (0.073190) test_query_len: .: (0.063646) test_statistics: .: (0.057360) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.066032) test_hits: .: (0.075340) test_message: .: (0.073210) test_num: .: (0.074818) test_query_def: .: (0.077099) test_query_id: .: (0.073764) test_query_len: .: (0.077386) test_statistics: .: (0.078879) Bio::TestBlastReportIterationREXML: test_hits: .: (0.026743) test_message: .: (0.024606) test_num: .: (0.027427) test_statistics: .: (0.026661) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000751) test_message: .: (0.000506) test_num: .: (0.000334) test_statistics: .: (0.000337) Bio::TestBlastReportMulti: test_db: .: (0.077480) test_db_len: .: (0.081457) test_db_num: .: (0.058855) test_each_hit: .: (0.063035) test_each_iteration: .: (0.072202) test_eff_space: .: (0.076425) test_entropy: .: (0.071753) test_expect: .: (0.073265) test_filter: .: (0.056038) test_gap_extend: .: (0.075581) test_gap_open: .: (0.066019) test_hits: .: (0.065598) test_hsp_len: .: (0.062919) test_iterations: .: (0.060506) test_kappa: .: (0.064852) test_lambda: .: (0.061678) test_matrix: .: (0.065307) test_message: .: (0.076898) test_parameters: .: (0.071635) test_pattern: .: (0.060978) test_program: .: (0.101282) test_query_def: .: (0.092641) test_query_id: .: (0.066793) test_query_len: .: (0.070557) test_reference: .: (0.072758) test_reports: .: (0.070334) test_statistics: .: (0.069590) test_version: .: (0.069232) Bio::TestBlastReportMultiREXML: test_db: .: (0.068641) test_db_len: .: (0.066942) test_db_num: .: (0.067282) test_each_hit: .: (0.076295) test_each_iteration: .: (0.070538) test_eff_space: .: (0.068686) test_entropy: .: (0.071107) test_expect: .: (0.066267) test_filter: .: (0.062500) test_gap_extend: .: (0.069493) test_gap_open: .: (0.071034) test_hits: .: (0.071253) test_hsp_len: .: (0.071217) test_iterations: .: (0.072152) test_kappa: .: (0.069899) test_lambda: .: (0.068142) test_matrix: .: (0.070284) test_message: .: (0.070440) test_parameters: .: (0.070912) test_pattern: .: (0.069738) test_program: .: (0.063826) test_query_def: .: (0.060824) test_query_id: .: (0.060882) test_query_len: .: (0.063808) test_reference: .: (0.062835) test_reports: .: (0.064175) test_statistics: .: (0.058209) test_version: .: (0.060394) Bio::TestBlastReportREXML: test_db: .: (0.020788) test_db_len: .: (0.019191) test_db_num: .: (0.020487) test_each_hit: .: (0.019986) test_each_iteration: .: (0.020414) test_eff_space: .: (0.018913) test_entrez_query: .: (0.019076) test_entropy: .: (0.018945) test_expect: .: (0.020184) test_filter: .: (0.020982) test_gap_extend: .: (0.018751) test_gap_open: .: (0.018203) test_hits: .: (0.023342) test_hsp_len: .: (0.021567) test_inclusion: .: (0.019899) test_iterations: .: (0.020632) test_kappa: .: (0.018453) test_lambda: .: (0.020913) test_matrix: .: (0.022027) test_message: .: (0.019519) test_parameters: .: (0.020418) test_pattern: .: (0.023683) test_program: .: (0.019612) test_query_def: .: (0.020762) test_query_id: .: (0.021439) test_query_len: .: (0.021383) test_reference: .: (0.019056) test_sc_match: .: (0.021320) test_sc_mismatch: .: (0.018568) test_statistics: .: (0.021158) test_version: .: (0.021212) Bio::TestBlastReportTabular: test_db: .: (0.000516) test_db_len: .: (0.000330) test_db_num: .: (0.000287) test_each_hit: .: (0.000291) test_each_iteration: .: (0.000298) test_eff_space: .: (0.000282) test_entrez_query: .: (0.000532) test_entropy: .: (0.000344) test_expect: .: (0.000285) test_filter: .: (0.000311) test_gap_extend: .: (0.000311) test_gap_open: .: (0.000386) test_hits: .: (0.000343) test_hsp_len: .: (0.000313) test_inclusion: .: (0.000289) test_iterations: .: (0.000285) test_kappa: .: (0.000301) test_lambda: .: (0.000284) test_matrix: .: (0.000341) test_message: .: (0.000534) test_parameters: .: (0.000332) test_pattern: .: (0.000286) test_program: .: (0.000322) test_query_def: .: (0.000321) test_query_id: .: (0.000342) test_query_len: .: (0.000293) test_reference: .: (0.000284) test_sc_match: .: (0.000367) test_sc_mismatch: .: (0.000298) test_statistics: .: (0.000308) test_version: .: (0.000285) Bio::TestChain: test_aaseq: .: (0.001131) test_addLigand: .: (0.000362) test_addResidue: .: (0.000287) test_atom_seq: .: (0.000369) test_comp: .: (0.000310) test_each: .: (0.000267) test_each_heterogen: .: (0.000277) test_each_residue: .: (0.000340) test_get_heterogen_by_id: .: (0.000277) test_get_residue_by_id: .: (0.000329) test_inspect: .: (0.000392) test_rehash: .: (0.000292) test_rehash_heterogens: .: (0.000288) test_rehash_residues: .: (0.000339) test_square_brace: .: (0.000421) test_to_s: .: (0.000481) Bio::TestChainFinder: test_chains: .: (0.000466) test_each_chain: .: (0.000274) test_find_chain: .: (0.000259) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.014909) test_header: .: (0.001425) test_match_line: .: (0.001198) test_sequence0: .: (0.000994) test_sequence1: .: (0.000842) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.016507) test_header: .: (0.001406) test_match_line: .: (0.001222) test_sequence0: .: (0.001409) test_sequence1: .: (0.001251) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.021501) test_header: .: (0.001127) test_match_line: .: (0.001253) test_sequence0: .: (0.001164) test_sequence1: .: (0.000994) Bio::TestCodonTable: test_Tables: .: (0.000480) test_accessor: .: (0.000310) test_definition: .: (0.000244) test_each: .: (0.000247) test_revtrans: .: (0.000414) test_self_accessor: .: (0.000265) test_self_copy: .: (0.001150) test_set_accessor: .: (0.157960) test_start: .: (0.000351) test_start_codon?: .: (0.000386) test_stop: .: (0.000232) test_stop_codon?: .: (0.000277) test_table: .: (0.000450) Bio::TestCodonTableConstants: test_Definitions: .: (0.000585) test_Starts: .: (0.000313) test_Tables: .: (0.000243) test_stops: .: (0.000257) Bio::TestColorScheme: test_buried: .: (0.001465) Bio::TestCommand: test_command_constants: .: (0.000398) test_escape_shell: .: (0.000303) test_escape_shell_unix: .: (0.000305) test_escape_shell_windows: .: (0.000469) test_make_cgi_params_by_array_of_array: .: (0.000693) test_make_cgi_params_by_array_of_hash: .: (0.000565) test_make_cgi_params_by_array_of_string: .: (0.000339) test_make_cgi_params_by_hash_in_string: .: (0.000737) test_make_cgi_params_by_hash_in_symbol: .: (0.000822) test_make_cgi_params_by_string: .: (0.000398) test_make_command_line: .: (0.000297) test_make_command_line_unix: .: (0.000255) test_make_command_line_windows: .: (0.000326) test_safe_command_line_array: .: (0.000306) test_safe_command_line_array_passthrough: .: (0.000362) Bio::TestContingencyTable: test_lite_example: .: (0.268666) Bio::TestDB: test_entry_id: .: (0.000526) test_exists: .: (0.000290) test_fetch: .: (0.000365) test_get: .: (0.000321) test_open: .: (0.000286) test_tags: .: (0.000282) Bio::TestDataType: test_const_like_method: .: (0.000936) test_pdb_achar: .: (0.000442) test_pdb_atom: .: (0.000404) test_pdb_character: .: (0.000394) test_pdb_date: .: (0.000471) test_pdb_idcode: .: (0.000544) test_pdb_integer: .: (0.000258) test_pdb_list: .: (0.000290) test_pdb_lstring: .: (0.000404) test_pdb_real: .: (0.000355) test_pdb_resudue_name: .: (0.000464) test_pdb_slist: .: (0.000293) test_pdb_string: .: (0.000421) test_pdb_stringrj: .: (0.000276) test_pdb_symop: .: (0.000560) test_specification_list: .: (0.000286) Bio::TestEMBL: test_ac: .: (0.002466) test_accession: .: (0.000608) test_cc: .: (0.000663) test_de: .: (0.000670) test_division: .: (0.000645) test_dr: .: (0.000555) test_dt: .: (0.000705) test_dt_created: .: (0.000731) test_dt_iterator: .: (0.000721) test_dt_updated: .: (0.000655) test_each_cds: .: (0.000906) test_each_gene: .: (0.000937) test_entry: .: (0.000640) test_fh: .: (0.000623) test_ft: .: (0.000905) test_ft_accessor: .: (0.001051) test_ft_iterator: .: (0.003304) test_id_line: .: (0.000648) test_id_line_data_class: .: (0.000663) test_id_line_division: .: (0.000795) test_id_line_entry_name: .: (0.000791) test_id_line_iterator: .: (0.000669) test_id_line_molecule_type: .: (0.000675) test_id_line_sequence_length: .: (0.000563) test_kw: .: (0.000732) test_molecule: .: (0.000637) test_oc: .: (0.000838) test_og: .: (0.000669) test_os: .: (0.000897) test_ref: .: (0.000751) test_references: .: (0.000892) test_seq: .: (0.001040) test_sequence_length: .: (0.000749) test_sq: .: (0.000778) test_sq_get: .: (0.000623) test_sv: .: (0.000717) test_version: .: (0.000639) Bio::TestEMBL89: test_ac: .: (0.001578) test_accession: .: (0.000608) test_cc: .: (0.001015) test_de: .: (0.000757) test_division: .: (0.000763) test_dr: .: (0.000554) test_dt: .: (0.000667) test_dt_created: .: (0.000541) test_dt_iterator: .: (0.000659) test_dt_updated: .: (0.000657) test_each_cds: .: (0.000967) test_each_gene: .: (0.000953) test_entry: .: (0.000750) test_fh: .: (0.000683) test_ft: .: (0.001226) test_ft_accessor: .: (0.000723) test_ft_iterator: .: (0.001010) test_id_line: .: (0.000761) test_id_line_data_class: .: (0.000710) test_id_line_division: .: (0.000637) test_id_line_entry_name: .: (0.000786) test_id_line_iterator: .: (0.000707) test_id_line_molecule_type: .: (0.000801) test_id_line_sequence_length: .: (0.000570) test_id_line_sequence_version: .: (0.000432) test_kw: .: (0.000620) test_molecule: .: (0.000645) test_oc: .: (0.000807) test_og: .: (0.000575) test_os: .: (0.000823) test_ref: .: (0.000834) test_references: .: (0.001269) test_seq: .: (0.001111) test_sequence_length: .: (0.000685) test_sq: .: (0.000815) test_sq_get: .: (0.000716) test_sv: .: (0.000812) test_version: .: (0.000731) Bio::TestEMBLAPI: test_ac: .: (0.000674) test_accessions: .: (0.000537) Bio::TestEMBLCommon: test_ac: .: (0.000458) test_accession: .: (0.000244) test_accessions: .: (0.000300) test_de: .: (0.000342) test_definition: .: (0.000262) test_description: .: (0.000313) test_dr: .: (0.000233) test_keywords: .: (0.000251) test_kw: .: (0.000282) test_oc: .: (0.000315) test_og: .: (0.000292) test_os: .: (0.000254) test_ref: .: (0.000287) test_references: .: (0.000240) Bio::TestEMBLDB: test_fetch: .: (0.000791) test_p_entry2hash: .: (0.000319) Bio::TestEMBLToBioSequence: test_classification: .: (0.005287) test_date_created: .: (0.001060) test_date_modified: .: (0.000896) test_definition: .: (0.000882) test_division: .: (0.000901) test_entry_id: .: (0.000811) test_entry_version: .: (0.000738) test_features: .: (0.001274) test_keywords: .: (0.000788) test_molecule_type: .: (0.000768) test_primary_accession: .: (0.000727) test_references: .: (0.001421) test_release_created: .: (0.000751) test_release_modified: .: (0.000731) test_secondary_accessions: .: (0.000740) test_sequence_version: .: (0.001236) test_species: .: (0.000782) test_topology: .: (0.000819) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.006265) test_date_created: .: (0.021644) test_date_modified: .: (0.025213) test_definition: .: (0.022401) test_division: .: (0.004742) test_entry_id: .: (0.003898) test_entry_version: .: (0.003550) test_features: .: (0.004102) test_keywords: .: (0.004339) test_molecule_type: .: (0.003821) test_primary_accession: .: (0.003902) test_references: .: (0.004234) test_release_created: .: (0.003767) test_release_modified: .: (0.003637) test_secondary_accessions: .: (0.004755) test_sequence_version: .: (0.004271) test_species: .: (0.004442) test_topology: .: (0.004630) Bio::TestFasta: test_db: .: (0.000486) test_format: .: (0.000267) test_format_arg_integer: .: (0.000303) test_format_arg_str: .: (0.000283) test_ktup: .: (0.000287) test_matrix: .: (0.000286) test_option: .: (0.000360) test_options: .: (0.000290) test_output: .: (0.000249) test_program: .: (0.000294) test_server: .: (0.000301) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000490) test_accession: .: (0.000616) test_accessions: .: (0.000307) test_description: .: (0.000311) test_descriptions: .: (0.000292) test_entry_id: .: (0.000298) test_get_all_by_type: .: (0.000275) test_gi: .: (0.000290) test_id_strings: .: (0.000404) test_list_ids: .: (0.000288) test_locus: .: (0.000289) test_words: .: (0.000347) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000463) test_accession: .: (0.000650) test_accessions: .: (0.000311) test_description: .: (0.000319) test_descriptions: .: (0.000288) test_emb: .: (0.000327) test_entry_id: .: (0.000309) test_get_all_by_type: .: (0.000311) test_get_emb: .: (0.000322) test_gi: .: (0.000329) test_id_strings: .: (0.000365) test_list_ids: .: (0.000314) test_locus: .: (0.000292) test_words: .: (0.000362) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000439) test_accession: .: (0.000331) test_accessions: .: (0.000649) test_description: .: (0.000292) test_descriptions: .: (0.000275) test_entry_id: .: (0.000275) test_get_all_by_type: .: (0.000275) test_gi: .: (0.000287) test_id_strings: .: (0.000393) test_list_ids: .: (0.000283) test_locus: .: (0.000297) test_sp: .: (0.000306) test_words: .: (0.000361) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000525) test_accession: .: (0.000385) test_accessions: .: (0.000365) test_description: .: (0.000326) test_descriptions: .: (0.000351) test_entry_id: .: (0.000337) test_get_all_by_type: .: (0.000343) test_gi: .: (0.000351) test_id_strings: .: (0.000556) test_list_ids: .: (0.000409) test_locus: .: (0.000389) test_words: .: (0.000923) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000567) test_accession: .: (0.000367) test_accessions: .: (0.000364) test_description: .: (0.000290) test_descriptions: .: (0.000299) test_entry_id: .: (0.000268) test_get_all_by_type: .: (0.000332) test_gi: .: (0.000299) test_id_strings: .: (0.000400) test_list_ids: .: (0.000648) test_locus: .: (0.000292) test_words: .: (0.000380) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000498) test_accession: .: (0.000260) test_accessions: .: (0.000240) test_description: .: (0.000235) test_descriptions: .: (0.000243) test_entry_id: .: (0.000240) test_get_all_by_type: .: (0.000239) test_gi: .: (0.000233) test_id_strings: .: (0.000295) test_list_ids: .: (0.000237) test_locus: .: (0.000307) test_words: .: (0.000333) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000754) test_accession: .: (0.000375) test_accessions: .: (0.000319) test_description: .: (0.000331) test_descriptions: .: (0.000305) test_entry_id: .: (0.000368) test_get: .: (0.000353) test_get_all_by_type: .: (0.000318) test_id_strings: .: (0.004688) test_list_ids: .: (0.000305) test_locus: .: (0.000256) test_sp: .: (0.000290) test_words: .: (0.000407) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000538) test_accession: .: (0.000316) test_accessions: .: (0.000325) test_description: .: (0.000301) test_descriptions: .: (0.000335) test_entry_id: .: (0.000342) test_get: .: (0.000335) test_get_all_by_type: .: (0.000310) test_id_strings: .: (0.000505) test_list_ids: .: (0.000378) test_locus: .: (0.000411) test_tr: .: (0.000347) test_words: .: (0.000536) Bio::TestFastaFirstName: test_first_name1: .: (0.000559) test_first_name_multi_identifier: .: (0.000340) test_first_name_single_worded_defintion: .: (0.000299) test_no_definition: .: (0.000298) test_space_before_first_name: .: (0.000303) test_tabbed_defintion: .: (0.000279) Bio::TestFastaFormat: test_aalen: .: (0.000872) test_aaseq: .: (0.000277) test_acc_version: .: (0.000321) test_accession: .: (0.000320) test_accessions: .: (0.000331) test_data: .: (0.000300) test_definition: .: (0.000272) test_entry: .: (0.000259) test_entry_id: .: (0.000292) test_entry_overrun: .: (0.000248) test_first_name: .: (0.000286) test_gi: .: (0.000298) test_identifiers: .: (0.000303) test_length: .: (0.000304) test_query: .: (0.000525) test_seq: .: (0.000322) Bio::TestFastaFormatConst: test_delimiter: .: (0.000412) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000450) test_data: .: (0.000309) test_definition: .: (0.000311) test_entry: .: (0.000325) test_entry_id: .: (0.000396) test_first_name: .: (0.000318) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000398) test_naseq: .: (0.000249) test_naseq_class: .: (0.000521) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000522) Bio::TestFastaInitialize: test_new_1: .: (0.000958) test_option: .: (0.000314) test_option_backward_compatibility: .: (0.000353) Bio::TestFastaNumericFormat: test_arg: .: (0.000483) test_data: .: (0.000293) test_definition: .: (0.000284) test_each: .: (0.000577) test_entry: .: (0.000281) test_entry_id: .: (0.000318) test_length: .: (0.000272) test_to_biosequence: .: (0.001135) Bio::TestFastaQuery: test_query: .: (0.000341) test_self_local: .: (0.000194) test_self_parser: .: (0.000213) test_self_remote: .: (0.000206) Bio::TestFastacmd: test_database: .: (0.000355) test_fastacmd: .: (0.000208) test_methods: .: (0.000290) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.017749) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.011914) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001236) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.001336) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.013349) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.002239) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.020805) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.001355) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001478) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001306) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.001273) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.003366) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.008103) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.002914) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.002268) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.001194) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001336) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.019275) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.029536) test_error_probabilities_as_sanger: .: (0.008949) test_error_probabilities_as_solexa: .: (0.014651) test_quality_scores_as_illumina: .: (0.000628) test_quality_scores_as_sanger: .: (0.000350) test_quality_scores_as_solexa: .: (0.000469) test_validate_format: .: (0.000662) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.011790) test_entry_id: .: (0.001665) test_error_probabilities: .: (0.209669) test_nalen: .: (0.001676) test_naseq: .: (0.001312) test_quality_scores: .: (0.003495) test_quality_string: .: (0.001191) test_roundtrip: .: (0.224598) test_seq: .: (0.001246) test_sequence_string: .: (0.001269) test_to_biosequence: .: (0.241089) test_to_biosequence_and_output: .: (0.009159) test_to_s: .: (0.002243) test_validate_format: .: (0.002078) test_validate_format_with_array: .: (0.002049) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.001691) test_mask_20_with_empty_string: .: (0.000984) test_mask_20_with_longer_string: .: (0.000726) test_mask_20_with_x: .: (0.000627) test_mask_60: .: (0.000764) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.021431) test_error_probabilities_as_sanger: .: (0.014806) test_error_probabilities_as_solexa: .: (0.017974) test_quality_scores_as_illumina: .: (0.000837) test_quality_scores_as_sanger: .: (0.000472) test_quality_scores_as_solexa: .: (0.001175) test_validate_format: .: (0.000929) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.010910) test_error_probabilities_as_sanger: .: (0.010712) test_error_probabilities_as_solexa: .: (0.010981) test_quality_scores_as_illumina: .: (0.000790) test_quality_scores_as_sanger: .: (0.000602) test_quality_scores_as_solexa: .: (0.000421) test_validate_format: .: (0.001154) Bio::TestFeature: test_append: .: (0.000410) test_append_nil: .: (0.000181) test_assoc: .: (0.000146) test_each: .: (0.000138) test_feature: .: (0.000141) test_locations: .: (0.000239) test_new: .: (0.000150) test_position: .: (0.000151) test_qualifiers: .: (0.000106) Bio::TestFeatures: test_append: .: (0.000391) test_arg: .: (0.000245) test_each: .: (0.000201) test_features: .: (0.000165) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.003427) test_aaindex2: .: (0.000350) test_blast: .: (0.000300) test_blastxml: .: (0.002009) test_embl: .: (0.000431) test_embl_oldrelease: .: (0.000386) test_fastaformat: .: (0.001477) test_fastanumericformat: .: (0.000254) test_fastq: .: (0.000313) test_genbank: .: (0.000645) test_genpept: .: (0.000340) test_hmmer: .: (0.002680) test_maxml_cluster: .: (0.005215) test_maxml_sequence: .: (0.000170) test_medline: .: (0.000262) test_prosite: .: (0.005291) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.012113) test_transfac: .: (0.002619) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000447) test_auto_1arg_filename: .: (0.000625) test_auto_1arg_io: .: (0.000491) test_auto_1arg_io_with_block: .: (0.001036) test_auto_1arg_with_block: .: (0.001255) test_auto_2arg_filename_mode: .: (0.000534) test_auto_2arg_filename_mode_with_block: .: (0.000965) test_auto_3arg: .: (0.000512) test_auto_3arg_with_block: .: (0.001218) test_foreach: .: (0.000768) test_new_2arg_class: .: (0.000281) test_new_2arg_nil: .: (0.000424) test_open_0arg: .: (0.000193) test_open_1arg_class: .: (0.000148) test_open_1arg_filename: .: (0.000520) test_open_1arg_io: .: (0.000479) test_open_1arg_io_with_block: .: (0.001344) test_open_1arg_nil: .: (0.000191) test_open_1arg_with_block: .: (0.000948) test_open_2arg_autodetect: .: (0.000493) test_open_2arg_autodetect_io: .: (0.000428) test_open_2arg_autodetect_io_with_block: .: (0.001251) test_open_2arg_autodetect_with_block: .: (0.000944) test_open_2arg_class: .: (0.000292) test_open_2arg_class_io: .: (0.000214) test_open_2arg_class_io_with_block: .: (0.000655) test_open_2arg_class_with_block: .: (0.000777) test_open_2arg_filename_mode: .: (0.000474) test_open_2arg_filename_mode_with_block: .: (0.000744) test_open_3arg: .: (0.000913) test_open_3arg_with_block: .: (0.002266) test_open_4arg: .: (0.001908) test_to_a: .: (0.000723) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000561) test_close: .: (0.000212) test_dbclass: .: (0.000205) test_dbclass_eq: .: (0.000248) test_dbclass_nil: .: (0.000564) test_each: .: (0.000430) test_each_entry: .: (0.000597) test_ended_pos: .: (0.000351) test_entry_pos_flag: .: (0.000241) test_entry_raw: .: (0.000464) test_eof?: .: (0.000422) test_next_entry: .: (0.000560) test_path: .: (0.000197) test_pos: .: (0.000614) test_raw: .: (0.000473) test_rewind: .: (0.000308) test_start_pos: .: (0.000340) test_start_pos_ended_pos_not_recorded: .: (0.000361) test_to_io: .: (0.000237) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000584) test_simpleformat2: .: (0.000282) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000339) test_eof_false_after_prefetch: .: (0.000607) test_eof_false_first: .: (0.000180) test_eof_true: .: (0.000289) test_getc: .: (0.000171) test_getc_after_prefetch: .: (0.000156) test_gets: .: (0.000185) test_gets_equal_prefetch_gets: .: (0.000183) test_gets_paragraph_mode: .: (0.000210) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000447) test_gets_paragraph_mode_within_buffer: .: (0.000490) test_gets_rs: .: (0.000230) test_gets_rs_equal_prefetch_gets: .: (0.000229) test_gets_rs_within_buffer: .: (0.000499) test_pos: .: (0.000183) test_pos=: .: (0.000191) test_prefetch_buffer: .: (0.000432) test_prefetch_gets: .: (0.000235) test_prefetch_gets_with_arg: .: (0.000223) test_rewind: .: (0.000161) test_skip_spaces: .: (0.000174) test_to_io: .: (0.000202) test_ungetc: .: (0.000153) test_ungetc_after_prefetch: .: (0.000198) test_ungets: .: (0.000235) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000345) test_self_open_file: .: (0.000198) test_self_open_file_with_block: .: (0.000216) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000581) test_parse_file_open_arg_int_perm: .: (0.000120) test_parse_file_open_arg_int_perm_opt: .: (0.000180) test_parse_file_open_arg_integer: .: (0.000113) test_parse_file_open_arg_nil: .: (0.000132) test_parse_file_open_arg_opt: .: (0.000192) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000170) test_parse_file_open_arg_str: .: (0.000169) test_parse_file_open_arg_str_opt: .: (0.000152) test_parse_file_open_arg_str_perm: .: (0.000165) test_parse_file_open_arg_str_perm_opt: .: (0.000134) test_parse_file_open_arg_str_with_enc: .: (0.000158) test_parse_file_open_arg_str_with_ext_enc: .: (0.000173) test_parse_file_open_mode_integer: .: (0.000122) test_parse_file_open_mode_nil: .: (0.000133) test_parse_file_open_mode_str: .: (0.000154) test_parse_file_open_mode_str_with_enc: .: (0.000161) test_parse_file_open_mode_str_with_ext_enc: .: (0.000351) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000318) test_entry: .: (0.000173) test_entry_ended_pos: .: (0.000156) test_entry_pos_flag: .: (0.000209) test_entry_start_pos: .: (0.000148) test_get_entry: .: (0.000208) test_rewind: .: (0.000197) test_skip_leader: .: (0.000145) test_stream: .: (0.000157) test_stream_pos: .: (0.000171) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000285) test_delimiter_overrun: .: (0.000152) test_entry: .: (0.000445) test_entry_ended_pos: .: (0.000173) test_entry_ended_pos_default_nil: .: (0.000189) test_entry_start_pos: .: (0.000140) test_entry_start_pos_default_nil: .: (0.000175) test_get_entry: .: (0.000336) test_get_parsed_entry: .: (0.000369) test_header: .: (0.000187) test_skip_leader: .: (0.000174) test_skip_leader_without_header: .: (0.000227) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000435) test_entry_ended_pos: .: (0.000635) test_entry_start_pos: .: (0.000356) test_flag_to_fetch_header: .: (0.000344) test_get_entry: .: (0.000470) test_get_parsed_entry: .: (0.000529) test_rewind: .: (0.000378) test_skip_leader: .: (0.000477) Bio::TestGCGMsf: test_alignment: .: (0.001563) test_checksum: .: (0.000347) test_compcheck: .: (0.000357) test_date: .: (0.000372) test_description: .: (0.000486) test_entry_id: .: (0.000333) test_gap_length_weight: .: (0.011640) test_gap_weight: .: (0.000353) test_heading: .: (0.000376) test_length: .: (0.011930) test_seq_type: .: (0.000364) test_symbol_comparison_table: .: (0.000350) test_validate_checksum: .: (0.013375) Bio::TestGFF: test_record_class: .: (0.010481) test_records: .: (0.010835) Bio::TestGFF2: test_const_version: .: (0.007736) test_gff_version: .: (0.000723) test_metadata: .: (0.010548) test_metadata_size: .: (0.003228) test_records_size: .: (0.000623) test_to_s: .: (0.001768) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000389) test_attributes_case2: .: (0.000251) test_attributes_incompatible_backslash_semicolon: .: (0.000333) Bio::TestGFF2MetaData: test_data: .: (0.000298) test_directive: .: (0.000117) test_parse: .: (0.000158) Bio::TestGFF2Record: test_attribute: .: (0.001155) test_attribute_nonexistent: .: (0.000372) test_attributes: .: (0.000376) test_attributes_to_hash: .: (0.000417) test_comment_only?: .: (0.000393) test_delete_attribute: .: (0.000427) test_delete_attribute_multiple: .: (0.000460) test_delete_attribute_multiple2: .: (0.000944) test_delete_attribute_multiple_nil: .: (0.000417) test_delete_attribute_nil: .: (0.000448) test_delete_attribute_nonexistent: .: (0.000392) test_delete_attributes: .: (0.000442) test_delete_attributes_multiple: .: (0.000792) test_delete_attributes_nonexistent: .: (0.000447) test_end: .: (0.000365) test_eqeq: .: (0.000987) test_eqeq_false: .: (0.001279) test_feature: .: (0.000368) test_frame: .: (0.000378) test_get_attribute: .: (0.000489) test_get_attribute_nonexistent: .: (0.000333) test_get_attributes: .: (0.000892) test_get_attributes_nonexistent: .: (0.000370) test_replace_attributes: .: (0.000489) test_replace_attributes_multiple_multiple_over: .: (0.000407) test_replace_attributes_multiple_multiple_same: .: (0.000617) test_replace_attributes_multiple_multiple_two: .: (0.000828) test_replace_attributes_multiple_single: .: (0.000422) test_replace_attributes_nonexistent: .: (0.000416) test_replace_attributes_nonexistent_multiple: .: (0.000412) test_replace_attributes_single_multiple: .: (0.000474) test_score: .: (0.000356) test_self_parse: .: (0.001224) test_seqname: .: (0.000344) test_set_attribute: .: (0.000441) test_set_attribute_multiple: .: (0.000422) test_set_attribute_nonexistent: .: (0.000425) test_sort_attributes_by_tag!: .: (0.000907) test_sort_attributes_by_tag_bang_test2: .: (0.000501) test_sort_attributes_by_tag_bang_with_block: .: (0.000514) test_source: .: (0.000358) test_start: .: (0.000341) test_strand: .: (0.000763) test_to_s: .: (0.000624) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000345) test_comment_eq: .: (0.000155) test_comment_only?: .: (0.000154) test_comment_only_false: .: (0.000159) test_to_s: .: (0.000140) test_to_s_not_empty: .: (0.000259) Bio::TestGFF3: test_const_version: .: (0.001462) test_gff_version: .: (0.000812) test_records: .: (0.001416) test_sequence_regions: .: (0.000819) test_sequences: .: (0.000922) test_to_s: .: (0.002133) Bio::TestGFF3MetaData: test_data: .: (0.000314) test_directive: .: (0.000104) test_parse: .: (0.000159) Bio::TestGFF3Record: test_attributes: .: (0.000942) test_end: .: (0.000395) test_feature: .: (0.000363) test_frame: .: (0.000338) test_id: .: (0.000330) test_score: .: (0.000718) test_seqname: .: (0.000352) test_source: .: (0.000343) test_start: .: (0.000366) test_strand: .: (0.000390) test_to_s: .: (0.000590) test_to_s_attr_order_changed: .: (0.000723) Bio::TestGFF3RecordEscape: test_escape: .: (0.000430) test_escape_attribute: .: (0.000204) test_escape_seqid: .: (0.000231) test_unescape: .: (0.000210) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.001080) test_eqeq: .: (0.000318) test_new_from_sequences_na: .: (0.000378) test_new_from_sequences_na_aa: .: (0.000482) test_new_from_sequences_na_aa_boundary_gap: .: (0.000688) test_new_from_sequences_na_aa_example: .: (0.000536) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000476) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000874) test_process_sequences_na: .: (0.000337) test_process_sequences_na_aa: .: (0.000316) test_process_sequences_na_aa_reverse_frameshift: .: (0.000314) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000375) test_process_sequences_na_aa_tooshort: .: (0.000466) test_process_sequences_na_tooshort: .: (0.000423) test_to_s: .: (0.000648) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000514) test_attributes_one: .: (0.000182) test_attributes_with_escaping: .: (0.000237) test_id_multiple: .: (0.000411) test_id_multiple2: .: (0.000343) test_id_replace: .: (0.000248) test_id_set: .: (0.000695) test_initialize_9: .: (0.000122) test_phase: .: (0.000245) test_score: .: (0.000219) test_to_s_void: .: (0.000150) Bio::TestGFF3RecordTarget: test_end: .: (0.000332) test_parse: .: (0.000234) test_start: .: (0.000175) test_strand: .: (0.000195) test_target_id: .: (0.000148) test_to_s: .: (0.000294) Bio::TestGFF3SequenceRegion: test_end: .: (0.000299) test_parse: .: (0.000535) test_seqid: .: (0.000203) test_start: .: (0.000141) test_to_s: .: (0.000274) Bio::TestGFFRecord: test_attributes: .: (0.000392) test_comment: .: (0.000187) test_end: .: (0.000183) test_feature: .: (0.000196) test_frame: .: (0.000163) test_score: .: (0.000180) test_seqname: .: (0.000209) test_source: .: (0.000154) test_start: .: (0.000202) test_strand: .: (0.000419) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000315) Bio::TestGeneAssociation: test_aspect: .: (0.000401) test_assigned_by: .: (0.000167) test_date: .: (0.000188) test_db: .: (0.000142) test_db_object_id: .: (0.000210) test_db_object_name: .: (0.000178) test_db_object_symbol: .: (0.000178) test_db_object_synonym: .: (0.000164) test_db_object_type: .: (0.000189) test_db_reference: .: (0.000133) test_evidence: .: (0.000174) test_goid: .: (0.000431) test_parser: .: (0.001405) test_qualifier: .: (0.000172) test_taxon: .: (0.000178) test_to_str: .: (0.000186) test_with: .: (0.000191) Bio::TestGenscanReport: test_date_run: .: (0.002277) test_gccontent: .: (0.001023) test_genscan_version: .: (0.001027) test_isochore: .: (0.001301) test_length: .: (0.001057) test_matrix: .: (0.001013) test_predictions_size: .: (0.001391) test_query_name: .: (0.001026) test_time: .: (0.001439) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.001326) test_donor_score: .: (0.000999) test_exon_type: .: (0.001323) test_exon_type_long: .: (0.001013) test_first: .: (0.006157) test_initiation_score: .: (0.001073) test_last: .: (0.001015) test_number: .: (0.001375) test_p_value: .: (0.000958) test_phase: .: (0.001086) test_range: .: (0.001014) test_score: .: (0.001286) test_strand: .: (0.001037) test_t_score: .: (0.000969) test_termination_score: .: (0.001268) Bio::TestGenscanReportGene: test_aaseq: .: (0.001314) test_naseq: .: (0.001281) test_number: .: (0.000982) test_polyA: .: (0.001264) test_promoter: .: (0.001069) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.001365) test_reports_ary_contents: .: (0.001254) Bio::TestHMMERReportConstants: test_rs: .: (0.000268) Bio::TestHMMERReportHit: test_accession: .: (0.001170) test_append_hsp: .: (0.001005) test_bit_score: .: (0.001241) test_definition: .: (0.001061) test_description: .: (0.001090) test_each: .: (0.001083) test_each_hsp: .: (0.001131) test_entry_id: .: (0.001055) test_evalue: .: (0.001033) test_hit: .: (0.001158) test_hit_id: .: (0.001018) test_hsps: .: (0.001029) test_num: .: (0.000992) test_score: .: (0.001218) test_target_def: .: (0.001060) test_target_id: .: (0.001038) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.001505) test_each: .: (0.001071) test_each_hit: .: (0.001032) test_histogram: .: (0.000993) test_hits: .: (0.001258) test_hsps: .: (0.001153) test_parameter: .: (0.001135) test_program: .: (0.001208) test_query_info: .: (0.001493) test_statistical_detail: .: (0.001060) test_total_seq_searched: .: (0.001083) test_whole_seq_top_hits: .: (0.001377) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.001705) test_histogram: .: (0.001262) test_statistical_detail: .: (0.001683) test_total_seq_searched: .: (0.001303) test_whole_seq_top_hit: .: (0.001370) Bio::TestHMMERReportHsp: test_accession: .: (0.001234) test_bit_score: .: (0.001321) test_csline: .: (0.001145) test_domain: .: (0.001071) test_evalue: .: (0.001083) test_flatseq: .: (0.001381) test_hmm_f: .: (0.001075) test_hmm_t: .: (0.001048) test_hmmseq: .: (0.001064) test_hsp: .: (0.001432) test_midline: .: (0.001061) test_query_frame: .: (0.001069) test_query_from: .: (0.001568) test_query_seq: .: (0.001189) test_query_to: .: (0.001098) test_rfline: .: (0.001101) test_score: .: (0.001081) test_seq_f: .: (0.001195) test_seq_ft: .: (0.001138) test_seq_t: .: (0.001067) test_set_alignment: .: (0.001424) test_targat_to: .: (0.001187) test_target_frame: .: (0.001062) test_target_from: .: (0.001053) test_target_seq: .: (0.001445) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000747) test_find_hetatm: .: (0.000379) test_hetatms: .: (0.000417) Bio::TestHeterogen: test_addAtom: .: (0.000854) test_each: .: (0.000309) test_each_hetatm: .: (0.000335) test_get_residue_id_from_atom: .: (0.000273) test_het_atom: .: (0.000225) test_iCode: .: (0.000257) test_inspect: .: (0.000600) test_resSeq: .: (0.000214) test_sort: .: (0.000292) test_square_bracket: .: (0.000292) test_to_s: .: (0.000474) test_update_resudue_id: .: (0.000198) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000396) test_find_heterogen: .: (0.000206) test_heterogens: .: (0.000323) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000421) test_match_description: .: (0.003800) test_match_evalue: .: (0.000233) test_match_ipr_description: .: (0.000247) test_match_ipr_id: .: (0.000245) test_match_match_end: .: (0.000222) test_match_match_start: .: (0.000263) test_match_method: .: (0.000225) test_matches_size: .: (0.000246) test_query_id: .: (0.000244) test_query_length: .: (0.000756) Bio::TestIprscanRawReport: test_entry_id: .: (0.005200) test_match_accession: .: (0.003826) test_match_crc64: .: (0.003847) test_match_date: .: (0.004198) test_match_description: .: (0.003921) test_match_evalue: .: (0.003802) test_match_go_terms: .: (0.003778) test_match_ipr_description: .: (0.004036) test_match_ipr_id: .: (0.003765) test_match_match_end: .: (0.003293) test_match_match_start: .: (0.006146) test_match_method: .: (0.003654) test_match_query_id: .: (0.003573) test_match_query_length: .: (0.003666) test_match_status: .: (0.004131) test_obj: .: (0.003775) test_query_id: .: (0.003746) test_query_length: .: (0.003571) test_self_reports_in_raw: .: (0.082981) Bio::TestIprscanReport: test_output_raw: .: (0.002125) test_to_raw: .: (0.000793) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000917) test_match_accession: .: (0.001039) test_match_date: .: (0.000721) test_match_description: .: (0.000726) test_match_evalue: .: (0.000701) test_match_go_terms: .: (0.001023) test_match_ipr_description: .: (0.000774) test_match_ipr_id: .: (0.000727) test_match_match_end: .: (0.000742) test_match_match_start: .: (0.001061) test_match_method: .: (0.000755) test_match_status: .: (0.000686) test_matches_size: .: (0.000697) test_query_id: .: (0.001048) test_query_length: .: (0.000722) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000973) test_to_hash_match?: .: (0.001417) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.002070) Bio::TestKeggCompound: test_comment: .: (0.001765) test_dblinks_as_hash: .: (0.000563) test_dblinks_as_strings: .: (0.000427) test_entry_id: .: (0.000385) test_enzymes: .: (0.000868) test_formula: .: (0.000794) test_kcf: .: (0.000435) test_mass: .: (0.000400) test_name: .: (0.000428) test_names: .: (0.000483) test_pathways_as_hash: .: (0.000746) test_pathways_as_strings: .: (0.000552) test_reactions: .: (0.001001) test_remark: .: (0.000458) test_rpairs: .: (0.000405) Bio::TestKeggEnzyme: test_all_reac: .: (0.001883) test_classes: .: (0.001095) test_cofactors: .: (0.000744) test_comment: .: (0.000795) test_dblinks_as_hash: .: (0.000852) test_dblinks_as_strings: .: (0.000784) test_diseases: .: (0.000768) test_entry: .: (0.001234) test_entry_id: .: (0.000902) test_genes: .: (0.022029) test_genes_as_hash: .: (0.026627) test_genes_as_strings: .: (0.007030) test_inhibitors: .: (0.000713) test_iubmb_reactions: .: (0.000753) test_kegg_reactions: .: (0.000654) test_motifs: .: (0.000680) test_name: .: (0.000776) test_names: .: (0.001258) test_obsolete?: .: (0.000752) test_orthologs_as_hash: .: (0.000917) test_orthologs_as_strings: .: (0.000855) test_pathways_as_hash: .: (0.001034) test_pathways_as_strings: .: (0.001246) test_products: .: (0.001028) test_reaction: .: (0.000900) test_structures: .: (0.001273) test_substrates: .: (0.000880) test_sysname: .: (0.000883) Bio::TestKeggGenesDblinks: test_data: .: (0.001005) test_dblinks_0: .: (0.000219) test_dblinks_1: .: (0.000162) test_dblinks_2: .: (0.000202) Bio::TestKeggGenesStructure: test_data: .: (0.000357) test_ids: .: (0.000250) test_ids_in_array: .: (0.000222) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.015911) test_graphics__size: .: (0.013305) test_id: .: (0.013087) test_link: .: (0.011936) test_name: .: (0.012335) test_reaction: .: (0.012796) test_type: .: (0.012609) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.012899) test_graphics__size: .: (0.012487) test_id: .: (0.012820) test_link: .: (0.012722) test_name: .: (0.017186) test_reaction: .: (0.014448) test_type: .: (0.014843) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.013835) test_category: .: (0.012914) test_entry_id: .: (0.012886) test_fgcolor=: .: (0.012902) test_height=: .: (0.012961) test_label=: .: (0.012888) test_shape=: .: (0.012873) test_width=: .: (0.012953) test_x=: .: (0.012788) test_y=: .: (0.012754) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.013386) test_graphics__size: .: (0.015225) test_id: .: (0.014353) test_link: .: (0.013675) test_name: .: (0.013368) test_reaction: .: (0.013251) test_type: .: (0.013030) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000389) test_graphics=: .: (0.000194) test_id=: .: (0.000189) test_link=: .: (0.000202) test_name=: .: (0.000177) test_reaction=: .: (0.000225) test_type=: .: (0.000447) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000542) test_category=: .: (0.000269) test_entry_id=: .: (0.000223) test_fgcolor=: .: (0.000261) test_height=: .: (0.000253) test_label=: .: (0.000231) test_pathway=: .: (0.000215) test_shape=: .: (0.000233) test_width=: .: (0.000252) test_x=: .: (0.000485) test_y=: .: (0.000236) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.013258) test_coords: .: (0.012969) test_fgcolor: .: (0.013304) test_height: .: (0.012698) test_name: .: (0.013515) test_type: .: (0.013103) test_width: .: (0.012595) test_x: .: (0.013101) test_y: .: (0.014444) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.010978) test_coords: .: (0.010773) test_fgcolor: .: (0.010581) test_height: .: (0.010685) test_name: .: (0.010427) test_type: .: (0.010460) test_width: .: (0.010385) test_x: .: (0.010279) test_y: .: (0.011987) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000402) test_coords=: .: (0.000189) test_fgcolor=: .: (0.000178) test_height=: .: (0.000199) test_name=: .: (0.000216) test_type=: .: (0.000201) test_width=: .: (0.000410) test_x=: .: (0.000222) test_y=: .: (0.000202) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.013247) test_entries__size: .: (0.012152) test_image: .: (0.010882) test_link: .: (0.010880) test_name: .: (0.012114) test_number: .: (0.011187) test_org: .: (0.010879) test_reactions=: .: (0.011026) test_reactions__size: .: (0.010639) test_relations=: .: (0.010487) test_relations__size: .: (0.010566) test_title: .: (0.010365) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.020688) test_name: .: (0.020181) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000377) test_initialize_0: .: (0.000115) test_initialize_1: .: (0.000251) test_initialize_2: .: (0.000121) test_name=: .: (0.000150) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.010522) test_name: .: (0.010334) test_products: .: (0.012002) test_substrates: .: (0.011654) test_type: .: (0.013264) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000451) test_name=: .: (0.000193) test_products=: .: (0.000201) test_substraces=: .: (0.000185) test_type=: .: (0.000187) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000373) test_entry_id=: .: (0.000224) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.013115) test_entry2: .: (0.010714) test_name: .: (0.012347) test_type: .: (0.010931) test_value: .: (0.012176) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000275) test_node1=: .: (0.000188) test_node2=: .: (0.000188) test_rel=: .: (0.000212) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000267) test_entry2=: .: (0.000164) test_name=: .: (0.000158) test_type=: .: (0.000155) test_value=: .: (0.000153) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.023942) test_name: .: (0.024940) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000380) test_initialize_0: .: (0.000150) test_initialize_1: .: (0.000169) test_initialize_2: .: (0.000144) test_name=: .: (0.000235) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000525) test_initialize_0: .: (0.000158) test_initialize_1: .: (0.000139) test_initialize_2: .: (0.000165) test_name=: .: (0.000176) Bio::TestKeggModule: test_compounds: .: (0.001336) test_compounds_as_hash: .: (0.000444) test_compounds_as_strings: .: (0.000356) test_definition: .: (0.000362) test_entry_id: .: (0.000297) test_keggclass: .: (0.000353) test_name: .: (0.000319) test_new: .: (0.000309) test_orthologs: .: (0.000424) test_orthologs_as_array: .: (0.000455) test_orthologs_as_hash: .: (0.000438) test_orthologs_as_strings: .: (0.000375) test_pathways: .: (0.000243) test_pathways_as_hash: .: (0.000228) test_pathways_as_strings: .: (0.000412) test_reactions: .: (0.000435) test_reactions_as_hash: .: (0.000376) test_reactions_as_strings: .: (0.000362) Bio::TestKeggOrthology: test_dblinks: .: (0.002457) test_dblinks_as_hash: .: (0.000686) test_dblinks_as_strings: .: (0.000611) test_definition: .: (0.000770) test_entry_id: .: (0.001229) test_genes_as_hash: .: (0.036573) test_genes_as_strings: .: (0.006263) test_keggclass: .: (0.000830) test_keggclasses: .: (0.000696) test_modules: .: (0.000587) test_modules_as_hash: .: (0.000566) test_modules_as_strings: .: (0.000770) test_name: .: (0.000597) test_names: .: (0.000538) test_pathways_as_strings: .: (0.000563) test_pathways_in_keggclass: .: (0.000782) test_references: .: (0.000750) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.002242) test_compounds_as_strings: .: (0.000612) test_dblinks_as_hash: .: (0.000286) test_dblinks_as_strings: .: (0.000299) test_description: .: (0.000377) test_diseases_as_hash: .: (0.000320) test_diseases_as_strings: .: (0.000317) test_entry_id: .: (0.000339) test_enzymes_as_strings: .: (0.000313) test_genes_as_hash: .: (0.000253) test_genes_as_strings: .: (0.000283) test_keggclass: .: (0.000624) test_ko_pathway: .: (0.000346) test_modules_as_hash: .: (0.000403) test_modules_as_strings: .: (0.000368) test_name: .: (0.000336) test_organism: .: (0.000261) test_orthologs_as_hash: .: (0.000239) test_orthologs_as_strings: .: (0.000249) test_pathways_as_hash: .: (0.000276) test_pathways_as_strings: .: (0.000342) test_reactions_as_hash: .: (0.000309) test_reactions_as_strings: .: (0.000254) test_references: .: (0.000241) test_rel_pathways_as_hash: .: (0.000302) test_rel_pathways_as_strings: .: (0.000260) Bio::TestKeggReaction: test_definition: .: (0.001209) test_entry_id: .: (0.000395) test_enzymes: .: (0.000554) test_equation: .: (0.000390) test_name: .: (0.000399) test_orthologs_as_hash: .: (0.000390) test_orthologs_as_strings: .: (0.000356) test_pathways_as_hash: .: (0.000429) test_pathways_as_strings: .: (0.000338) test_rpairs_as_hash: .: (0.000625) test_rpairs_as_strings: .: (0.000311) test_rpairs_as_tokens: .: (0.000315) Bio::TestLasergene: test_methods: .: (0.010358) Bio::TestLocations: test_complement: .: (0.000453) test_hat: .: (0.000227) test_normal: .: (0.000231) test_replace_single_base: .: (0.000186) test_should_not_modify_argument: .: (0.000436) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.005298) test_locations_to_s: .: (0.002311) Bio::TestMEDLINE: test_authors: .: (0.001306) test_authors_with_last_name_all_caps: .: (0.000164) test_authors_with_suffix: .: (0.000185) Bio::TestMEDLINE_20146148: test_ab: .: (0.001511) test_ad: .: (0.000577) test_au: .: (0.000573) test_authors: .: (0.000795) test_doi: .: (0.000565) test_dp: .: (0.000464) test_ip: .: (0.000565) test_mh: .: (0.000824) test_pages: .: (0.000625) test_pg: .: (0.000495) test_pii: .: (0.000433) test_pmid: .: (0.000681) test_pt: .: (0.000579) test_reference: .: (0.000766) test_self_new: .: (0.000460) test_so: .: (0.000659) test_ta: .: (0.000590) test_ti: .: (0.000589) test_ui: .: (0.000600) test_vi: .: (0.000590) test_year: .: (0.000741) Bio::TestMapSimple: test_attributes: .: (0.000527) Bio::TestMapping: test_add_mapping_as_map: .: (0.000482) test_add_mapping_as_marker: .: (0.000199) test_contains_marker?: .: (0.000156) test_mapped_to?: .: (0.000143) test_mapping_location_comparison: .: (0.000390) test_mappings_as_map_each: .: (0.000138) test_mappings_as_marker_each: .: (0.000504) test_mappings_on: .: (0.000253) test_multiple_mappings_between_same_marker_and_map: .: (0.000559) test_positions_on: .: (0.000319) test_raise_error_kind_of: .: (0.000532) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000476) test_check_options_with_invalid_opts: .: (0.000263) test_check_options_with_valid_opts: .: (0.000283) test_command_to_be_run: .: (0.000276) test_config_defaults: .: (0.000250) test_minimal_config: .: (0.000257) test_more_config: .: (0.000196) test_run: .: (0.000196) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.001307) test_report_has_motifs: .: (0.000356) Bio::TestModel: test_addChain: .: (0.000339) test_comp: .: (0.000183) test_each: .: (0.000185) test_each_chain: .: (0.000185) test_inspect: .: (0.000171) test_rehash: .: (0.000120) test_square_brace: .: (0.000151) test_to_s: .: (0.000143) Bio::TestModelFinder: test_find_model: .: (0.000283) Bio::TestMotif: test_creation_and_attributes: .: (0.000393) test_length: .: (0.000153) Bio::TestMyGraph: test_cliquishness: .: (0.000750) Bio::TestNA: test_accessor: .: (0.000230) test_na: .: (0.000105) test_name: .: (0.000251) test_names: .: (0.000106) test_to_re: .: (0.000288) test_weight: .: (0.000128) test_weight_rna: .: (0.000153) Bio::TestNAConstants: test_NAMES: .: (0.000301) test_NAMES_1_to_name: .: (0.000109) test_WEIGHT: .: (0.000165) Bio::TestNATranslate: test_translate: .: (0.000478) test_translate_1: .: (0.000231) test_translate_2: .: (0.000173) test_translate_3: .: (0.000149) test_translate_4: .: (0.000246) test_translate_5: .: (0.000291) test_translate_6: .: (0.000186) Bio::TestNCBIDB: test_fetch: .: (0.000398) test_p_entry2hash: .: (0.000109) test_p_subtag2array: .: (0.000134) test_p_toptag2array: .: (0.000134) Bio::TestNewick: test_reparse: .: (0.001857) test_reparse_before_lazy_parsing: .: (0.000852) test_string_tree: .: (0.001228) Bio::TestNewick2: test_string_tree: .: (0.000865) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000259) test_parse_newick_leaf: .: (0.000303) test_parse_newick_tokenize: .: (0.000661) Bio::TestNexus: test_nexus: .: (0.017652) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000422) test_uncapitalized_letter_Q32725_9POAL: .: (0.000206) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000331) test_load_parameters: .: (0.000178) test_parameters: .: (0.000109) test_set_default_parameters: .: (0.000139) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.001393) test_expected_parameters_set_in_control_file: .: (0.000935) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000510) test_new_with_parameters: .: (0.000212) test_new_with_two_argument: .: (0.000200) test_new_without_argument: .: (0.000161) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.002682) test_rates_hundred_and_fiftieth_position: .: (0.001834) test_rates_last_position: .: (0.002077) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.013814) test_tree: .: (0.013046) test_tree_length: .: (0.013542) test_tree_log_likelihood: .: (0.013499) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.001499) test_parameters_should_be_loaded_from_control: .: (0.000480) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.002244) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.001139) test_dN_dS: .: (0.000405) test_kappa: .: (0.000333) test_lnL: .: (0.000332) test_m3_classes: .: (0.000488) test_m3_lnL: .: (0.000284) test_m3_to_s: .: (0.000334) test_m3_tree: .: (0.001033) test_omega: .: (0.000374) test_to_s: .: (0.000492) test_tree: .: (0.000900) test_tree_length: .: (0.000310) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000829) test_p: .: (0.000658) test_position: .: (0.000718) test_probability: .: (0.000535) test_w: .: (0.000631) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.001020) test_graph_omega: .: (0.000651) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000455) test_footer: .: (0.000340) test_header: .: (0.000315) test_initialize: .: (0.000323) test_models: .: (0.000569) test_nb_sites: .: (0.001089) test_num_codons: .: (0.000308) test_num_sequences: .: (0.000335) test_significant: .: (0.000345) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.001448) test_nb_sites: .: (0.000851) test_significant: .: (0.000357) test_sites: .: (0.002193) Bio::TestPDB: test_accession: .: (0.001694) test_addModel: .: (0.001604) test_authors: .: (0.001334) test_bracket: .: (0.001682) test_classification: .: (0.001308) test_dbref: .: (0.001570) test_definition: .: (0.001173) test_each: .: (0.001168) test_each_model: .: (0.001398) test_entry_id: .: (0.001048) test_helix: .: (0.001690) test_inspect: .: (0.001503) test_jrnl: .: (0.001202) test_keywords: .: (0.012305) test_record: .: (0.001405) test_remark: .: (0.001925) test_seqres: .: (0.001712) test_sheet: .: (0.001872) test_ssbond: .: (0.001562) test_to_s: .: (0.001882) test_turn: .: (0.001687) test_version: .: (0.001289) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000460) test_U12: .: (0.000197) test_U13: .: (0.000202) test_U22: .: (0.000582) test_U23: .: (0.000258) test_U33: .: (0.000228) test_altLoc: .: (0.000269) test_chainID: .: (0.000268) test_charge: .: (0.000277) test_element: .: (0.000271) test_iCode: .: (0.000266) test_name: .: (0.000231) test_resName: .: (0.000269) test_resSeq: .: (0.000270) test_segID: .: (0.000248) test_serial: .: (0.000240) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000710) test_anisou: .: (0.000162) test_chainID: .: (0.000162) test_charge: .: (0.000158) test_comparable: .: (0.000246) test_do_parse: .: (0.000217) test_element: .: (0.000214) test_iCode: .: (0.000204) test_name: .: (0.000202) test_occupancy: .: (0.000289) test_original_data: .: (0.000207) test_record_name: .: (0.000198) test_resName: .: (0.000171) test_resSeq: .: (0.000221) test_residue: .: (0.000162) test_segID: .: (0.000586) test_serial: .: (0.000203) test_sigatm: .: (0.000244) test_tempFactor: .: (0.000225) test_ter: .: (0.000202) test_to_a: .: (0.000205) test_to_s: .: (0.000215) test_x: .: (0.000192) test_xyz: .: (0.000341) test_y: .: (0.000207) test_z: .: (0.000249) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000878) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000313) test_idcode: .: (0.000162) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000433) test_chainID2: .: (0.000235) test_icode1: .: (0.000240) test_icode2: .: (0.000252) test_measure: .: (0.000195) test_modNum: .: (0.000192) test_pep1: .: (0.000189) test_pep2: .: (0.000180) test_seqNum1: .: (0.000207) test_seqNum2: .: (0.000544) test_serNum: .: (0.000245) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000405) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000416) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000394) test_alpha: .: (0.000174) test_b: .: (0.000206) test_beta: .: (0.000183) test_c: .: (0.000210) test_gamma: .: (0.000197) test_sGroup: .: (0.000201) test_z: .: (0.000221) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000841) test_database: .: (0.000215) test_dbAccession: .: (0.000221) test_dbIdCode: .: (0.000270) test_dbseqBegin: .: (0.000304) test_dbseqEnd: .: (0.000323) test_idCode: .: (0.000278) test_idbnsBeg: .: (0.000307) test_insertBegin: .: (0.000276) test_insertEnd: .: (0.000279) test_seqBegin: .: (0.000288) test_seqEnd: .: (0.000800) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000447) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000276) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000281) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000306) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000379) test_depDate: .: (0.000227) test_idCode: .: (0.000202) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000447) test_hetID: .: (0.000238) test_iCode: .: (0.000615) test_numHetAtoms: .: (0.000198) test_seqNum: .: (0.000221) test_text: .: (0.000228) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000646) test_anisou: .: (0.000195) test_chainID: .: (0.000176) test_charge: .: (0.000184) test_comparable: .: (0.000192) test_do_parse: .: (0.000160) test_element: .: (0.000211) test_iCode: .: (0.000199) test_name: .: (0.000171) test_occupancy: .: (0.000596) test_original_data: .: (0.000201) test_record_name: .: (0.000207) test_resName: .: (0.000180) test_resSeq: .: (0.000152) test_residue: .: (0.000160) test_segID: .: (0.000173) test_serial: .: (0.000147) test_sigatm: .: (0.000147) test_tempFactor: .: (0.000250) test_ter: .: (0.000204) test_to_a: .: (0.000169) test_to_s: .: (0.000252) test_x: .: (0.000215) test_xyz: .: (0.000491) test_y: .: (0.000196) test_z: .: (0.000182) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000758) test_ChainH: .: (0.000316) test_ICode1: .: (0.000299) test_altLoc1: .: (0.000321) test_altLoc2: .: (0.000328) test_altLocH: .: (0.000312) test_chainID2: .: (0.000282) test_iCode2: .: (0.000269) test_iCodeH: .: (0.000342) test_name1: .: (0.000255) test_name2: .: (0.000259) test_nameH: .: (0.000228) test_resName1: .: (0.000228) test_resName2: .: (0.000225) test_resSeq1: .: (0.000237) test_resSeq2: .: (0.000270) test_resSeqH: .: (0.000317) test_sym1: .: (0.000282) test_sym2: .: (0.000275) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000457) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000489) test_altLoc2: .: (0.000294) test_chainID1: .: (0.000272) test_chainID2: .: (0.000274) test_iCode1: .: (0.000216) test_iCode2: .: (0.000202) test_name1: .: (0.000225) test_name2: .: (0.000204) test_resName1: .: (0.000200) test_resName2: .: (0.000238) test_resSeq1: .: (0.000273) test_resSeq2: .: (0.000237) test_sym1: .: (0.000710) test_sym2: .: (0.000256) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000493) test_numCoord: .: (0.000235) test_numHelix: .: (0.000198) test_numHet: .: (0.000197) test_numRemark: .: (0.000242) test_numSeq: .: (0.000214) test_numSheet: .: (0.000214) test_numSite: .: (0.000195) test_numTer: .: (0.000230) test_numTurn: .: (0.000214) test_numXform: .: (0.000171) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000362) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000384) test_comment: .: (0.000198) test_iCode: .: (0.000234) test_idCode: .: (0.000243) test_resName: .: (0.000187) test_seqNum: .: (0.000173) test_stdRes: .: (0.000171) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000325) test_Mn2: .: (0.000192) test_Mn3: .: (0.000210) test_Vn: .: (0.000207) test_iGiven: .: (0.000186) test_serial: .: (0.000155) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000300) test_Mn2: .: (0.000170) test_Mn3: .: (0.000173) test_Vn: .: (0.000199) test_iGiven: .: (0.000214) test_serial: .: (0.000188) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000416) test_Mn2: .: (0.000197) test_Mn3: .: (0.000209) test_Vn: .: (0.000216) test_iGiven: .: (0.000168) test_serial: .: (0.000215) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000427) test_rIdCode: .: (0.000216) test_repDate: .: (0.000188) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000649) test_On2: .: (0.000153) test_On3: .: (0.000160) test_Tn: .: (0.000153) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000375) test_modId: .: (0.000227) test_modNum: .: (0.000201) test_modType: .: (0.000191) test_record: .: (0.000223) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000396) test_text: .: (0.000213) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000400) test_Sn2: .: (0.000192) test_Sn3: .: (0.000177) test_Un: .: (0.000205) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000297) test_Sn2: .: (0.000159) test_Sn3: .: (0.000153) test_Un: .: (0.000151) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000354) test_Sn2: .: (0.000240) test_Sn3: .: (0.000166) test_Un: .: (0.000229) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000485) test_conflict: .: (0.000272) test_database: .: (0.000215) test_dbIdCode: .: (0.000282) test_dbRes: .: (0.000229) test_dbSeq: .: (0.000243) test_iCode: .: (0.000637) test_idCode: .: (0.000260) test_resName: .: (0.000214) test_seqNum: .: (0.000233) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000381) test_numRes: .: (0.000222) test_resName: .: (0.000273) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000498) test_curChainId: .: (0.000289) test_curICode: .: (0.000319) test_curResName: .: (0.000327) test_curResSeq: .: (0.000488) test_endChainID: .: (0.000250) test_endICode: .: (0.000262) test_endResName: .: (0.000284) test_endSeqNum: .: (0.000277) test_initChainID: .: (0.000303) test_initICode: .: (0.000278) test_initResName: .: (0.000228) test_initSeqNum: .: (0.000226) test_numStrands: .: (0.000236) test_prevAtom: .: (0.000290) test_prevChainId: .: (0.000311) test_prevICode: .: (0.000255) test_prevResName: .: (0.000281) test_prevResSeq: .: (0.000311) test_sense: .: (0.000289) test_sheetID: .: (0.000305) test_strand: .: (0.000250) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000607) test_chainID: .: (0.000648) test_charge: .: (0.000220) test_element: .: (0.000198) test_iCode: .: (0.000192) test_name: .: (0.000201) test_resName: .: (0.000212) test_resSeq: .: (0.000257) test_segID: .: (0.000254) test_serial: .: (0.000227) test_sigOcc: .: (0.000267) test_sigTemp: .: (0.000258) test_sigX: .: (0.000282) test_sigY: .: (0.000278) test_sigZ: .: (0.000260) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000890) test_SigmaU12: .: (0.000271) test_SigmaU13: .: (0.000265) test_SigmaU22: .: (0.000213) test_SigmaU23: .: (0.000196) test_SigmaU33: .: (0.000194) test_altLoc: .: (0.000197) test_chainID: .: (0.000196) test_charge: .: (0.000229) test_element: .: (0.000260) test_iCode: .: (0.000240) test_name: .: (0.000265) test_resName: .: (0.000613) test_resSeq: .: (0.000276) test_segID: .: (0.000268) test_serial: .: (0.000217) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000552) test_chainID2: .: (0.000258) test_chainID3: .: (0.000270) test_chainID4: .: (0.000272) test_iCode1: .: (0.000251) test_iCode2: .: (0.000305) test_iCode3: .: (0.000271) test_iCode4: .: (0.000532) test_numRes: .: (0.000279) test_resName1: .: (0.000233) test_resName2: .: (0.000252) test_resName3: .: (0.000282) test_resName4: .: (0.000280) test_seq1: .: (0.000312) test_seq2: .: (0.000214) test_seq3: .: (0.000214) test_seq4: .: (0.000208) test_seqNum: .: (0.000203) test_siteID: .: (0.000268) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000834) test_altLoc2: .: (0.000190) test_atom1: .: (0.000180) test_atom2: .: (0.000193) test_chainID1: .: (0.000182) test_chainID2: .: (0.000185) test_iCode1: .: (0.000241) test_iCode2: .: (0.000252) test_resName1: .: (0.000203) test_resName2: .: (0.000253) test_resSeq1: .: (0.000233) test_resSeq2: .: (0.000259) test_sym1: .: (0.000239) test_sym2: .: (0.000237) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000779) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000395) test_sIdCode: .: (0.000193) test_sprsdeDate: .: (0.000200) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000313) test_iCode: .: (0.000162) test_resName: .: (0.000170) test_resSeq: .: (0.000163) test_serial: .: (0.000204) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000375) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000383) test_t1: .: (0.000228) test_t2: .: (0.000224) test_t3: .: (0.000217) test_text: .: (0.000503) Bio::TestPROSITE: test_ac: .: (0.002672) test_cc: .: (0.002537) test_de: .: (0.002869) test_division: .: (0.002685) test_dr: .: (0.056282) test_dt: .: (0.012288) test_false_neg: .: (0.007223) test_false_pos: .: (0.011821) test_false_positive_sequences: .: (0.012429) test_list_falsenegative: .: (0.041086) test_list_falsepositive: .: (0.026370) test_list_potentialhit: .: (0.025560) test_list_truepositive: .: (0.026726) test_list_unknown: .: (0.024495) test_list_xref: .: (0.025381) test_ma: .: (0.002586) test_max_repeat: .: (0.003005) test_name: .: (0.002773) test_nr: .: (0.002930) test_pa: .: (0.002364) test_pa2re: .: (0.002472) test_partial: .: (0.002877) test_pdb_xref: .: (0.003492) test_pdoc_xref: .: (0.003430) test_positive: .: (0.003309) test_positive_hits: .: (0.002982) test_positive_sequences: .: (0.003662) test_release: .: (0.003732) test_ru: .: (0.003298) test_self_pa2re: .: (0.003137) test_site: .: (0.003413) test_skip_flag: .: (0.007918) test_swissprot_release_number: .: (0.003715) test_swissprot_release_sequences: .: (0.003863) test_taxon_range: .: (0.003511) test_total: .: (0.002725) test_total_hits: .: (0.003176) test_total_sequences: .: (0.003297) test_unknown: .: (0.003519) test_unknown_hits: .: (0.003282) test_unknown_sequences: .: (0.004002) Bio::TestPROSITEConst: test_delimiter: .: (0.000519) test_tagsize: .: (0.000256) Bio::TestPTS1: test_function_set: .: (0.000375) test_function_set_number_1: .: (0.000898) test_function_set_number_2: .: (0.000279) test_function_set_number_3: .: (0.000271) test_function_show: .: (0.000249) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000348) Bio::TestPTS1New: test_fungi: .: (0.000428) test_general: .: (0.000224) test_metazoa: .: (0.000225) Bio::TestQualifier: test_qualifier: .: (0.000312) test_value: .: (0.000188) Bio::TestREBASE: test_methods: .: (0.002637) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.002583) test_bit_score: .: (0.001677) test_evalue: .: (0.001479) test_gaps: .: (0.001055) test_hit_from: .: (0.001045) test_hit_to: .: (0.000906) test_hseq: .: (0.001099) test_identity: .: (0.001854) test_midline: .: (0.001137) test_percent_identity: .: (0.001036) test_positive: .: (0.000973) test_qseq: .: (0.001107) test_query_from: .: (0.001595) test_query_to: .: (0.001096) test_score: .: (0.000834) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.001167) test_hits_size: .: (0.003436) test_iterations_size: .: (0.001769) test_program: .: (0.000925) test_query_def: .: (0.002265) test_query_len: .: (0.002785) test_version: .: (0.000816) test_version_date: .: (0.000905) test_version_number: .: (0.000950) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.002109) test_definition: .: (0.001368) test_evalue: .: (0.001085) test_hsps_size: .: (0.000961) test_identity: .: (0.000974) test_lap_at: .: (0.001658) test_len: .: (0.000999) test_midline: .: (0.001032) test_overlap: .: (0.001097) test_query_end: .: (0.001575) test_query_seq: .: (0.001250) test_query_start: .: (0.000960) test_target_def: .: (0.000997) test_target_end: .: (0.001674) test_target_len: .: (0.001249) test_target_seq: .: (0.001122) test_target_start: .: (0.000946) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001000) test_get_entry: .: (0.001661) test_rewind: .: (0.000312) test_skip_leader: .: (0.000642) Bio::TestReference: test_abstract: .: (0.000465) test_affiliations: .: (0.000282) test_authors: .: (0.000197) test_format_bibitem: .: (0.000378) test_format_bibtex: .: (0.000476) test_format_bibtex_with_arguments: .: (0.000463) test_format_cell: .: (0.000312) test_format_current: .: (0.000252) test_format_endnote: .: (0.000258) test_format_general: .: (0.000717) test_format_genome_biol: .: (0.000367) test_format_genome_res: .: (0.000327) test_format_nar: .: (0.000250) test_format_nature: .: (0.000258) test_format_rd: .: (0.000254) test_format_science: .: (0.000304) test_format_trends: .: (0.000277) test_issue: .: (0.000234) test_journal: .: (0.000271) test_mesh: .: (0.000264) test_pages: .: (0.000248) test_pubmed: .: (0.000276) test_pubmed_url: .: (0.001093) test_url: .: (0.000269) test_volume: .: (0.000324) test_year: .: (0.000195) Bio::TestReference_noURL: test_format_endnote: .: (0.000453) test_url: .: (0.000253) Bio::TestReferences: test_append: .: (0.001051) test_each: .: (0.000316) Bio::TestRelation: test_comparison_operator: .: (0.000557) test_uniq: .: (0.000330) Bio::TestResidue: test_addAtom: .: (0.001330) test_each: .: (0.000416) test_each_atom: .: (0.000417) test_get_residue_id_from_atom: .: (0.000372) test_het_atom: .: (0.000368) test_iCode: .: (0.000384) test_inspect: .: (0.000439) test_resSeq: .: (0.000374) test_sort: .: (0.000424) test_square_bracket: .: (0.000893) test_to_s: .: (0.000507) test_update_resudue_id: .: (0.000362) Bio::TestResidueFinder: test_each_residue: .: (0.000526) test_find_residue: .: (0.000307) test_residues: .: (0.000376) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.214885) test_cut_from_bio_sequence_na: .: (0.050126) test_cut_without_permutations: .: (0.033320) test_view_ranges: .: (0.038951) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.002704) test_cuts_after_remove_incomplete_cuts: .: (0.001285) test_strands_for_display: .: (0.005361) test_strands_for_display_current: .: (0.001294) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000942) test_fragments_for_display_1: .: (0.001658) test_fragments_for_display_10: .: (0.001954) test_fragments_for_display_2: .: (0.001765) test_fragments_for_display_3: .: (0.002060) test_fragments_for_display_4: .: (0.001783) test_fragments_for_display_5: .: (0.001089) test_fragments_for_display_6: .: (0.001355) test_fragments_for_display_7: .: (0.000991) test_fragments_for_display_8: .: (0.001054) test_fragments_for_display_9: .: (0.001188) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000951) test_obj_3: .: (0.000571) test_obj_7: .: (0.000496) test_obj_z: .: (0.000514) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000756) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000583) test_bracket_eq: .: (0.000397) test_concat: .: (0.000498) test_delete: .: (0.000252) test_dup: .: (0.000335) test_each: .: (0.000388) test_eqeq: .: (0.000325) test_eqeq_false: .: (0.000231) test_eqeq_other: .: (0.000201) test_eqeq_self: .: (0.000199) test_include?: .: (0.000223) test_internal_data: .: (0.000282) test_internal_data_eq: .: (0.000315) test_length: .: (0.000289) test_ltlt: .: (0.000311) test_ltlt_larger: .: (0.000326) test_ltlt_middle: .: (0.000542) test_plus: .: (0.000338) test_plus_error: .: (0.000357) test_push: .: (0.000323) test_reverse_each: .: (0.000450) test_self_bracket: .: (0.000213) test_self_new: .: (0.000279) test_size: .: (0.000206) test_sort!: .: (0.000215) test_to_a: .: (0.000268) test_uniq!: .: (0.000301) test_unshift: .: (0.000337) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.008001) test_complement: .: (0.006671) test_complement_with_cut_symbols: .: (0.007182) test_cut_locations: .: (0.006872) test_cut_locations_in_enzyme_notation: .: (0.006603) test_primary: .: (0.006749) test_primary_with_cut_symbols: .: (0.007123) test_to_re: .: (0.007033) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.001736) test_align_with_cuts: .: (0.001390) test_argument_error: .: (0.001936) test_ds: .: (0.001268) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.001118) test_complement: .: (0.000487) test_contents: .: (0.000410) test_primary: .: (0.000390) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000730) test_complement: .: (0.000349) test_contents: .: (0.000346) test_primary: .: (0.000463) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000722) test_contents: .: (0.000378) test_primary: .: (0.000377) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000577) test_complement_to_array_index: .: (0.000530) test_complement_to_array_index_class: .: (0.000385) test_contents: .: (0.000303) test_primary: .: (0.000283) test_primary_to_array_index: .: (0.000520) test_primary_to_array_index_class: .: (0.000699) test_to_array_index: .: (0.000943) test_to_array_index_class: .: (0.000839) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000925) test_rebase: .: (0.000344) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001798) test_creation_with_no_cuts: .: (0.000985) test_cut_locations: .: (0.000730) test_cut_locations_in_enzyme_notation: .: (0.001092) test_orientation: .: (0.000697) test_pattern: .: (0.000757) test_pattern_palindromic?: .: (0.001084) test_stripped: .: (0.001106) test_to_re: .: (0.000750) test_with_cut_symbols: .: (0.000891) test_with_spaces: .: (0.001021) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.001560) test_creation_with_no_cuts: .: (0.001062) test_cut_locations: .: (0.001096) test_cut_locations_in_enzyme_notation: .: (0.000942) test_orientation: .: (0.000680) test_pattern: .: (0.001051) test_pattern_palindromic?: .: (0.001130) test_stripped: .: (0.000868) test_to_re: .: (0.000966) test_with_cut_symbols: .: (0.000917) test_with_spaces: .: (0.000921) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.001108) test_initialize_with_pattern: .: (0.000728) test_max: .: (0.000278) test_min: .: (0.006619) test_to_array_index: .: (0.000497) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000583) test_bracket_eq: .: (0.000293) test_concat: .: (0.000238) test_delete: .: (0.000214) test_dup: .: (0.000304) test_each: .: (0.000488) test_eqeq: .: (0.000326) test_eqeq_false: .: (0.000280) test_eqeq_other: .: (0.000268) test_eqeq_self: .: (0.000306) test_include?: .: (0.000607) test_internal_data_hash: .: (0.000283) test_internal_data_hash_eq: .: (0.000310) test_length: .: (0.000309) test_ltlt: .: (0.000219) test_ltlt_noeffect: .: (0.000212) test_plus: .: (0.000208) test_plus_error: .: (0.000352) test_private_push_element: .: (0.000303) test_private_push_element_intermediate: .: (0.000301) test_private_push_element_last: .: (0.000305) test_private_push_element_noeffect: .: (0.000301) test_private_sorted_keys: .: (0.000269) test_private_unshift_element: .: (0.000305) test_private_unshift_element_first: .: (0.000316) test_private_unshift_element_intermediate: .: (0.000259) test_private_unshift_element_noeffect: .: (0.000263) test_push: .: (0.000218) test_reverse_each: .: (0.000305) test_self_bracket: .: (0.000191) test_self_new: .: (0.000303) test_size: .: (0.000261) test_sort!: .: (0.000270) test_to_a: .: (0.000272) test_uniq!: .: (0.000279) test_unshift: .: (0.000298) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000549) test_left_padding: .: (0.000526) test_right_padding: .: (0.000296) test_strip_padding: .: (0.000308) Bio::TestSOFT: test_dataset: .: (0.015893) test_series: .: (0.012300) Bio::TestSOSUIReport: test_entry_id: .: (0.000587) test_prediction: .: (0.000270) test_tmh: .: (0.000271) test_tmhs: .: (0.000359) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000384) test_rs: .: (0.000190) Bio::TestSOSUITMH: test_grade: .: (0.000408) test_range: .: (0.000332) test_sequence: .: (0.000340) Bio::TestSampleGraph: test_bellman_ford: .: (0.001051) test_bfs_shortest_path: .: (0.000412) test_breadth_first_search: .: (0.000385) test_depth_first_search: .: (0.000673) test_dijkstra: .: (0.000442) test_dump_list: .: (0.000668) test_dump_matrix: .: (0.000674) test_extract_subgraph_by_label: .: (0.000466) test_extract_subgraph_by_list: .: (0.000505) test_extract_subgraph_retains_disconnected_nodes: .: (0.000407) test_small_world_aka_node_degree_histogram: .: (0.000377) test_to_matrix: .: (0.000783) test_to_matrix_fixed_index: .: (0.000568) test_undirected_cliquishness: .: (0.000777) Bio::TestScf_version_2: test_complement: .: (0.018617) test_seq: .: (0.016711) test_to_biosequence: .: (0.016830) Bio::TestScf_version_3: test_complement: .: (0.052001) test_seq: .: (0.047965) test_to_biosequence: .: (0.047850) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000507) test_AA_new_sequence_all_legal_symbols: .: (0.000252) test_AA_new_sequence_removes_whitespace: .: (0.000253) test_AA_new_sequence_upcases_symbols: .: (0.000270) test_DNA_new_blank_sequence: .: (0.000263) test_DNA_new_sequence_downcases_symbols: .: (0.000282) test_DNA_new_sequence_removes_whitespace: .: (0.000229) test_NA_randomize_with_counts: .: (0.001606) test_NA_randomize_with_counts_and_block: .: (0.001683) test_RNA_new_sequence: .: (0.000273) test_ambiguous_dna_sequence_complement: .: (0.000297) test_ambiguous_rna_sequence_complement: .: (0.000277) test_amino_acid_codes: .: (0.000370) test_amino_acid_molecular_weight: .: (0.000407) test_amino_acid_names: .: (0.000246) test_amino_acid_randomize_can_be_chained: .: (0.002081) test_amino_acid_randomize_has_same_composition: .: (0.000998) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.001383) test_dna_composition: .: (0.000358) test_dna_gc_percent: .: (0.000331) test_dna_molecular_weight: .: (0.000436) test_dna_pikachu: .: (0.000300) test_dna_sequence_complement: .: (0.000252) test_dna_sequence_translate: .: (0.000764) test_dna_to_re: .: (0.000336) test_element_reference_operator_with_one_argument: .: (0.000201) test_element_reference_operator_with_two_arguments: .: (0.000195) test_invalid_nucleic_acid_illegal_bases: .: (0.000260) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000343) test_nucleic_acid_names: .: (0.000539) test_randomize_dna_can_be_chained: .: (0.000778) test_randomize_dna_retains_composition: .: (0.000600) test_randomize_dna_with_block: .: (0.000608) test_rna_composition: .: (0.000289) test_rna_gc_percent: .: (0.000317) test_rna_molecular_weight: .: (0.000530) test_rna_pikachu: .: (0.000209) test_rna_sequence_complement: .: (0.000232) test_rna_sequence_translate: .: (0.000725) test_rna_to_re: .: (0.000418) test_total: .: (0.000292) test_two_consecutive_dna_randomizations_not_equal: .: (0.000572) test_valid_dna_sequence_illegal_bases: .: (0.000244) Bio::TestSequenceAA: test_codes: .: (0.000499) test_molecular_weight: .: (0.000465) test_names: .: (0.000347) test_to_re: .: (0.000368) test_to_s: .: (0.000198) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000560) Bio::TestSequenceAANew: test_new: .: (0.000353) test_new_n: .: (0.000270) test_new_r: .: (0.000200) test_new_t: .: (0.000206) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000441) test_concat: .: (0.000424) test_push: .: (0.000211) test_seq: .: (0.000183) test_splicing: .: (0.000330) test_sum: .: (0.000184) test_to_s: .: (0.000212) test_to_str: .: (0.000250) test_total: .: (0.000225) test_window_search: .: (0.000639) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000431) test_normalize_A: .: (0.000235) test_normalize_a: .: (0.000269) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.001974) test_randomize_with_block: .: (0.007411) test_randomize_with_hash: .: (0.002416) test_randomize_with_hash_block: .: (0.016880) 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' =============================================================================== : (0.002101) 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' =============================================================================== : (0.002273) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000563) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000279) test_subseq_returns_subsequence: .: (0.000233) test_to_s_returns_self_as_string: .: (0.000271) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000431) test_window_search_with_width_3_step_two_with_residual: .: (0.000740) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000495) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000391) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000569) test_na_self_randomize: .: (0.000384) Bio::TestSequenceDBLink: test_database: .: (0.000418) test_id: .: (0.000236) test_secondary_ids: .: (0.000189) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000740) test_parse_uniprot_DR_line: .: (0.000330) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.001409) test_output_width_35: .: (0.001128) test_output_width_nil: .: (0.000679) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000906) test_output_after_adding_sequence: .: (0.000606) test_output_after_truncating_sequence: .: (0.000836) test_output_from_error_probabilities: .: (0.006702) test_output_width45: .: (0.000530) test_output_with_converting_score_phred2solexa: .: (0.001607) test_output_with_converting_score_solexa2phred: .: (0.000651) test_output_with_default_score: .: (0.000440) Bio::TestSequenceMasker: test_mask: .: (0.001007) test_mask_with_enumerator: .: (0.000410) test_mask_with_enumerator_empty_mask_char: .: (0.000401) test_mask_with_enumerator_excess: .: (0.001051) test_mask_with_enumerator_longer_mask_char: .: (0.000376) test_mask_with_enumerator_shorter: .: (0.000449) test_mask_with_error_probability: .: (0.000371) test_mask_with_quality_score: .: (0.000631) Bio::TestSequenceNA: test_at_content: .: (0.000862) test_at_skew: .: (0.000608) test_codon_usage: .: (0.000258) test_complement: .: (0.000224) test_dna: .: (0.000266) test_dna!: .: (0.000264) test_forward_complement: .: (0.000370) test_gc_content: .: (0.000731) test_gc_percent: .: (0.000318) test_gc_skew: .: (0.000763) test_iliegal_bases: .: (0.000252) test_molecular_weight: .: (0.000349) test_names: .: (0.000351) test_reverse_complement: .: (0.000402) test_rna: .: (0.000247) test_rna!: .: (0.000255) test_splicing: .: (0.000391) test_to_re: .: (0.000407) test_to_s: .: (0.000197) Bio::TestSequenceNACommon: test_composition: .: (0.000432) test_concat: .: (0.000247) test_push: .: (0.000255) test_seq: .: (0.000242) test_splicing: .: (0.000404) test_sum: .: (0.000268) test_to_s: .: (0.000290) test_to_str: .: (0.000245) test_total: .: (0.000241) test_window_search: .: (0.000831) Bio::TestSequenceNANew: test_new: .: (0.000376) test_new_n: .: (0.000199) test_new_r: .: (0.000189) test_new_t: .: (0.000224) Bio::TestSequenceNATranslation: test_translate: .: (0.000788) test_translate_0: .: (0.001513) test_translate_1: .: (0.000458) test_translate_2: .: (0.000754) test_translate_3: .: (0.000502) test_translate_4: .: (0.000506) test_translate_5: .: (0.000393) test_translate_6: .: (0.000451) test_translate_7: .: (0.000905) test_translate_given_codon_table: .: (0.168173) test_translate_n1: .: (0.001023) test_translate_n2: .: (0.000815) test_translate_n3: .: (0.000891) test_translate_unknown_o: .: (0.000533) test_translate_unknown_x: .: (0.000605) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000497) test_convert_scores_from_phred_to_solexa: .: (0.000904) test_convert_scores_from_solexa_to_phred: .: (0.000774) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000488) test_convert_scores_from_phred: .: (0.000263) test_convert_scores_from_phred_to_solexa: .: (0.000987) test_convert_scores_from_solexa: .: (0.000998) test_convert_scores_from_solexa_to_phred: .: (0.000492) test_convert_scores_to_phred: .: (0.000218) test_convert_scores_to_solexa: .: (0.001181) test_p2q: .: (0.000436) test_phred_p2q: .: (0.000396) test_phred_q2p: .: (0.010417) test_q2p: .: (0.009906) test_quality_score_type: .: (0.000315) test_self_convert_scores_to_solexa: .: (0.001408) test_self_p2q: .: (0.000399) test_self_q2p: .: (0.010058) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000476) test_convert_scores_from_phred: .: (0.001093) test_convert_scores_from_phred_to_solexa: .: (0.000752) test_convert_scores_from_solexa: .: (0.000257) test_convert_scores_from_solexa_to_phred: .: (0.000673) test_convert_scores_to_phred: .: (0.000361) test_convert_scores_to_solexa: .: (0.000205) test_p2q: .: (0.000480) test_q2p: .: (0.010987) test_quality_score_type: .: (0.000227) test_self_convert_scores_to_phred: .: (0.000391) test_self_p2q: .: (0.000439) test_self_q2p: .: (0.011435) test_solexa_p2q: .: (0.000435) test_solexa_q2p: .: (0.010765) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000602) test_center: .: (0.000248) test_chomp: .: (0.000262) test_chop: .: (0.000271) test_delete: .: (0.000293) test_delete_prefix: .: (0.000307) test_delete_suffix: .: (0.000284) test_downcase: .: (0.000287) test_each_char: .: (0.000455) test_each_char_enum: .: (0.000384) test_each_grapheme_cluster: .: (0.000841) test_each_grapheme_cluster_enum: .: (0.000406) test_each_line: .: (0.000393) test_each_line_enum: .: (0.000355) test_gsub: .: (0.000272) test_gsub_with_block: .: (0.000904) test_ljust: .: (0.000345) test_lstrip: .: (0.000339) test_multiply: .: (0.000280) test_next: .: (0.000219) test_reverse: .: (0.000214) test_rjust: .: (0.000235) test_rstrip: .: (0.000257) test_slice: .: (0.000357) test_slice2: .: (0.000234) test_split: .: (0.000294) test_squeeze: .: (0.000221) test_strip: .: (0.000211) test_sub: .: (0.000299) test_sub_with_block: .: (0.000517) test_succ: .: (0.000248) test_swapcase: .: (0.000325) test_tr: .: (0.000326) test_tr_s: .: (0.000275) test_upcase: .: (0.000335) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000825) test_partition_nomatch: .: (0.000282) test_partition_sep_TSeq: .: (0.000265) test_partition_sep_regexp: .: (0.000284) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000574) test_rpartition_nomatch: .: (0.000315) test_rpartition_sep_TSeq: .: (0.000373) test_rpartition_sep_regexp: .: (0.000360) Bio::TestShRNA: test_blocK_it: .: (0.045049) test_blocK_it_: .: (0.041470) test_blocK_it_BLOCK_IT: .: (0.040942) test_blocK_it_BLOCK_iT: .: (0.042952) test_blocK_it_piGene: .: (0.041168) test_bottom_strand: .: (0.041546) test_bottom_strand_class: .: (0.041852) test_bottom_strand_nil: .: (0.042598) test_design: .: (0.041351) test_design_BLOCK_IT: .: (0.040568) test_report: .: (0.043973) test_report_before_design: .: (0.040683) test_top_strand: .: (0.043120) test_top_strand_class: .: (0.052447) test_top_strand_nil: .: (0.049977) Bio::TestShRNANew: test_new: .: (0.000897) Bio::TestSiRNA: test_antisense_size: .: (0.000408) test_design: .: (0.045139) test_design_reynolds: .: (0.059166) test_design_uitei: .: (0.048213) test_max_gc_percent: .: (0.000235) test_min_gc_percent: .: (0.000209) test_reynolds: .: (0.079222) test_reynolds?: .: (0.000328) test_uitei: .: (0.047323) test_uitei?: .: (0.000392) Bio::TestSiRNANew: test_new: .: (0.000729) Bio::TestSiRNAPair: test_antisense: .: (0.042500) test_gc_percent: .: (0.042566) test_report: .: (0.045481) test_rule: .: (0.044865) test_sense: .: (0.042796) test_start: .: (0.042826) test_stop: .: (0.044817) test_target: .: (0.043849) Bio::TestSiRNAPairNew: test_new: .: (0.000876) Bio::TestSim4Report: test_all_hits: .: (0.004232) test_each: .: (0.000876) test_each_hit: .: (0.000552) test_hits: .: (0.000458) test_num_hits: .: (0.000405) test_query_def: .: (0.000420) test_query_id: .: (0.000355) test_query_len: .: (0.000327) test_seq1: .: (0.000474) Bio::TestSim4Report2: test_all_hits: .: (0.001226) test_each: .: (0.000378) test_each_hit: .: (0.000391) test_hits: .: (0.000736) test_num_hits: .: (0.000391) test_query_def: .: (0.000277) test_query_id: .: (0.000288) test_query_len: .: (0.000381) test_seq1: .: (0.000492) Bio::TestSim4Report4: test_all_hits: .: (0.001291) test_each: .: (0.000450) test_each_hit: .: (0.000456) test_hits: .: (0.000819) test_num_hits: .: (0.000374) test_query_def: .: (0.000296) test_query_id: .: (0.000309) test_query_len: .: (0.000442) test_seq1: .: (0.000535) Bio::TestSim4ReportHit: test_align: .: (0.000813) test_complement?: .: (0.000377) test_definition: .: (0.000380) test_each: .: (0.001115) test_exons: .: (0.000561) test_hit_id: .: (0.000314) test_hsps: .: (0.000606) test_introns: .: (0.000653) test_len: .: (0.000424) test_query_def: .: (0.000538) test_query_id: .: (0.000413) test_query_len: .: (0.000686) test_segmentpairs: .: (0.000976) test_seq1: .: (0.000468) test_seq2: .: (0.000393) test_target_def: .: (0.000389) test_target_id: .: (0.000420) test_target_len: .: (0.000377) Bio::TestSim4ReportHit2: test_align: .: (0.000645) test_complement?: .: (0.000293) test_definition: .: (0.000415) test_each: .: (0.000618) test_exons: .: (0.000490) test_hit_id: .: (0.000309) test_hsps: .: (0.000500) test_introns: .: (0.000603) test_len: .: (0.000709) test_query_def: .: (0.000464) test_query_id: .: (0.000370) test_query_len: .: (0.000444) test_segmentpairs: .: (0.000691) test_seq1: .: (0.000497) test_seq2: .: (0.000381) test_target_def: .: (0.000301) test_target_id: .: (0.000281) test_target_len: .: (0.000371) Bio::TestSim4ReportHit4: test_align: .: (0.001331) test_complement?: .: (0.000391) test_definition: .: (0.000397) test_each: .: (0.000835) test_exons: .: (0.000680) test_hit_id: .: (0.000382) test_hsps: .: (0.001136) test_introns: .: (0.000857) test_len: .: (0.000426) test_query_def: .: (0.000368) test_query_id: .: (0.000375) test_query_len: .: (0.000370) test_segmentpairs: .: (0.000914) test_seq1: .: (0.000510) test_seq2: .: (0.000765) test_target_def: .: (0.000424) test_target_id: .: (0.000355) test_target_len: .: (0.000419) Bio::TestSim4ReportSegment: test_from: .: (0.000372) test_self_new: .: (0.000261) test_seq: .: (0.000201) test_to: .: (0.000236) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000813) test_direction: .: (0.000395) test_hit_from: .: (0.000653) test_hit_to: .: (0.000585) test_hseq: .: (0.000513) test_midline: .: (0.000590) test_percent_identity: .: (0.000505) test_qseq: .: (0.000501) test_query_from: .: (0.000531) test_query_to: .: (0.000769) test_seq1: .: (0.000606) test_seq2: .: (0.000440) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000948) test_direction: .: (0.000531) test_hit_from: .: (0.000662) test_hit_to: .: (0.000621) test_hseq: .: (0.000476) test_midline: .: (0.000396) test_percent_identity: .: (0.000401) test_qseq: .: (0.000661) test_query_from: .: (0.000520) test_query_to: .: (0.000951) test_seq1: .: (0.000799) test_seq2: .: (0.000820) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000854) test_direction: .: (0.000657) test_hit_from: .: (0.001165) test_hit_to: .: (0.000933) test_hseq: .: (0.000547) test_midline: .: (0.000553) test_percent_identity: .: (0.000752) test_qseq: .: (0.000587) test_query_from: .: (0.000998) test_query_to: .: (0.000635) test_seq1: .: (0.000793) test_seq2: .: (0.000820) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.001860) test_direction: .: (0.000615) test_hit_from: .: (0.000660) test_hit_to: .: (0.000504) test_hseq: .: (0.000518) test_midline: .: (0.000678) test_percent_identity: .: (0.001940) test_qseq: .: (0.001182) test_query_from: .: (0.000705) test_query_to: .: (0.000688) test_seq1: .: (0.000713) test_seq2: .: (0.000902) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000992) test_direction: .: (0.000690) test_hit_from: .: (0.000628) test_hit_to: .: (0.000605) test_hseq: .: (0.000997) test_midline: .: (0.000565) test_percent_identity: .: (0.000498) test_qseq: .: (0.000808) test_query_from: .: (0.000670) test_query_to: .: (0.001025) test_seq1: .: (0.000787) test_seq2: .: (0.000731) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000709) test_direction: .: (0.000452) test_hit_from: .: (0.000465) test_hit_to: .: (0.000923) test_hseq: .: (0.000725) test_midline: .: (0.000459) test_percent_identity: .: (0.000391) test_qseq: .: (0.000516) test_query_from: .: (0.000559) test_query_to: .: (0.000396) test_seq1: .: (0.000777) test_seq2: .: (0.000658) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000787) test_direction: .: (0.000532) test_hit_from: .: (0.000525) test_hit_to: .: (0.000493) test_hseq: .: (0.000838) test_midline: .: (0.000516) test_percent_identity: .: (0.000382) test_qseq: .: (0.000492) test_query_from: .: (0.000564) test_query_to: .: (0.000644) test_seq1: .: (0.000997) test_seq2: .: (0.001210) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000535) test_entry_id: .: (0.000319) test_filename: .: (0.000222) test_len: .: (0.000249) test_self_new: .: (0.000249) test_self_parse: .: (0.000280) Bio::TestTMHMMReport: test_entry_id: .: (0.001303) test_exp_aas_in_tmhs: .: (0.000640) test_exp_first_60aa: .: (0.000594) test_helix: .: (0.000668) test_predicted_tmhs: .: (0.000596) test_query_len: .: (0.000607) test_tmhs: .: (0.000619) test_to_s: .: (0.005228) test_total_prob_of_N_in: .: (0.000486) Bio::TestTMHMMReport_reports: test_reports: .: (0.000609) Bio::TestTMHMMTMH: test_entry_id: .: (0.000948) test_pos: .: (0.001324) test_range: .: (0.000612) test_status: .: (0.000622) test_version: .: (0.000636) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000687) test_cutoff: .: (0.000483) test_entry_id: .: (0.000835) test_length: .: (0.000480) test_loc: .: (0.000451) test_name: .: (0.000494) test_networks: .: (0.000437) test_prediction: .: (0.000464) test_query_len: .: (0.000356) test_query_sequences: .: (0.000350) test_rc: .: (0.000335) test_version: .: (0.000462) Bio::TestTargetPReportConst: test_delimiter: .: (0.000838) test_rs: .: (0.000245) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000391) test_togows_access_wait: .: (2.005985) Bio::TestTogoWSREST: test_debug: .: (0.001008) test_debug_default: .: (0.000363) test_internal_http: .: (0.000625) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000413) test_entry: .: (0.000242) test_entry_database_list: .: (0.000233) test_new: .: (0.000586) test_new_with_uri_object: .: (0.000476) test_new_with_uri_string: .: (0.000415) test_retrieve: .: (0.000234) test_search: .: (0.000242) test_search_database_list: .: (0.000241) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000661) test_prepare_return_value: .: (0.000468) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.001224) Bio::TestTree: test_get_edge_distance: .: (0.000503) test_get_edge_distance_string: .: (0.000361) test_get_node_name: .: (0.000270) test_initialize: .: (0.000287) test_options: .: (0.000265) test_root: .: (0.000230) test_root=: .: (0.000267) Bio::TestTree2: test_add_edge: .: (0.000916) test_add_node: .: (0.000478) test_adjacency_matrix: .: (0.000834) test_adjacency_matrix_with_block: .: (0.000490) test_adjacent_nodes: .: (0.000500) test_adjacent_nodes_nonexistent: .: (0.000540) test_ancestors: .: (0.000417) test_children: .: (0.000365) test_clear: .: (0.000397) test_clear_node: .: (0.000472) test_clear_node_nonexistent: .: (0.000442) test_collect_edge!: .: (0.001073) test_collect_node!: .: (0.000618) test_concat: .: (0.000576) test_descendents: .: (0.000428) test_distance_matrix: .: (0.001088) test_each_edge: .: (0.000496) test_each_node: .: (0.000464) test_each_out_edge: .: (0.000806) test_each_out_edge_chimpanzee: .: (0.000442) test_each_out_edge_human: .: (0.000428) test_each_out_edge_mammals: .: (0.000498) test_each_out_edge_nonexistent: .: (0.000366) test_each_out_edge_primates: .: (0.000887) test_each_out_edge_rat: .: (0.000421) test_each_out_edge_rodents: .: (0.000550) test_edges: .: (0.000389) test_get_edge: .: (0.001163) test_get_edge_indirect: .: (0.000373) test_get_edge_merged: .: (0.000379) test_get_edge_nonexistent: .: (0.000366) test_get_node_bootstrap: .: (0.000346) test_get_node_bootstrap_string=: .: (0.000362) test_get_node_by_name: .: (0.000512) test_get_node_by_name_noexistent: .: (0.000343) test_include?: .: (0.000470) test_include_nonexistent: .: (0.000354) test_insert_node: .: (0.000513) test_leaves: .: (0.000441) test_leaves_noargs: .: (0.000361) test_lowest_common_ancestor: .: (0.000404) test_nodes: .: (0.000353) test_number_of_edges: .: (0.000377) test_number_of_nodes: .: (0.000340) test_out_degree: .: (0.000468) test_out_degree_nonexistent: .: (0.000358) test_out_edges: .: (0.000775) test_out_edges_mammals: .: (0.000780) test_out_edges_nonexistent: .: (0.000348) test_out_edges_primates: .: (0.000558) test_out_edges_rodents: .: (0.000544) test_parent: .: (0.000418) test_path: .: (0.000395) test_remove_edge: .: (0.000436) test_remove_edge_if: .: (0.000435) test_remove_edge_if_nothing_removed: .: (0.000865) test_remove_edge_nonexistent: .: (0.000417) test_remove_node: .: (0.000485) test_remove_node_if: .: (0.000383) test_remove_node_if_false: .: (0.000410) test_remove_node_nonexistent: .: (0.000396) test_remove_nonsense_nodes: .: (0.000411) test_subtree: .: (0.000503) test_subtree_with_all_paths: .: (0.000728) test_total_distance: .: (0.000387) Bio::TestTreeEdge: test_distance: .: (0.000882) test_distance=: .: (0.000321) test_distance_string: .: (0.000260) test_distance_string=: .: (0.000338) test_initialize: .: (0.000309) test_inspect: .: (0.000257) test_to_s: .: (0.000239) Bio::TestTreeNode: test_bootstrap: .: (0.000410) test_bootstrap=: .: (0.000317) test_bootstrap_string: .: (0.000233) test_bootstrap_string=: .: (0.000358) test_initialize: .: (0.000294) test_inspect: .: (0.000293) test_name: .: (0.000264) test_to_s: .: (0.000247) Bio::TestUniProt: test_gene_name: .: (0.010556) Bio::TestUniProtKB: test_ac: .: (0.010693) test_accession: .: (0.009730) test_cc: .: (0.011928) test_cc_alternative_products: .: (0.011557) test_cc_database: .: (0.012220) test_cc_mass_spectrometry: .: (0.011512) test_de: .: (0.016868) test_dr: .: (0.052057) test_dr_with_key: .: (0.053492) test_dr_with_key_empty: .: (0.011487) test_dt: .: (0.008096) test_dt_annotation: .: (0.007759) test_dt_created: .: (0.008624) test_dt_sequence: .: (0.008352) test_entry: .: (0.008464) test_ft: .: (0.022836) test_gene_name: .: (0.008534) test_gene_names: .: (0.008968) test_gn: .: (0.009517) test_gn_old_parser: .: (0.008569) test_gn_uniprot_parser: .: (0.008923) test_id_line: .: (0.011271) test_id_line_data_class: .: (0.008811) test_id_line_entry_name: .: (0.008471) test_id_line_molecule_type: .: (0.008381) test_id_line_sequence_length: .: (0.008546) test_kw: .: (0.008810) test_molecule: .: (0.008762) test_oc: .: (0.008706) test_og_1: .: (0.009377) test_og_2: .: (0.009131) test_og_3: .: (0.008554) test_og_4: .: (0.008913) test_og_5: .: (0.008942) test_og_6: .: (0.008548) test_os: .: (0.008375) test_os_access: .: (0.010135) test_os_access2: .: (0.008321) test_ox: .: (0.008671) test_protein_name: .: (0.008450) test_ref: .: (0.020026) test_seq: .: (0.008736) test_sequence_length: .: (0.008475) test_sq: .: (0.008747) test_sq_crc64: .: (0.008183) test_sq_len: .: (0.008941) test_sq_mw: .: (0.008526) test_synonyms: .: (0.008575) Bio::TestUniProtKB_CC: test_allergen: .: (0.000635) test_alternative_products_access_as_hash: .: (0.000774) test_alternative_products_ai: .: (0.000650) test_alternative_products_apu: .: (0.000896) test_alternative_products_as: .: (0.000603) test_alternative_products_rf: .: (0.000241) test_biophysicochemical_properties: .: (0.000831) test_biotechnology: .: (0.000475) test_catalytic_activity: .: (0.000684) test_caution: .: (0.000515) test_cofactor: .: (0.000427) test_developmental_stage: .: (0.000450) test_disease: .: (0.000625) test_domain: .: (0.000687) test_enzyme_regulation: .: (0.000453) test_function: .: (0.000479) test_induction: .: (0.000381) test_interaction: .: (0.000803) test_mass_spectrometry: .: (0.000573) test_miscellaneous: .: (0.000388) test_pathway: .: (0.000448) test_pharmaceutical: .: (0.000448) test_polymorphism: .: (0.000584) test_ptm: .: (0.000387) test_rna_editing: .: (0.000504) test_similarity: .: (0.000422) test_subcellular_location: .: (0.000456) test_subunit: .: (0.000472) test_tissue_specificity: .: (0.000446) test_toxic_dose: .: (0.000351) test_web_resource: .: (0.002903) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000776) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.001002) test_protein_name: .: (0.000714) test_synonyms: .: (0.001308) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000469) test_entry: .: (0.000275) test_entry_id: .: (0.000267) test_entry_name: .: (0.000274) test_id_line: .: (0.000265) test_molecule: .: (0.000273) test_sequence_length: .: (0.000252) Bio::TestUniProtKB_P03589: test_ac: .: (0.013593) test_accession: .: (0.001254) test_cc: .: (0.002044) test_cc_alternative_products: .: (0.001390) test_cc_database: .: (0.001452) test_cc_mass_spectrometry: .: (0.001446) test_de: .: (0.000915) test_dr: .: (0.001773) test_dr_with_key: .: (0.001483) test_dr_with_key_empty: .: (0.001561) test_dt: .: (0.001052) test_dt_annotation: .: (0.000861) test_dt_created: .: (0.001209) test_dt_sequence: .: (0.001074) test_entry: .: (0.001128) test_ft: .: (0.001803) test_gene_name: .: (0.001115) test_gene_names: .: (0.001022) test_gn: .: (0.001214) test_gn_old_parser: .: (0.001087) test_gn_uniprot_parser: .: (0.001096) test_id_line: .: (0.001292) test_id_line_data_class: .: (0.000915) test_id_line_entry_name: .: (0.000923) test_id_line_sequence_length: .: (0.001303) test_kw: .: (0.001158) test_oc: .: (0.001245) test_oh: .: (0.002033) test_os: .: (0.001040) test_os_access: .: (0.000743) test_os_access2: .: (0.001149) test_ox: .: (0.001010) test_protein_name: .: (0.001115) test_protein_name_after_calling_de: .: (0.001418) test_ref: .: (0.001110) test_seq: .: (0.001797) test_sequence_length: .: (0.001035) test_sq: .: (0.000995) test_sq_crc64: .: (0.001393) test_sq_len: .: (0.000851) test_sq_mw: .: (0.000963) test_synonyms: .: (0.001594) Bio::TestUniProtKB_P28907: test_ac: .: (0.004433) test_accession: .: (0.002688) test_cc: .: (0.003610) test_cc_alternative_products: .: (0.003553) test_cc_database: .: (0.003145) test_cc_mass_spectrometry: .: (0.003345) test_de: .: (0.002521) test_dr: .: (0.005820) test_dr_with_key: .: (0.005753) test_dr_with_key_empty: .: (0.005717) test_dt: .: (0.002546) test_dt_annotation: .: (0.002396) test_dt_created: .: (0.002208) test_dt_sequence: .: (0.002494) test_entry: .: (0.002405) test_ft: .: (0.004570) test_gene_name: .: (0.002512) test_gene_names: .: (0.002392) test_gn: .: (0.002480) test_gn_old_parser: .: (0.002752) test_gn_uniprot_parser: .: (0.002483) test_id_line: .: (0.005601) test_id_line_data_class: .: (0.002665) test_id_line_entry_name: .: (0.002417) test_id_line_sequence_length: .: (0.002417) test_kw: .: (0.002920) test_oc: .: (0.002448) test_os: .: (0.002388) test_os_access: .: (0.002324) test_os_access2: .: (0.002600) test_ox: .: (0.002730) test_protein_name: .: (0.002428) test_protein_name_after_calling_de: .: (0.002438) test_ref: .: (0.003889) test_seq: .: (0.002812) test_sequence_length: .: (0.002412) test_sq: .: (0.002311) test_sq_crc64: .: (0.002351) test_sq_len: .: (0.002660) test_sq_mw: .: (0.002489) test_synonyms: .: (0.002983) test_synonyms_after_calling_de: .: (0.002689) Bio::TestUniProtKB_P49144: test_ac: .: (0.001876) test_accession: .: (0.001155) test_cc: .: (0.002150) test_cc_alternative_products: .: (0.001584) test_cc_database: .: (0.001911) test_cc_mass_spectrometry: .: (0.002045) test_de: .: (0.001051) test_dr: .: (0.002246) test_dr_with_key: .: (0.002202) test_dr_with_key_empty: .: (0.002122) test_dt: .: (0.001277) test_dt_annotation: .: (0.001078) test_dt_created: .: (0.001272) test_dt_sequence: .: (0.001052) test_entry: .: (0.001101) test_ft: .: (0.002766) test_gene_name: .: (0.001367) test_gene_names: .: (0.001375) test_gn: .: (0.001125) test_gn_old_parser: .: (0.001146) test_gn_uniprot_parser: .: (0.001442) test_id_line: .: (0.001027) test_id_line_data_class: .: (0.001342) test_id_line_entry_name: .: (0.001352) test_id_line_sequence_length: .: (0.001074) test_kw: .: (0.001364) test_oc: .: (0.001119) test_os: .: (0.001412) test_os_access: .: (0.001029) test_os_access2: .: (0.001373) test_ox: .: (0.001107) test_protein_name: .: (0.001417) test_protein_name_after_calling_de: .: (0.001167) test_ref: .: (0.001613) test_seq: .: (0.001369) test_sequence_length: .: (0.001071) test_sq: .: (0.003656) test_sq_crc64: .: (0.001523) test_sq_len: .: (0.001113) test_sq_mw: .: (0.001445) test_synonyms: .: (0.001146) test_synonyms_after_calling_de: .: (0.001503) Bio::TestUniProtKB_Ref: test_RA: .: (0.000621) test_RC: .: (0.000418) test_RG: .: (0.000698) test_RL: .: (0.000435) test_RN: .: (0.000408) test_RP: .: (0.000449) test_RT: .: (0.000435) test_RX: .: (0.000708) test_ref: .: (0.000426) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000429) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000732) test_alternative_products_with_ft: .: (0.001337) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000504) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000472) test_RL_lines: .: (0.000241) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000993) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000391) test_RG_line: .: (0.000263) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000742) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000664) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000369) test_RL_line: .: (0.000253) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000986) test_RP_line: .: (0.000379) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000253) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000680) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000352) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000355) test_CC_interaction_isoform: .: (0.000313) test_CC_interaction_no_gene_name: .: (0.000313) test_CC_interaction_self_association: .: (0.000336) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000396) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000453) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000605) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000455) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000428) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000385) test_DT_line: .: (0.000303) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.005223) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000887) test_CC_web_resource: .: (0.000473) test_FT_VER_SEQ: .: (0.000306) test_OH_line_exception: .: (0.000352) test_OH_lines: .: (0.000517) Bio::TestUtils: test_centreOfGravity: .: (0.000777) test_dihedral_angle: .: (0.000869) test_distance: .: (0.000526) test_geometricCentre: .: (0.000484) test_rad2deg: .: (0.000311) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000433) test_dijkstra_on_weighted_graph: .: (0.000262) Finished in 26.188401986 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 150.49 tests/s, 824.83 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_i386.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_i386.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/48915/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/48915/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/48915 and its subdirectories I: Current time: Fri Mar 22 06:28:27 +14 2024 I: pbuilder-time-stamp: 1711038507