I: pbuilder: network access will be disabled during build I: Current time: Thu May 9 22:23:57 +14 2024 I: pbuilder-time-stamp: 1715243037 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: 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/5016/tmp/hooks/D01_modify_environment starting debug: Running on virt64a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 9 08:24 /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/5016/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/5016/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=dcca6f3b01bd463ca30cd4015466b904 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=5016 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.aBFbAFjm/pbuilderrc_1xiM --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.aBFbAFjm/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 8 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5016/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: armhf 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 ... 19445 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libb-hooks-op-check-perl{a} libbsd0{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap-2.5-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0t64{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-override-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjs-jquery libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc strace unzip wget zip 0 packages upgraded, 135 newly installed, 0 to remove and 0 not upgraded. Need to get 46.7 MB of archives. After unpacking 156 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.2.1-3 [1326 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libassuan0 armhf 2.5.6-1+b1 [43.8 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf gpgconf armhf 2.2.40-3 [547 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libksba8 armhf 1.6.6-1 [112 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-6 [18.0 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-6 [50.1 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.17+dfsg-1 [161 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libnpth0t64 armhf 1.6-3.1 [16.9 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf dirmngr armhf 2.2.40-3 [750 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf gnupg-l10n all 2.2.40-3 [1094 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf gnupg-utils armhf 2.2.40-3 [853 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf gpg armhf 2.2.40-3 [885 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf pinentry-curses armhf 1.2.1-3+b2 [74.2 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf gpg-agent armhf 2.2.40-3 [654 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf gpg-wks-client armhf 2.2.40-3 [525 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf gpg-wks-server armhf 2.2.40-3 [518 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf gpgsm armhf 2.2.40-3 [638 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf gnupg all 2.2.40-3 [847 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libfile-dirlist-perl all 0.05-3 [7600 B] Get: 65 http://deb.debian.org/debian trixie/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libfile-touch-perl all 0.12-2 [8816 B] Get: 68 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1+b1 [33.9 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libipc-run-perl all 20231003.0-2 [101 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libclass-xsaccessor-perl armhf 1.19-4+b3 [35.4 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libb-hooks-op-check-perl armhf 0.22-3+b1 [10.2 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libdevel-callchecker-perl armhf 0.009-1 [15.7 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libparams-classify-perl armhf 0.015-2+b3 [21.3 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libimport-into-perl all 1.002005-2 [11.3 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libmoo-perl all 2.005005-1 [58.0 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libhttp-date-perl all 6.06-1 [10.7 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libfile-listing-perl all 6.16-1 [12.4 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf liburi-perl all 5.28-1 [98.6 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libhtml-parser-perl armhf 3.82-1 [95.6 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libclone-perl armhf 0.46-1+b2 [13.1 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libhttp-message-perl all 6.45-1 [82.0 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf perl-openssl-defaults armhf 7+b2 [6708 B] Get: 96 http://deb.debian.org/debian trixie/main armhf libnet-ssleay-perl armhf 1.94-1+b1 [319 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libnet-http-perl all 6.23-1 [23.9 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libwww-perl all 6.77-1 [183 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf wdiff armhf 1.2.2-6 [118 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf devscripts all 2.23.7 [1068 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libosp5 armhf 1.5.2-15 [883 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf opensp armhf 1.5.2-15 [434 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf docbook-to-man armhf 1:2.0.0-46 [69.1 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian trixie/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf ruby-sdbm armhf 1.0.0-5+b4 [13.3 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20230828-1+b1 [77.6 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.4+20240414-1 [81.8 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-1+b1 [45.5 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libruby3.1t64 armhf 3.1.2-8.3 [5068 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf ruby3.1 armhf 3.1.2-8.3 [663 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 124 http://deb.debian.org/debian trixie/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 126 http://deb.debian.org/debian trixie/main armhf rake all 13.0.6-3 [83.9 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf gem2deb-test-runner armhf 2.2.3 [17.8 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b1 [328 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b1 [591 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf ruby3.1-dev armhf 3.1.2-8.3 [1002 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf ruby-all-dev armhf 1:3.1+nmu1 [5676 B] Get: 132 http://deb.debian.org/debian trixie/main armhf gem2deb armhf 2.2.3 [47.8 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf ruby-libxml armhf 3.2.4-2+b2 [72.5 kB] Fetched 46.7 MB in 1s (41.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19445 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19761 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_armhf.deb ... Unpacking python3-minimal (3.11.8-1) ... 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-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../5-libreadline8t64_8.2-4_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20753 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_armhf.deb ... Unpacking python3 (3.11.8-1) ... 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) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.2.1-3_armhf.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-4_armhf.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../012-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.1-1_armhf.deb ... 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Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../026-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../028-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../029-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... 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Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../038-libsasl2-2_2.1.28+dfsg1-6_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../039-libldap-2.5-0_2.5.17+dfsg-1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.17+dfsg-1) ... Selecting previously unselected package libnpth0t64:armhf. Preparing to unpack .../040-libnpth0t64_1.6-3.1_armhf.deb ... Unpacking libnpth0t64:armhf (1.6-3.1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../041-dirmngr_2.2.40-3_armhf.deb ... Unpacking dirmngr (2.2.40-3) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../042-gnupg-l10n_2.2.40-3_all.deb ... Unpacking gnupg-l10n (2.2.40-3) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../043-gnupg-utils_2.2.40-3_armhf.deb ... Unpacking gnupg-utils (2.2.40-3) ... Selecting previously unselected package gpg. Preparing to unpack .../044-gpg_2.2.40-3_armhf.deb ... Unpacking gpg (2.2.40-3) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../045-pinentry-curses_1.2.1-3+b2_armhf.deb ... Unpacking pinentry-curses (1.2.1-3+b2) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../046-gpg-agent_2.2.40-3_armhf.deb ... Unpacking gpg-agent (2.2.40-3) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../047-gpg-wks-client_2.2.40-3_armhf.deb ... Unpacking gpg-wks-client (2.2.40-3) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../048-gpg-wks-server_2.2.40-3_armhf.deb ... Unpacking gpg-wks-server (2.2.40-3) ... Selecting previously unselected package gpgsm. Preparing to unpack .../049-gpgsm_2.2.40-3_armhf.deb ... Unpacking gpgsm (2.2.40-3) ... Selecting previously unselected package gnupg. 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Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../067-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../068-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../069-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../070-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../071-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../072-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../073-liburi-perl_5.28-1_all.deb ... Unpacking liburi-perl (5.28-1) ... Selecting previously unselected package libhtml-parser-perl:armhf. Preparing to unpack .../074-libhtml-parser-perl_3.82-1_armhf.deb ... Unpacking libhtml-parser-perl:armhf (3.82-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../075-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:armhf. Preparing to unpack .../076-libclone-perl_0.46-1+b2_armhf.deb ... Unpacking libclone-perl:armhf (0.46-1+b2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../077-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../078-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../079-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../080-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../081-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:armhf. Preparing to unpack .../082-perl-openssl-defaults_7+b2_armhf.deb ... Unpacking perl-openssl-defaults:armhf (7+b2) ... Selecting previously unselected package libnet-ssleay-perl:armhf. Preparing to unpack .../083-libnet-ssleay-perl_1.94-1+b1_armhf.deb ... Unpacking libnet-ssleay-perl:armhf (1.94-1+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../084-libio-socket-ssl-perl_2.085-1_all.deb ... Unpacking libio-socket-ssl-perl (2.085-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../085-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../086-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../087-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../088-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../089-libwww-perl_6.77-1_all.deb ... Unpacking libwww-perl (6.77-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../090-patchutils_0.4.2-1_armhf.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../091-wdiff_1.2.2-6_armhf.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_armhf.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../097-opensp_1.5.2-15_armhf.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_armhf.deb ... Unpacking docbook-to-man (1:2.0.0-46) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../099-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../100-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../101-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../102-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../103-ruby-sdbm_1.0.0-5+b4_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../104-libbsd0_0.12.2-1_armhf.deb ... Unpacking libbsd0:armhf (0.12.2-1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../105-libedit2_3.1-20230828-1+b1_armhf.deb ... Unpacking libedit2:armhf (3.1-20230828-1+b1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../106-libncurses6_6.4+20240414-1_armhf.deb ... Unpacking libncurses6:armhf (6.4+20240414-1) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../107-libyaml-0-2_0.2.5-1+b1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:armhf. Preparing to unpack .../108-libruby3.1t64_3.1.2-8.3_armhf.deb ... Unpacking libruby3.1t64:armhf (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../109-ruby3.1_3.1.2-8.3_armhf.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../110-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../111-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../112-ruby_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby (1:3.1+nmu1) ... 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_2.2.3_armhf.deb ... Unpacking gem2deb-test-runner (2.2.3) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../115-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b1_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../116-libgmp-dev_2%3a6.3.0+dfsg-2+b1_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2+b1) ... Selecting previously unselected package ruby3.1-dev:armhf. Preparing to unpack .../117-ruby3.1-dev_3.1.2-8.3_armhf.deb ... Unpacking ruby3.1-dev:armhf (3.1.2-8.3) ... Selecting previously unselected package ruby-all-dev:armhf. Preparing to unpack .../118-ruby-all-dev_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby-all-dev:armhf (1:3.1+nmu1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../119-gem2deb_2.2.3_armhf.deb ... Unpacking gem2deb (2.2.3) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../120-ruby-rd_0.6.38-4.1_all.deb ... Unpacking ruby-rd (0.6.38-4.1) ... Selecting previously unselected package rdtool. Preparing to unpack .../121-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:armhf. Preparing to unpack .../122-ruby-libxml_3.2.4-2+b2_armhf.deb ... Unpacking ruby-libxml:armhf (3.2.4-2+b2) ... Setting up libksba8:armhf (1.6.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:armhf (1.6-3.1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:armhf (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:armhf (7+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up file (1:5.45-3) ... Setting up libassuan0:armhf (2.5.6-1+b1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-6) ... Setting up libosp5 (1.5.2-15) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 9 08:27:09 UTC 2024. Universal Time is now: Thu May 9 08:27:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b1) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up libncurses6:armhf (6.4+20240414-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:armhf (0.22-3+b1) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:armhf (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgmp-dev:armhf (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:armhf (3.1-20230828-1+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:armhf (0.009-1) ... Setting up libldap-2.5-0:armhf (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:armhf (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-3) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up libparams-classify-perl:armhf (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gpg-wks-server (2.2.40-3) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up gnupg (2.2.40-3) ... Setting up libruby:armhf (1:3.1+nmu1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up ruby-sdbm:armhf (1.0.0-5+b4) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.0.6-3) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:armhf (3.1.2-8.3) ... Setting up ruby3.1-dev:armhf (3.1.2-8.3) ... Setting up ruby-libxml:armhf (3.2.4-2+b2) ... Setting up gem2deb-test-runner (2.2.3) ... Setting up ruby-all-dev:armhf (1:3.1+nmu1) ... Setting up gem2deb (2.2.3) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-10) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-46) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/5016/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/5016/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 armhf 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/arm-linux-gnueabihf/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/arm-linux-gnueabihf/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: .: (0.001670) test_dbs: .: (0.000862) test_go_ids: .: (0.000595) test_go_terms: .: (0.000530) test_parser: .: (0.001065) test_set_date: .: (0.000558) test_set_desc: .: (0.000561) test_to_str: .: (0.000653) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.002094) test_mktmpdir_without_block: .: (0.002122) test_remove_entry_secure: .: (0.001021) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.005746) test_call_command_fork: .: (0.000392) test_call_command_open3: .: (0.005719) test_call_command_popen: .: (0.006611) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.007829) test_call_command_fork: .: (0.000372) test_call_command_open3: .: (0.006783) test_call_command_popen: .: (0.005586) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.005398) test_call_command_fork: .: (0.000364) test_call_command_open3: .: (0.005190) test_call_command_popen: .: (0.004824) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.005048) test_call_command_fork_chdir: .: (0.000705) test_call_command_popen_chdir: .: (0.003298) test_query_command_chdir: .: (0.003346) test_query_command_fork_chdir: .: (0.000875) test_query_command_popen_chdir: .: (0.003085) Bio::FuncTestCommandQuery: test_query_command: .: (0.014230) test_query_command_fork: .: (0.003857) test_query_command_open3: .: (0.013124) test_query_command_popen: .: (0.015065) Bio::FuncTestCommandTmpdir: test_close!: .: (0.002989) test_initialize: .: (0.000929) test_path: .: (0.002296) test_path_after_close: .: (0.001499) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.044229) test_output_fasta: .: (0.021885) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000959) test_accession: .: (0.000674) test_accessions: .: (0.000574) test_comment: .: (0.000585) test_common_name: .: (0.000608) test_definition: .: (0.000702) test_features: .: (0.000994) test_gi: .: (0.000599) test_keywords: .: (0.000617) test_locus: .: (0.000438) test_nid: .: (0.000521) test_organism: .: (0.000585) test_origin: .: (0.000613) test_references: .: (0.001538) test_segment: .: (0.000605) test_source: .: (0.000902) test_taxonomy: .: (0.000574) test_version: .: (0.000661) test_versions: .: (0.000534) Bio::TestAA: test_13: .: (0.000652) test_1n: .: (0.000364) test_name2one: .: (0.000444) test_name2three: .: (0.000505) test_one2name: .: (0.000349) test_one2three: .: (0.000338) test_three2name: .: (0.000381) test_three2one: .: (0.000397) test_to_1_1: .: (0.000361) test_to_1_3: .: (0.000495) test_to_1_name: .: (0.000508) test_to_3_1: .: (0.000340) test_to_3_3: .: (0.000368) test_to_3_name: .: (0.000419) test_to_re: .: (0.000432) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000676) Bio::TestAAindex: test_api: .: (0.000572) test_auto_aax1: .: (0.000698) test_auto_aax2: .: (0.000692) Bio::TestAAindex1: test_author: .: (0.001009) test_comment: .: (0.000658) test_correlation_coefficient: .: (0.001312) test_dblinks: .: (0.000674) test_definition: .: (0.000711) test_entry_id: .: (0.000654) test_index: .: (0.001050) test_journal: .: (0.000728) test_title: .: (0.000729) Bio::TestAAindex2: test_access_A_R: .: (0.002339) test_access_R_A: .: (0.001968) test_author: .: (0.000681) test_cols: .: (0.000633) test_comment: .: (0.000760) test_dblinks: .: (0.000655) test_definition: .: (0.000692) test_entry_id: .: (0.000647) test_journal: .: (0.000773) test_matrix: .: (0.001915) test_matrix_1_2: .: (0.001929) test_matrix_2_2: .: (0.001926) test_matrix_A_R: .: (0.002003) test_matrix_R_A: .: (0.001913) test_matrix_determinant: .: (0.011663) test_matrix_rank: .: (0.011384) test_matrix_transpose: .: (0.002258) test_rows: .: (0.000651) test_title: .: (0.000697) Bio::TestAAindexConstant: test_delimiter: .: (0.000797) test_tagsize: .: (0.000354) Bio::TestAbif: test_complement: .: (0.020897) test_seq: .: (0.019651) test_to_biosequence: .: (0.021846) Bio::TestActsLikeMap: test_mixin: .: (0.000998) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.001010) Bio::TestActsLikeMarker: test_mixin: .: (0.000737) Bio::TestAlignment: test_add_seq_no_key: .: (0.000885) test_add_seq_using_seq_with_aaseq_method: .: (0.000521) test_add_seq_using_seq_with_definition_method: .: (0.000417) test_add_seq_using_seq_with_entry_id_method: .: (0.000441) test_add_seq_using_seq_with_naseq_method: .: (0.000466) test_add_seq_using_seq_with_seq_method: .: (0.001094) test_consensus_iupac_gap_modes: .: (0.001145) test_consensus_iupac_missing_char: .: (0.000657) test_consensus_iupac_missing_char_option: .: (0.000677) test_consensus_iupac_no_gaps: .: (0.000836) test_consensus_iupac_of_ambiguous_bases: .: (0.001142) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.014453) test_consensus_opt_gap_mode: .: (0.001793) test_consensus_opt_missing_char: .: (0.000749) test_consensus_string_no_gaps: .: (0.000744) test_consensus_threshold_four_sequences: .: (0.001648) test_consensus_threshold_two_sequences: .: (0.001129) test_convert_match: .: (0.000908) test_convert_unmatch: .: (0.000540) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000542) test_convert_unmatch_different_match_char: .: (0.000505) test_convert_unmatch_multiple_sequences: .: (0.001058) test_default_gap_char: .: (0.000352) test_default_gap_regexp_matches_default_gap_char: .: (0.000447) test_default_missing_char: .: (0.000349) test_each_site_equal_length: .: (0.000546) test_each_site_unequal_length: .: (0.000558) test_equals: .: (0.000638) test_match_line_protein: .: (0.001357) test_normalizebang_extends_sequences_with_gaps: .: (0.000528) test_seq_length_is_max_seq_length: .: (0.002423) test_seq_length_when_one_sequence: .: (0.000389) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000396) test_seqclass_when_seqclass_set: .: (0.000375) test_seqclass_when_sequence_used: .: (0.000377) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000374) test_set_and_get_gap_char: .: (0.000375) test_store_cannot_override_key: .: (0.000395) test_store_with_default_keys_and_user_defined_keys: .: (0.000415) test_store_with_nil_key_uses_next_number_for_key: .: (0.000399) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000712) test_alignment_concat: .: (0.000484) test_alignment_length: .: (0.000349) test_alignment_lstrip!: .: (0.000581) test_alignment_lstrip_nil: .: (0.000435) test_alignment_normalize!: .: (0.000376) test_alignment_rstrip!: .: (0.000645) test_alignment_rstrip_nil: .: (0.000956) test_alignment_site: .: (0.000507) test_alignment_slice: .: (0.000369) test_alignment_strip!: .: (0.000635) test_alignment_strip_nil: .: (0.000462) test_alignment_subseq: .: (0.000465) test_alignment_window: .: (0.000405) test_collect_each_site: .: (0.000478) test_consensus_each_site_default: .: (0.000519) test_consensus_each_site_gap_mode_1: .: (0.000637) test_consensus_each_site_gap_mode_minus1: .: (0.000552) test_consensus_iupac: .: (0.001701) test_consensus_string_default: .: (0.000579) test_consensus_string_half: .: (0.000501) test_convert_match: .: (0.000460) test_convert_unmatch: .: (0.000397) test_each_seq: .: (0.000419) test_each_site: .: (0.000591) test_each_site_step: .: (0.000473) test_each_window: .: (0.000566) test_match_line: .: (0.002938) test_match_line_amino: .: (0.003693) test_match_line_nuc: .: (0.000606) test_private_alignment_site: .: (0.000402) test_remove_all_gaps!: .: (0.000916) test_seqclass: .: (0.000424) test_seqclass=: .: (0.000461) test_seqclass_default: .: (0.000333) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.009393) test_determine_seq_method: .: (0.005251) test_entries: .: (0.001066) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000899) test_avoid_same_name_numbering: .: (0.000506) test_clustal_have_same_name_true: .: (0.000457) test_have_same_name_false: .: (0.000420) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.001393) test_gap_char_default: .: (0.000402) test_gap_char_never_nil: .: (0.000391) test_gap_regexp: .: (0.000423) test_gap_regexp=: .: (0.000406) test_gap_regexp_never_nil: .: (0.000391) test_get_all_property_default: .: (0.000400) test_get_all_property_nodefault: .: (0.000446) test_is_gap_default_false: .: (0.000407) test_is_gap_default_true: .: (0.000413) test_is_gap_nodefault_false: .: (0.000405) test_is_gap_nodefault_true: .: (0.000406) test_missing_char=: .: (0.000399) test_missing_char_default: .: (0.000409) test_missing_char_never_nil: .: (0.000384) test_seqclass=: .: (0.000396) test_seqclass_default: .: (0.000399) test_seqclass_never_nil: .: (0.000386) test_set_all_property: .: (0.000441) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001660) test_consensus_string_50percent: .: (0.000399) test_consensus_string_50percent_nil: .: (0.000412) test_consensus_string_default: .: (0.000350) test_consensus_string_default_nil: .: (0.000362) test_has_gap_false: .: (0.000363) test_has_gap_true: .: (0.000396) test_match_line_amino_100percent: .: (0.000460) test_match_line_amino_missing: .: (0.001203) test_match_line_amino_strong: .: (0.000478) test_match_line_amino_weak: .: (0.000706) test_match_line_nuc_100percent: .: (0.000441) test_match_line_nuc_missing: .: (0.000442) test_remove_gaps!: .: (0.000374) test_remove_gaps_bang_not_removed: .: (0.000343) Bio::TestAtomFinder: test_atoms: .: (0.050503) test_each_atom: .: (0.000752) test_find_atom: .: (0.000702) Bio::TestBioFastaDefline: test_acc_version: .: (0.001313) test_accession: .: (0.001283) test_accessions: .: (0.001160) test_description: .: (0.000943) test_descriptions: .: (0.000989) test_entry_id: .: (0.000917) test_get: .: (0.001118) test_get_all_by_type: .: (0.000988) test_get_by_type: .: (0.000941) test_gi: .: (0.000901) test_id_strings: .: (0.002042) test_locus: .: (0.000890) test_method_missing: .: (0.001055) test_to_s: .: (0.001054) test_words: .: (0.001999) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.002417) test_goid2term: .: (0.001076) test_parse_goids: .: (0.001177) Bio::TestBioGenBank: test_basecount: .: (0.001034) test_circular: .: (0.000729) test_classification: .: (0.000984) test_date: .: (0.000725) test_date_modified: .: (0.001736) test_division: .: (0.000711) test_each_cds_feature: .: (0.002115) test_each_cds_qualifiers: .: (0.002275) test_each_gene: .: (0.002175) test_entry_id: .: (0.000754) test_length: .: (0.000776) test_locus_circular: .: (0.000843) test_locus_class: .: (0.001030) test_locus_date: .: (0.000849) test_locus_division: .: (0.000829) test_locus_entry_id: .: (0.000892) test_locus_length: .: (0.000824) test_locus_natype: .: (0.000872) test_locus_strand: .: (0.000831) test_natype: .: (0.000800) test_seq: .: (0.000977) test_seq_len: .: (0.000920) test_strand: .: (0.000902) test_strandedness: .: (0.000924) test_to_biosequence: .: (0.005979) Bio::TestBioGenPept: test_circular: .: (0.000981) test_date: .: (0.000651) test_dbsource: .: (0.014350) test_division: .: (0.000799) test_entry_id: .: (0.000770) test_length: .: (0.000754) test_locus: .: (0.000692) test_seq: .: (0.000749) test_seq_len: .: (0.000675) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.001111) test_aaseq: .: (0.001324) test_chromosome: .: (0.000734) test_codon_usage: .: (0.001054) test_cu_list: .: (0.000684) test_dblinks_as_hash: .: (0.000813) test_dblinks_as_strings: .: (0.000797) test_definition: .: (0.000749) test_division: .: (0.000704) test_eclinks: .: (0.001204) test_entry: .: (0.000683) test_entry_id: .: (0.000661) test_gbposition: .: (0.000730) test_gene: .: (0.000722) test_genes: .: (0.000789) test_keggclass: .: (0.000776) test_keggclasses: .: (0.000847) test_locations: .: (0.001067) test_motifs_as_hash: .: (0.001310) test_motifs_as_strings: .: (0.000680) test_name: .: (0.000701) test_names_as_array: .: (0.000757) test_new: .: (0.000697) test_ntlen: .: (0.000868) test_ntseq: .: (0.001051) test_organism: .: (0.000651) test_orthologs_as_hash: .: (0.000746) test_orthologs_as_strings: .: (0.001137) test_pathway: .: (0.000760) test_pathway_after_pathways_as_strings: .: (0.000925) test_pathway_before_pathways_as_strings: .: (0.000887) test_pathways_as_hash: .: (0.000800) test_pathways_as_strings: .: (0.000689) test_position: .: (0.000853) test_structure: .: (0.000712) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.004047) test_comment: .: (0.001337) test_data_source: .: (0.001134) test_definition: .: (0.001143) test_disease: .: (0.001122) test_entry_id: .: (0.001312) test_lineage: .: (0.001222) test_nalen: .: (0.001098) test_name: .: (0.001082) test_new: .: (0.001047) test_num_gene: .: (0.001325) test_num_rna: .: (0.001152) test_original_databases: .: (0.001048) test_original_db: .: (0.001131) test_plasmids: .: (0.001341) test_references: .: (0.007821) test_statistics: .: (0.001730) test_taxid: .: (0.001339) test_taxonomy: .: (0.001314) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001436) test_comment: .: (0.000946) test_data_source: .: (0.001163) test_definition: .: (0.000999) test_disease: .: (0.000783) test_entry_id: .: (0.000787) test_lineage: .: (0.000844) test_nalen: .: (0.000760) test_name: .: (0.000805) test_new: .: (0.000734) test_num_gene: .: (0.001239) test_num_rna: .: (0.000833) test_original_databases: .: (0.000754) test_original_db: .: (0.000769) test_plasmids: .: (0.001036) test_references: .: (0.001122) test_statistics: .: (0.000738) test_taxid: .: (0.001261) test_taxonomy: .: (0.000849) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.001072) test_compounds_as_strings: .: (0.000667) test_dblinks_as_hash: .: (0.000625) test_dblinks_as_strings: .: (0.000591) test_description: .: (0.000690) test_diseases_as_hash: .: (0.000668) test_diseases_as_strings: .: (0.000595) test_entry_id: .: (0.001340) test_enzymes_as_strings: .: (0.000896) test_genes_as_hash: .: (0.000612) test_genes_as_strings: .: (0.000626) test_keggclass: .: (0.000676) test_ko_pathway: .: (0.000639) test_modules_as_hash: .: (0.000640) test_modules_as_strings: .: (0.000655) test_name: .: (0.000660) test_new: .: (0.000632) test_organism: .: (0.000702) test_orthologs_as_hash: .: (0.001294) test_orthologs_as_strings: .: (0.000774) test_pathways_as_hash: .: (0.000696) test_pathways_as_strings: .: (0.000626) test_reactions_as_hash: .: (0.000630) test_reactions_as_strings: .: (0.000593) test_references: .: (0.000613) test_rel_pathways_as_hash: .: (0.000749) test_rel_pathways_as_strings: .: (0.000648) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001428) test_compounds_as_strings: .: (0.001432) test_dblinks_as_hash: .: (0.000693) test_dblinks_as_strings: .: (0.000827) test_description: .: (0.000776) test_diseases_as_hash: .: (0.000710) test_diseases_as_strings: .: (0.000682) test_entry_id: .: (0.000717) test_enzymes_as_strings: .: (0.000853) test_genes_as_hash: .: (0.001377) test_genes_as_strings: .: (0.000936) test_keggclass: .: (0.000806) test_ko_pathway: .: (0.000702) test_modules_as_hash: .: (0.000712) test_modules_as_strings: .: (0.000677) test_name: .: (0.000780) test_new: .: (0.000677) test_organism: .: (0.000743) test_orthologs_as_hash: .: (0.000940) test_orthologs_as_strings: .: (0.000700) test_pathways_as_hash: .: (0.000714) test_pathways_as_strings: .: (0.000662) test_reactions_as_hash: .: (0.000678) test_reactions_as_strings: .: (0.000754) test_references: .: (0.000763) test_rel_pathways_as_hash: .: (0.000892) test_rel_pathways_as_strings: .: (0.000877) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000968) test_compounds_as_strings: .: (0.001128) test_dblinks_as_hash: .: (0.000591) test_dblinks_as_strings: .: (0.000588) test_description: .: (0.000633) test_diseases_as_hash: .: (0.000583) test_diseases_as_strings: .: (0.000633) test_entry_id: .: (0.000647) test_enzymes_as_strings: .: (0.000605) test_genes_as_hash: .: (0.000572) test_genes_as_strings: .: (0.000574) test_keggclass: .: (0.000695) test_ko_pathway: .: (0.000616) test_modules_as_hash: .: (0.000603) test_modules_as_strings: .: (0.001223) test_name: .: (0.000759) test_new: .: (0.000618) test_organism: .: (0.000626) test_orthologs_as_hash: .: (0.000750) test_orthologs_as_strings: .: (0.000721) test_pathways_as_hash: .: (0.000616) test_pathways_as_strings: .: (0.000602) test_reactions_as_hash: .: (0.000575) test_reactions_as_strings: .: (0.000812) test_references: .: (0.000615) test_rel_pathways_as_hash: .: (0.001356) test_rel_pathways_as_strings: .: (0.000605) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000919) test_compounds_as_strings: .: (0.000658) test_dblinks_as_hash: .: (0.000687) test_dblinks_as_strings: .: (0.000728) test_description: .: (0.000995) test_diseases_as_hash: .: (0.000693) test_diseases_as_strings: .: (0.001230) test_entry_id: .: (0.000801) test_enzymes_as_strings: .: (0.000691) test_genes_as_hash: .: (0.000655) test_genes_as_strings: .: (0.000703) test_keggclass: .: (0.000717) test_ko_pathway: .: (0.000743) test_modules_as_hash: .: (0.001068) test_modules_as_strings: .: (0.001169) test_name: .: (0.000786) test_new: .: (0.000662) test_organism: .: (0.000703) test_orthologs_as_hash: .: (0.000651) test_orthologs_as_strings: .: (0.000664) test_pathways_as_hash: .: (0.000680) test_pathways_as_strings: .: (0.000664) test_reactions_as_hash: .: (0.000724) test_reactions_as_strings: .: (0.000906) test_references: .: (0.001950) test_rel_pathways_as_hash: .: (0.000835) test_rel_pathways_as_strings: .: (0.000735) Bio::TestBioKeggDRUG: test_activity: .: (0.001030) test_comment: .: (0.000957) test_dblinks_as_hash: .: (0.000949) test_dblinks_as_strings: .: (0.000759) test_entry_id: .: (0.000796) test_formula: .: (0.000741) test_kcf: .: (0.000681) test_mass: .: (0.000736) test_name: .: (0.000870) test_names: .: (0.001098) test_pathways_as_hash: .: (0.000799) test_pathways_as_strings: .: (0.000734) test_products: .: (0.000826) test_remark: .: (0.001067) Bio::TestBioKeggGLYCAN: test_comment: .: (0.001120) test_composition: .: (0.000938) test_compounds: .: (0.000838) test_dblinks_as_hash: .: (0.001632) test_dblinks_as_strings: .: (0.000901) test_entry_id: .: (0.000874) test_enzymes: .: (0.001047) test_kcf: .: (0.000737) test_keggclass: .: (0.000845) test_mass: .: (0.000857) test_name: .: (0.000830) test_orthologs_as_hash: .: (0.001356) test_orthologs_as_strings: .: (0.000852) test_pathways_as_hash: .: (0.000799) test_pathways_as_strings: .: (0.000796) test_reactions: .: (0.000839) test_references: .: (0.001001) test_remark: .: (0.000742) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000992) test_composition: .: (0.001183) test_compounds: .: (0.000738) test_dblinks_as_hash: .: (0.000752) test_dblinks_as_strings: .: (0.000712) test_entry_id: .: (0.000677) test_enzymes: .: (0.000670) test_kcf: .: (0.000599) test_keggclass: .: (0.000657) test_mass: .: (0.000666) test_name: .: (0.000630) test_orthologs_as_hash: .: (0.000617) test_orthologs_as_strings: .: (0.001042) test_pathways_as_hash: .: (0.000660) test_pathways_as_strings: .: (0.000594) test_reactions: .: (0.000617) test_references: .: (0.000582) test_remark: .: (0.000692) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.001395) test_compounds_as_strings: .: (0.000891) test_dblinks_as_hash: .: (0.001181) test_dblinks_as_strings: .: (0.000712) test_description: .: (0.000712) test_diseases_as_hash: .: (0.000811) test_diseases_as_strings: .: (0.000710) test_entry_id: .: (0.000756) test_enzymes_as_strings: .: (0.000661) test_genes_as_hash: .: (0.000753) test_genes_as_strings: .: (0.000663) test_keggclass: .: (0.000768) test_ko_pathway: .: (0.001140) test_modules_as_hash: .: (0.000988) test_modules_as_strings: .: (0.000813) test_name: .: (0.000813) test_new: .: (0.000725) test_organism: .: (0.000711) test_orthologs_as_hash: .: (0.000703) test_orthologs_as_strings: .: (0.000660) test_pathways_as_hash: .: (0.000702) test_pathways_as_strings: .: (0.001068) test_reactions_as_hash: .: (0.001390) test_reactions_as_strings: .: (0.001224) test_references: .: (0.001558) test_rel_pathways_as_hash: .: (0.008082) test_rel_pathways_as_strings: .: (0.000949) Bio::TestBioLITDB: test_author: .: (0.001043) test_entry_id: .: (0.000672) test_field: .: (0.000722) test_journal: .: (0.000676) test_keyword: .: (0.001450) test_reference: .: (0.001341) test_title: .: (0.000774) test_volume: .: (0.000674) Bio::TestBioNBRF: test_aalen: .: (0.000923) test_aaseq: .: (0.000574) test_entry: .: (0.000557) test_length: .: (0.000548) test_nalen: .: (0.000652) test_naseq: .: (0.000593) test_seq: .: (0.001111) test_seq_class: .: (0.000605) test_to_nbrf: .: (0.000560) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000906) test_to_newick_format_leaf: .: (0.000822) test_to_newick_format_leaf_NHX: .: (0.000584) Bio::TestBl2seqReport: test_db_len: .: (0.001789) test_db_num: .: (0.001872) test_new: .: (0.001039) test_undefed_methods: .: (0.002791) test_undefed_methods_for_iteration: .: (0.002922) Bio::TestBl2seqReportConstants: test_rs: .: (0.000644) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.001657) test_hits: .: (0.001005) Bio::TestBlast: test_blast_reports_format0: .: (0.014435) test_blast_reports_format0_with_block: .: (0.002075) test_blast_reports_format7: .: (0.042420) test_blast_reports_format7_with_block: .: (0.039971) test_blast_reports_format7_with_parser: .: (0.039790) test_blast_reports_format7_with_parser_with_block: .: (0.045924) test_blast_reports_format8: .: (0.002643) test_blast_reports_format8_with_block: .: (0.001670) test_blast_reports_format8_with_parser: .: (0.000972) test_blast_reports_format8_with_parser_with_block: .: (0.000912) test_blast_reports_xml: .: (0.037429) test_blast_reports_xml_with_block: .: (0.037311) test_blastll: .: (0.000728) test_db: .: (0.000712) test_exec_genomenet: .: (0.000633) test_exec_local: .: (0.000628) test_exec_ncbi: .: (0.000625) test_filter: .: (0.000677) test_format: .: (0.000711) test_make_command_line: .: (0.001703) test_make_command_line_2: .: (0.001310) test_matrix: .: (0.000700) test_new: .: (0.000932) test_new_opt_string: .: (0.000943) test_option: .: (0.001085) test_option_set: .: (0.000975) test_option_set_m0: .: (0.000863) test_options: .: (0.000670) test_output: .: (0.000701) test_parse_result: .: (0.065497) test_parser: .: (0.000776) test_program: .: (0.008244) test_query: .: (0.000649) test_self_local: .: (0.000854) test_self_remote: .: (0.009249) test_server: .: (0.000784) Bio::TestBlastNCBIOptions: test_add_options: .: (0.010316) test_delete: .: (0.001330) test_equal_equal: .: (0.011044) test_get: .: (0.001258) test_make_command_line_options: .: (0.001158) test_normalize!: .: (0.008647) test_parse: .: (0.000992) test_set: .: (0.010881) Bio::TestBlastReport: test_db: .: (0.064086) test_db_len: .: (0.038901) test_db_num: .: (0.038265) test_each_hit: .: (0.039030) test_each_iteration: .: (0.039459) test_eff_space: .: (0.038083) test_entrez_query: .: (0.038261) test_entropy: .: (0.037068) test_expect: .: (0.037579) test_filter: .: (0.039433) test_gap_extend: .: (0.038160) test_gap_open: .: (0.037455) test_hits: .: (0.036854) test_hsp_len: .: (0.037371) test_inclusion: .: (0.039875) test_iterations: .: (0.037686) test_kappa: .: (0.037256) test_lambda: .: (0.037333) test_matrix: .: (0.036329) test_message: .: (0.039567) test_parameters: .: (0.037830) test_pattern: .: (0.036794) test_program: .: (0.036883) test_query_def: .: (0.036948) test_query_id: .: (0.039048) test_query_len: .: (0.037119) test_reference: .: (0.036729) test_sc_match: .: (0.036820) test_sc_mismatch: .: (0.036723) test_statistics: .: (0.039305) test_version: .: (0.037119) Bio::TestBlastReportDefault: test_db: .: (0.001805) test_db_len: .: (0.001344) test_db_num: .: (0.001281) test_each_hit: .: (0.001285) test_each_iteration: .: (0.001249) test_eff_space: .: (0.001902) test_entropy: .: (0.001360) test_expect: .: (0.001450) test_gap_extend: .: (0.001422) test_gap_open: .: (0.001425) test_gapped_entropy: .: (0.001266) test_gapped_kappa: .: (0.001261) test_gapped_lambda: .: (0.001387) test_hits: .: (0.001240) test_iterations: .: (0.001163) test_kappa: .: (0.001303) test_lambda: .: (0.001284) test_matrix: .: (0.001471) test_message: .: (0.001202) test_pattern: .: (0.001450) test_program: .: (0.001288) test_query_def: .: (0.001309) test_query_len: .: (0.001278) test_reference: .: (0.001359) test_sc_match: .: (0.001454) test_sc_mismatch: .: (0.001490) test_version: .: (0.001225) Bio::TestBlastReportHit: test_Hit_accession: .: (0.036829) test_Hit_bit_score: .: (0.036359) test_Hit_definition: .: (0.040636) test_Hit_evalue: .: (0.039047) test_Hit_hit_id: .: (0.038582) test_Hit_hsps: .: (0.037241) test_Hit_identity: .: (0.036637) test_Hit_lap_at: .: (0.039275) test_Hit_len: .: (0.037126) test_Hit_midline: .: (0.036669) test_Hit_num: .: (0.036301) test_Hit_overlap: .: (0.038545) test_Hit_query_def: .: (0.038218) test_Hit_query_end: .: (0.036790) test_Hit_query_id: .: (0.036496) test_Hit_query_len: .: (0.036678) test_Hit_query_seq: .: (0.039016) test_Hit_query_start: .: (0.036858) test_Hit_taeget_def: .: (0.036650) test_Hit_target_end: .: (0.036265) test_Hit_target_id: .: (0.036574) test_Hit_target_len: .: (0.038772) test_Hit_target_seq: .: (0.036926) test_Hit_target_start: .: (0.036487) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001912) test_Hit_definition: .: (0.001327) test_Hit_evalue: .: (0.001346) test_Hit_hsps: .: (0.001247) test_Hit_identity: .: (0.001429) test_Hit_lap_at: .: (0.002045) test_Hit_len: .: (0.001288) test_Hit_midline: .: (0.001736) test_Hit_overlap: .: (0.001315) test_Hit_query_end: .: (0.001735) test_Hit_query_seq: .: (0.002117) test_Hit_query_start: .: (0.001783) test_Hit_taeget_def: .: (0.001284) test_Hit_target_end: .: (0.001765) test_Hit_target_id: .: (0.001295) test_Hit_target_len: .: (0.001287) test_Hit_target_seq: .: (0.001708) test_Hit_target_start: .: (0.001971) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.111741) test_Hit_bit_score: .: (0.114632) test_Hit_definition: .: (0.108173) test_Hit_evalue: .: (0.111243) test_Hit_hit_id: .: (0.111208) test_Hit_hsps: .: (0.107527) test_Hit_identity: .: (0.110597) test_Hit_lap_at: .: (0.111990) test_Hit_len: .: (0.107948) test_Hit_midline: .: (0.110972) test_Hit_num: .: (0.111714) test_Hit_overlap: .: (0.107438) test_Hit_query_def: .: (0.110676) test_Hit_query_end: .: (0.112489) test_Hit_query_id: .: (0.107887) test_Hit_query_len: .: (0.107474) test_Hit_query_seq: .: (0.112668) test_Hit_query_start: .: (0.119665) test_Hit_taeget_def: .: (0.109283) test_Hit_target_end: .: (0.112747) test_Hit_target_id: .: (0.112770) test_Hit_target_len: .: (0.108367) test_Hit_target_seq: .: (0.112287) test_Hit_target_start: .: (0.113252) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.110746) test_Hit_bit_score: .: (0.110074) test_Hit_definition: .: (0.112452) test_Hit_evalue: .: (0.113053) test_Hit_hit_id: .: (0.126532) test_Hit_hsps: .: (0.112728) test_Hit_identity: .: (0.112297) test_Hit_lap_at: .: (0.107227) test_Hit_len: .: (0.118338) test_Hit_midline: .: (0.112588) test_Hit_num: .: (0.152888) test_Hit_overlap: .: (0.108856) test_Hit_query_def: .: (0.112891) test_Hit_query_end: .: (0.120638) test_Hit_query_id: .: (0.118115) test_Hit_query_len: .: (0.112204) test_Hit_query_seq: .: (0.155371) test_Hit_query_start: .: (0.111090) test_Hit_taeget_def: .: (0.121121) test_Hit_target_end: .: (0.122904) test_Hit_target_id: .: (0.121293) test_Hit_target_len: .: (0.118162) test_Hit_target_seq: .: (0.120231) test_Hit_target_start: .: (0.114415) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.036951) test_Hit_bit_score: .: (0.037242) test_Hit_definition: .: (0.036977) test_Hit_evalue: .: (0.038981) test_Hit_hit_id: .: (0.037561) test_Hit_hsps: .: (0.037060) test_Hit_identity: .: (0.037333) test_Hit_lap_at: .: (0.038254) test_Hit_len: .: (0.037751) test_Hit_midline: .: (0.037084) test_Hit_num: .: (0.037033) test_Hit_overlap: .: (0.036672) test_Hit_query_def: .: (0.039441) test_Hit_query_end: .: (0.037189) test_Hit_query_id: .: (0.036918) test_Hit_query_len: .: (0.037233) test_Hit_query_seq: .: (0.038569) test_Hit_query_start: .: (0.037831) test_Hit_taeget_def: .: (0.037308) test_Hit_target_end: .: (0.036568) test_Hit_target_id: .: (0.036691) test_Hit_target_len: .: (0.039700) test_Hit_target_seq: .: (0.037182) test_Hit_target_start: .: (0.036844) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.001279) test_Hit_bit_score: .: (0.000706) test_Hit_definition: .: (0.000710) test_Hit_evalue: .: (0.000697) test_Hit_hit_id: .: (0.000699) test_Hit_hsps: .: (0.001132) test_Hit_identity: .: (0.000824) test_Hit_lap_at: .: (0.000714) test_Hit_len: .: (0.000722) test_Hit_midline: .: (0.000693) test_Hit_num: .: (0.000689) test_Hit_overlap: .: (0.000729) test_Hit_query_def: .: (0.000700) test_Hit_query_end: .: (0.000690) test_Hit_query_id: .: (0.000735) test_Hit_query_len: .: (0.000688) test_Hit_query_seq: .: (0.000680) test_Hit_query_start: .: (0.000713) test_Hit_taeget_def: .: (0.000682) test_Hit_target_end: .: (0.000685) test_Hit_target_id: .: (0.001034) test_Hit_target_len: .: (0.000759) test_Hit_target_seq: .: (0.000680) test_Hit_target_start: .: (0.000728) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.036968) test_Hsp_bit_score: .: (0.039881) test_Hsp_density: .: (0.037663) test_Hsp_evalue: .: (0.049674) test_Hsp_gaps: .: (0.037135) test_Hsp_hit_frame: .: (0.038641) test_Hsp_hit_from: .: (0.037853) test_Hsp_hit_to: .: (0.036857) test_Hsp_hseq: .: (0.036794) test_Hsp_identity: .: (0.039296) test_Hsp_midline: .: (0.039367) test_Hsp_mismatch_count: .: (0.037368) test_Hsp_num: .: (0.036514) test_Hsp_pattern_from: .: (0.037192) test_Hsp_pattern_to: .: (0.038979) test_Hsp_percent_identity: .: (0.038383) test_Hsp_positive: .: (0.037071) test_Hsp_qseq: .: (0.036624) test_Hsp_query_frame: .: (0.037357) test_Hsp_query_from: .: (0.039791) test_Hsp_query_to: .: (0.037372) test_Hsp_score: .: (0.037796) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.002114) test_Hsp_bit_score: .: (0.001421) test_Hsp_evalue: .: (0.001487) test_Hsp_gaps: .: (0.001372) test_Hsp_hit_frame: .: (0.001730) test_Hsp_hit_from: .: (0.002683) test_Hsp_hit_to: .: (0.002468) test_Hsp_hseq: .: (0.002407) test_Hsp_identity: .: (0.001977) test_Hsp_midline: .: (0.002501) test_Hsp_percent_identity: .: (0.001873) test_Hsp_positive: .: (0.001657) test_Hsp_qseq: .: (0.002457) test_Hsp_query_frame: .: (0.001372) test_Hsp_query_from: .: (0.001742) test_Hsp_query_to: .: (0.001731) test_Hsp_score: .: (0.001376) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.117254) test_Hsp_bit_score: .: (0.119083) test_Hsp_density: .: (0.109437) test_Hsp_evalue: .: (0.113796) test_Hsp_gaps: .: (0.113039) test_Hsp_hit_frame: .: (0.112288) test_Hsp_hit_from: .: (0.109998) test_Hsp_hit_to: .: (0.115238) test_Hsp_hseq: .: (0.113062) test_Hsp_identity: .: (0.110579) test_Hsp_midline: .: (0.109792) test_Hsp_mismatch_count: .: (0.114529) test_Hsp_num: .: (0.114269) test_Hsp_pattern_from: .: (0.109200) test_Hsp_pattern_to: .: (0.110919) test_Hsp_percent_identity: .: (0.114561) test_Hsp_positive: .: (0.112717) test_Hsp_qseq: .: (0.108546) test_Hsp_query_frame: .: (0.112326) test_Hsp_query_from: .: (0.112943) test_Hsp_query_to: .: (0.113141) test_Hsp_score: .: (0.115568) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.116999) test_Hsp_bit_score: .: (0.116821) test_Hsp_density: .: (0.112434) test_Hsp_evalue: .: (0.109302) test_Hsp_gaps: .: (0.112646) test_Hsp_hit_frame: .: (0.112819) test_Hsp_hit_from: .: (0.110539) test_Hsp_hit_to: .: (0.110327) test_Hsp_hseq: .: (0.112025) test_Hsp_identity: .: (0.111971) test_Hsp_midline: .: (0.107822) test_Hsp_mismatch_count: .: (0.113382) test_Hsp_num: .: (0.118393) test_Hsp_pattern_from: .: (0.123600) test_Hsp_pattern_to: .: (0.110023) test_Hsp_percent_identity: .: (0.112010) test_Hsp_positive: .: (0.113586) test_Hsp_qseq: .: (0.113311) test_Hsp_query_frame: .: (0.111659) test_Hsp_query_from: .: (0.113816) test_Hsp_query_to: .: (0.213199) test_Hsp_score: .: (0.111374) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.040576) test_Hsp_bit_score: .: (0.037828) test_Hsp_density: .: (0.037596) test_Hsp_evalue: .: (0.036889) test_Hsp_gaps: .: (0.037327) test_Hsp_hit_frame: .: (0.039652) test_Hsp_hit_from: .: (0.037324) test_Hsp_hit_to: .: (0.036836) test_Hsp_hseq: .: (0.037066) test_Hsp_identity: .: (0.037008) test_Hsp_midline: .: (0.039086) test_Hsp_mismatch_count: .: (0.037001) test_Hsp_num: .: (0.036927) test_Hsp_pattern_from: .: (0.037013) test_Hsp_pattern_to: .: (0.036521) test_Hsp_percent_identity: .: (0.038893) test_Hsp_positive: .: (0.037876) test_Hsp_qseq: .: (0.036646) test_Hsp_query_frame: .: (0.037016) test_Hsp_query_from: .: (0.036653) test_Hsp_query_to: .: (0.039527) test_Hsp_score: .: (0.037287) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.001181) test_Hsp_bit_score: .: (0.000697) test_Hsp_density: .: (0.000773) test_Hsp_evalue: .: (0.000710) test_Hsp_gaps: .: (0.000691) test_Hsp_hit_frame: .: (0.000788) test_Hsp_hit_from: .: (0.001125) test_Hsp_hit_to: .: (0.000833) test_Hsp_hseq: .: (0.000677) test_Hsp_identity: .: (0.000700) test_Hsp_midline: .: (0.000676) test_Hsp_mismatch_count: .: (0.000677) test_Hsp_num: .: (0.000702) test_Hsp_pattern_from: .: (0.000668) test_Hsp_pattern_to: .: (0.000714) test_Hsp_percent_identity: .: (0.000689) test_Hsp_positive: .: (0.000701) test_Hsp_qseq: .: (0.000745) test_Hsp_query_frame: .: (0.000714) test_Hsp_query_from: .: (0.000690) test_Hsp_query_to: .: (0.001114) test_Hsp_score: .: (0.000829) Bio::TestBlastReportIteration: test_hits: .: (0.037152) test_message: .: (0.036695) test_num: .: (0.039431) test_statistics: .: (0.039733) Bio::TestBlastReportIterationDefault: test_hits: .: (0.001961) test_message: .: (0.001351) test_num: .: (0.001305) Bio::TestBlastReportIterationMulti: test_each: .: (0.108043) test_hits: .: (0.112515) test_message: .: (0.112208) test_num: .: (0.107451) test_query_def: .: (0.111809) test_query_id: .: (0.112069) test_query_len: .: (0.107899) test_statistics: .: (0.111661) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.112701) test_hits: .: (0.108625) test_message: .: (0.112638) test_num: .: (0.114328) test_query_def: .: (0.108489) test_query_id: .: (0.112357) test_query_len: .: (0.111268) test_statistics: .: (0.109396) Bio::TestBlastReportIterationREXML: test_hits: .: (0.037469) test_message: .: (0.040117) test_num: .: (0.037613) test_statistics: .: (0.036664) Bio::TestBlastReportIterationTabular: test_hits: .: (0.001237) test_message: .: (0.000697) test_num: .: (0.000778) test_statistics: .: (0.000805) Bio::TestBlastReportMulti: test_db: .: (0.111935) test_db_len: .: (0.109240) test_db_num: .: (0.111717) test_each_hit: .: (0.112840) test_each_iteration: .: (0.107664) test_eff_space: .: (0.110413) test_entropy: .: (0.112470) test_expect: .: (0.107299) test_filter: .: (0.111523) test_gap_extend: .: (0.112833) test_gap_open: .: (0.108151) test_hits: .: (0.111406) test_hsp_len: .: (0.113222) test_iterations: .: (0.107780) test_kappa: .: (0.112304) test_lambda: .: (0.113818) test_matrix: .: (0.108820) test_message: .: (0.112394) test_parameters: .: (0.114506) test_pattern: .: (0.111136) test_program: .: (0.110211) test_query_def: .: (0.113026) test_query_id: .: (0.112630) test_query_len: .: (0.109678) test_reference: .: (0.113125) test_reports: .: (0.112476) test_statistics: .: (0.107796) test_version: .: (0.111382) Bio::TestBlastReportMultiREXML: test_db: .: (0.113203) test_db_len: .: (0.111179) test_db_num: .: (0.111487) test_each_hit: .: (0.112415) test_each_iteration: .: (0.112429) test_eff_space: .: (0.108811) test_entropy: .: (0.111829) test_expect: .: (0.112660) test_filter: .: (0.109834) test_gap_extend: .: (0.109519) test_gap_open: .: (0.112295) test_hits: .: (0.111147) test_hsp_len: .: (0.108783) test_iterations: .: (0.112264) test_kappa: .: (0.113345) test_lambda: .: (0.114577) test_matrix: .: (0.109555) test_message: .: (0.111255) test_parameters: .: (0.116333) test_pattern: .: (0.107412) test_program: .: (0.111250) test_query_def: .: (0.111645) test_query_id: .: (0.111455) test_query_len: .: (0.108474) test_reference: .: (0.111810) test_reports: .: (0.112423) test_statistics: .: (0.110903) test_version: .: (0.108279) Bio::TestBlastReportREXML: test_db: .: (0.039862) test_db_len: .: (0.037835) test_db_num: .: (0.036653) test_each_hit: .: (0.036236) test_each_iteration: .: (0.039155) test_eff_space: .: (0.037121) test_entrez_query: .: (0.036339) test_entropy: .: (0.036641) test_expect: .: (0.037552) test_filter: .: (0.037549) test_gap_extend: .: (0.036096) test_gap_open: .: (0.036024) test_hits: .: (0.036740) test_hsp_len: .: (0.038437) test_inclusion: .: (0.036937) test_iterations: .: (0.037185) test_kappa: .: (0.036679) test_lambda: .: (0.038122) test_matrix: .: (0.036841) test_message: .: (0.036786) test_parameters: .: (0.036737) test_pattern: .: (0.038690) test_program: .: (0.036734) test_query_def: .: (0.036385) test_query_id: .: (0.036376) test_query_len: .: (0.038217) test_reference: .: (0.036638) test_sc_match: .: (0.036616) test_sc_mismatch: .: (0.036498) test_statistics: .: (0.037649) test_version: .: (0.037291) Bio::TestBlastReportTabular: test_db: .: (0.001411) test_db_len: .: (0.000764) test_db_num: .: (0.000679) test_each_hit: .: (0.000688) test_each_iteration: .: (0.000677) test_eff_space: .: (0.000685) test_entrez_query: .: (0.000697) test_entropy: .: (0.000759) test_expect: .: (0.000710) test_filter: .: (0.000677) test_gap_extend: .: (0.000676) test_gap_open: .: (0.000714) test_hits: .: (0.000693) test_hsp_len: .: (0.000684) test_inclusion: .: (0.001193) test_iterations: .: (0.000855) test_kappa: .: (0.000687) test_lambda: .: (0.000675) test_matrix: .: (0.000722) test_message: .: (0.000705) test_parameters: .: (0.000696) test_pattern: .: (0.000687) test_program: .: (0.000682) test_query_def: .: (0.000704) test_query_id: .: (0.000694) test_query_len: .: (0.000699) test_reference: .: (0.000735) test_sc_match: .: (0.000719) test_sc_mismatch: .: (0.001247) test_statistics: .: (0.000860) test_version: .: (0.000731) Bio::TestChain: test_aaseq: .: (0.001138) test_addLigand: .: (0.000637) test_addResidue: .: (0.000630) test_atom_seq: .: (0.000686) test_comp: .: (0.000703) test_each: .: (0.000607) test_each_heterogen: .: (0.000599) test_each_residue: .: (0.000605) test_get_heterogen_by_id: .: (0.000631) test_get_residue_by_id: .: (0.000617) test_inspect: .: (0.000661) test_rehash: .: (0.000575) test_rehash_heterogens: .: (0.000585) test_rehash_residues: .: (0.000556) test_square_brace: .: (0.000630) test_to_s: .: (0.000632) Bio::TestChainFinder: test_chains: .: (0.000948) test_each_chain: .: (0.000613) test_find_chain: .: (0.000583) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.025361) test_header: .: (0.002267) test_match_line: .: (0.001755) test_sequence0: .: (0.002278) test_sequence1: .: (0.001876) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.025733) test_header: .: (0.002644) test_match_line: .: (0.002241) test_sequence0: .: (0.002710) test_sequence1: .: (0.002345) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.037153) test_header: .: (0.002449) test_match_line: .: (0.001938) test_sequence0: .: (0.001954) test_sequence1: .: (0.002235) Bio::TestCodonTable: test_Tables: .: (0.000805) test_accessor: .: (0.000682) test_definition: .: (0.000509) test_each: .: (0.000590) test_revtrans: .: (0.000749) test_self_accessor: .: (0.000629) test_self_copy: .: (0.002197) test_set_accessor: .: (0.251508) test_start: .: (0.000552) test_start_codon?: .: (0.000559) test_stop: .: (0.000519) test_stop_codon?: .: (0.000573) test_table: .: (0.000509) Bio::TestCodonTableConstants: test_Definitions: .: (0.000824) test_Starts: .: (0.000552) test_Tables: .: (0.000496) test_stops: .: (0.000542) Bio::TestColorScheme: test_buried: .: (0.002898) Bio::TestCommand: test_command_constants: .: (0.000807) test_escape_shell: .: (0.000653) test_escape_shell_unix: .: (0.000603) test_escape_shell_windows: .: (0.000591) test_make_cgi_params_by_array_of_array: .: (0.001124) test_make_cgi_params_by_array_of_hash: .: (0.001100) test_make_cgi_params_by_array_of_string: .: (0.000695) test_make_cgi_params_by_hash_in_string: .: (0.001624) test_make_cgi_params_by_hash_in_symbol: .: (0.001389) test_make_cgi_params_by_string: .: (0.000655) test_make_command_line: .: (0.000594) test_make_command_line_unix: .: (0.000566) test_make_command_line_windows: .: (0.000579) test_safe_command_line_array: .: (0.000620) test_safe_command_line_array_passthrough: .: (0.000585) Bio::TestContingencyTable: test_lite_example: .: (0.463954) Bio::TestDB: test_entry_id: .: (0.000948) test_exists: .: (0.000536) test_fetch: .: (0.000669) test_get: .: (0.000505) test_open: .: (0.000505) test_tags: .: (0.000652) Bio::TestDataType: test_const_like_method: .: (0.001457) test_pdb_achar: .: (0.000829) test_pdb_atom: .: (0.000779) test_pdb_character: .: (0.000800) test_pdb_date: .: (0.000830) test_pdb_idcode: .: (0.000786) test_pdb_integer: .: (0.000505) test_pdb_list: .: (0.000533) test_pdb_lstring: .: (0.000770) test_pdb_real: .: (0.000668) test_pdb_resudue_name: .: (0.000801) test_pdb_slist: .: (0.000572) test_pdb_string: .: (0.000797) test_pdb_stringrj: .: (0.000529) test_pdb_symop: .: (0.000957) test_specification_list: .: (0.000569) Bio::TestEMBL: test_ac: .: (0.001654) test_accession: .: (0.001269) test_cc: .: (0.001180) test_de: .: (0.001248) test_division: .: (0.001379) test_dr: .: (0.001113) test_dt: .: (0.001148) test_dt_created: .: (0.001137) test_dt_iterator: .: (0.001180) test_dt_updated: .: (0.001289) test_each_cds: .: (0.001657) test_each_gene: .: (0.001522) test_entry: .: (0.001331) test_fh: .: (0.001342) test_ft: .: (0.001588) test_ft_accessor: .: (0.001448) test_ft_iterator: .: (0.001561) test_id_line: .: (0.001360) test_id_line_data_class: .: (0.001219) test_id_line_division: .: (0.001246) test_id_line_entry_name: .: (0.001190) test_id_line_iterator: .: (0.001150) test_id_line_molecule_type: .: (0.001216) test_id_line_sequence_length: .: (0.001201) test_kw: .: (0.005396) test_molecule: .: (0.001280) test_oc: .: (0.001311) test_og: .: (0.001073) test_os: .: (0.001512) test_ref: .: (0.001378) test_references: .: (0.001901) test_seq: .: (0.002023) test_sequence_length: .: (0.001207) test_sq: .: (0.001126) test_sq_get: .: (0.001174) test_sv: .: (0.001356) test_version: .: (0.001146) Bio::TestEMBL89: test_ac: .: (0.001465) test_accession: .: (0.001147) test_cc: .: (0.001309) test_de: .: (0.001115) test_division: .: (0.001132) test_dr: .: (0.001008) test_dt: .: (0.001123) test_dt_created: .: (0.001302) test_dt_iterator: .: (0.001024) test_dt_updated: .: (0.001035) test_each_cds: .: (0.001442) test_each_gene: .: (0.001670) test_entry: .: (0.001228) test_fh: .: (0.001153) test_ft: .: (0.001452) test_ft_accessor: .: (0.001733) test_ft_iterator: .: (0.001514) test_id_line: .: (0.001207) test_id_line_data_class: .: (0.001355) test_id_line_division: .: (0.001127) test_id_line_entry_name: .: (0.001189) test_id_line_iterator: .: (0.001210) test_id_line_molecule_type: .: (0.001398) test_id_line_sequence_length: .: (0.001167) test_id_line_sequence_version: .: (0.001117) test_kw: .: (0.001103) test_molecule: .: (0.001169) test_oc: .: (0.001443) test_og: .: (0.001074) test_os: .: (0.001122) test_ref: .: (0.001189) test_references: .: (0.001977) test_seq: .: (0.001592) test_sequence_length: .: (0.001018) test_sq: .: (0.000929) test_sq_get: .: (0.001438) test_sv: .: (0.001042) test_version: .: (0.001005) Bio::TestEMBLAPI: test_ac: .: (0.000793) test_accessions: .: (0.000459) Bio::TestEMBLCommon: test_ac: .: (0.000837) test_accession: .: (0.000262) test_accessions: .: (0.000252) test_de: .: (0.000240) test_definition: .: (0.000248) test_description: .: (0.000244) test_dr: .: (0.000304) test_keywords: .: (0.000255) test_kw: .: (0.000237) test_oc: .: (0.000247) test_og: .: (0.000245) test_os: .: (0.000246) test_ref: .: (0.000241) test_references: .: (0.000233) Bio::TestEMBLDB: test_fetch: .: (0.000717) test_p_entry2hash: .: (0.000496) Bio::TestEMBLToBioSequence: test_classification: .: (0.008554) test_date_created: .: (0.001569) test_date_modified: .: (0.005006) test_definition: .: (0.001259) test_division: .: (0.001400) test_entry_id: .: (0.001831) test_entry_version: .: (0.001430) test_features: .: (0.001901) test_keywords: .: (0.001828) test_molecule_type: .: (0.001606) test_primary_accession: .: (0.001443) test_references: .: (0.002129) test_release_created: .: (0.002008) test_release_modified: .: (0.001407) test_secondary_accessions: .: (0.001460) test_sequence_version: .: (0.001541) test_species: .: (0.002051) test_topology: .: (0.001411) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.009506) test_date_created: .: (0.008066) test_date_modified: .: (0.038223) test_definition: .: (0.047804) test_division: .: (0.042408) test_entry_id: .: (0.008852) test_entry_version: .: (0.008551) test_features: .: (0.008563) test_keywords: .: (0.007739) test_molecule_type: .: (0.008571) test_primary_accession: .: (0.008332) test_references: .: (0.008706) test_release_created: .: (0.007623) test_release_modified: .: (0.008130) test_secondary_accessions: .: (0.008129) test_sequence_version: .: (0.008046) test_species: .: (0.007546) test_topology: .: (0.008166) Bio::TestFasta: test_db: .: (0.000845) test_format: .: (0.000621) test_format_arg_integer: .: (0.000569) test_format_arg_str: .: (0.001065) test_ktup: .: (0.000591) test_matrix: .: (0.000535) test_option: .: (0.000646) test_options: .: (0.000567) test_output: .: (0.000493) test_program: .: (0.000555) test_server: .: (0.000532) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000850) test_accession: .: (0.000589) test_accessions: .: (0.000613) test_description: .: (0.000569) test_descriptions: .: (0.000609) test_entry_id: .: (0.000566) test_get_all_by_type: .: (0.001191) test_gi: .: (0.000625) test_id_strings: .: (0.000706) test_list_ids: .: (0.000569) test_locus: .: (0.000595) test_words: .: (0.000707) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000869) test_accession: .: (0.000618) test_accessions: .: (0.000657) test_description: .: (0.000600) test_descriptions: .: (0.000606) test_emb: .: (0.000635) test_entry_id: .: (0.000592) test_get_all_by_type: .: (0.000629) test_get_emb: .: (0.000616) test_gi: .: (0.000602) test_id_strings: .: (0.001407) test_list_ids: .: (0.000699) test_locus: .: (0.000602) test_words: .: (0.000772) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000830) test_accession: .: (0.000634) test_accessions: .: (0.000590) test_description: .: (0.000561) test_descriptions: .: (0.000563) test_entry_id: .: (0.000563) test_get_all_by_type: .: (0.000603) test_gi: .: (0.000571) test_id_strings: .: (0.000716) test_list_ids: .: (0.000607) test_locus: .: (0.001174) test_sp: .: (0.000604) test_words: .: (0.000698) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.001006) test_accession: .: (0.000750) test_accessions: .: (0.000739) test_description: .: (0.000581) test_descriptions: .: (0.000803) test_entry_id: .: (0.000707) test_get_all_by_type: .: (0.000705) test_gi: .: (0.000719) test_id_strings: .: (0.000928) test_list_ids: .: (0.001337) test_locus: .: (0.000767) test_words: .: (0.000964) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000886) test_accession: .: (0.000568) test_accessions: .: (0.000616) test_description: .: (0.000546) test_descriptions: .: (0.000545) test_entry_id: .: (0.000738) test_get_all_by_type: .: (0.000620) test_gi: .: (0.000546) test_id_strings: .: (0.000759) test_list_ids: .: (0.001126) test_locus: .: (0.000547) test_words: .: (0.000751) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000936) test_accession: .: (0.000506) test_accessions: .: (0.000477) test_description: .: (0.000458) test_descriptions: .: (0.000465) test_entry_id: .: (0.000458) test_get_all_by_type: .: (0.000464) test_gi: .: (0.000461) test_id_strings: .: (0.000583) test_list_ids: .: (0.001273) test_locus: .: (0.000534) test_words: .: (0.000555) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000774) test_accession: .: (0.000519) test_accessions: .: (0.000548) test_description: .: (0.000482) test_descriptions: .: (0.000599) test_entry_id: .: (0.000508) test_get: .: (0.000559) test_get_all_by_type: .: (0.000489) test_id_strings: .: (0.000705) test_list_ids: .: (0.000500) test_locus: .: (0.001235) test_sp: .: (0.000672) test_words: .: (0.000773) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000759) test_accession: .: (0.000516) test_accessions: .: (0.000510) test_description: .: (0.000536) test_descriptions: .: (0.000494) test_entry_id: .: (0.000493) test_get: .: (0.000724) test_get_all_by_type: .: (0.000506) test_id_strings: .: (0.000736) test_list_ids: .: (0.000493) test_locus: .: (0.000490) test_tr: .: (0.000524) test_words: .: (0.001023) Bio::TestFastaFirstName: test_first_name1: .: (0.000980) test_first_name_multi_identifier: .: (0.000562) test_first_name_single_worded_defintion: .: (0.006889) test_no_definition: .: (0.000505) test_space_before_first_name: .: (0.000489) test_tabbed_defintion: .: (0.000480) Bio::TestFastaFormat: test_aalen: .: (0.000805) test_aaseq: .: (0.000520) test_acc_version: .: (0.000622) test_accession: .: (0.000898) test_accessions: .: (0.000737) test_data: .: (0.000601) test_definition: .: (0.000611) test_entry: .: (0.000667) test_entry_id: .: (0.000765) test_entry_overrun: .: (0.001268) test_first_name: .: (0.000747) test_gi: .: (0.000804) test_identifiers: .: (0.000736) test_length: .: (0.000586) test_query: .: (0.000754) test_seq: .: (0.000592) Bio::TestFastaFormatConst: test_delimiter: .: (0.000895) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.001040) test_data: .: (0.000667) test_definition: .: (0.000556) test_entry: .: (0.000562) test_entry_id: .: (0.001472) test_first_name: .: (0.000632) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000891) test_naseq: .: (0.000558) test_naseq_class: .: (0.000613) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000959) Bio::TestFastaInitialize: test_new_1: .: (0.001587) test_option: .: (0.000594) test_option_backward_compatibility: .: (0.001200) Bio::TestFastaNumericFormat: test_arg: .: (0.001139) test_data: .: (0.000729) test_definition: .: (0.000549) test_each: .: (0.000753) test_entry: .: (0.000609) test_entry_id: .: (0.000621) test_length: .: (0.000705) test_to_biosequence: .: (0.002514) Bio::TestFastaQuery: test_query: .: (0.001382) test_self_local: .: (0.000476) test_self_parser: .: (0.000512) test_self_remote: .: (0.000465) Bio::TestFastacmd: test_database: .: (0.000917) test_fastacmd: .: (0.000617) test_methods: .: (0.000669) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.002270) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.002401) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001846) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.001671) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.001824) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.002344) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.001589) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.001668) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001945) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001680) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.001499) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001523) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.002222) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.003701) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.003325) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.002012) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001663) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.001424) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.016095) test_error_probabilities_as_sanger: .: (0.015715) test_error_probabilities_as_solexa: .: (0.017962) test_quality_scores_as_illumina: .: (0.002158) test_quality_scores_as_sanger: .: (0.001413) test_quality_scores_as_solexa: .: (0.001501) test_validate_format: .: (0.002182) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.004037) test_entry_id: .: (0.003561) test_error_probabilities: .: (0.452668) test_nalen: .: (0.003403) test_naseq: .: (0.002837) test_quality_scores: .: (0.005641) test_quality_string: .: (0.002487) test_roundtrip: .: (0.421417) test_seq: .: (0.003116) test_sequence_string: .: (0.002499) test_to_biosequence: .: (0.393729) test_to_biosequence_and_output: .: (0.014168) test_to_s: .: (0.003271) test_validate_format: .: (0.002785) test_validate_format_with_array: .: (0.003391) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.001673) test_mask_20_with_empty_string: .: (0.001286) test_mask_20_with_longer_string: .: (0.001679) test_mask_20_with_x: .: (0.001335) test_mask_60: .: (0.001499) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.021041) test_error_probabilities_as_sanger: .: (0.020960) test_error_probabilities_as_solexa: .: (0.025304) test_quality_scores_as_illumina: .: (0.001435) test_quality_scores_as_sanger: .: (0.001005) test_quality_scores_as_solexa: .: (0.001921) test_validate_format: .: (0.001815) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.015764) test_error_probabilities_as_sanger: .: (0.015784) test_error_probabilities_as_solexa: .: (0.015630) test_quality_scores_as_illumina: .: (0.001487) test_quality_scores_as_sanger: .: (0.001246) test_quality_scores_as_solexa: .: (0.002964) test_validate_format: .: (0.001831) Bio::TestFeature: test_append: .: (0.000833) test_append_nil: .: (0.000548) test_assoc: .: (0.000555) test_each: .: (0.000449) test_feature: .: (0.000496) test_locations: .: (0.000697) test_new: .: (0.000524) test_position: .: (0.000637) test_qualifiers: .: (0.001032) Bio::TestFeatures: test_append: .: (0.001089) test_arg: .: (0.000569) test_each: .: (0.000563) test_features: .: (0.000573) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.002890) test_aaindex2: .: (0.001008) test_blast: .: (0.000822) test_blastxml: .: (0.001995) test_embl: .: (0.000993) test_embl_oldrelease: .: (0.000875) test_fastaformat: .: (0.001251) test_fastanumericformat: .: (0.000700) test_fastq: .: (0.000769) test_genbank: .: (0.000794) test_genpept: .: (0.000856) test_hmmer: .: (0.000799) test_maxml_cluster: .: (0.008287) test_maxml_sequence: .: (0.000619) test_medline: .: (0.000624) test_prosite: .: (0.006466) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.006068) test_transfac: .: (0.004524) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000972) test_auto_1arg_filename: .: (0.001195) test_auto_1arg_io: .: (0.001074) test_auto_1arg_io_with_block: .: (0.002486) test_auto_1arg_with_block: .: (0.001818) test_auto_2arg_filename_mode: .: (0.001090) test_auto_2arg_filename_mode_with_block: .: (0.001824) test_auto_3arg: .: (0.001048) test_auto_3arg_with_block: .: (0.002165) test_foreach: .: (0.001557) test_new_2arg_class: .: (0.000664) test_new_2arg_nil: .: (0.001000) test_open_0arg: .: (0.000526) test_open_1arg_class: .: (0.000520) test_open_1arg_filename: .: (0.001243) test_open_1arg_io: .: (0.001486) test_open_1arg_io_with_block: .: (0.001888) test_open_1arg_nil: .: (0.000510) test_open_1arg_with_block: .: (0.001784) test_open_2arg_autodetect: .: (0.001020) test_open_2arg_autodetect_io: .: (0.001502) test_open_2arg_autodetect_io_with_block: .: (0.001823) test_open_2arg_autodetect_with_block: .: (0.001774) test_open_2arg_class: .: (0.000671) test_open_2arg_class_io: .: (0.000715) test_open_2arg_class_io_with_block: .: (0.001954) test_open_2arg_class_with_block: .: (0.001488) test_open_2arg_filename_mode: .: (0.001189) test_open_2arg_filename_mode_with_block: .: (0.001816) test_open_3arg: .: (0.002298) test_open_3arg_with_block: .: (0.004243) test_open_4arg: .: (0.004025) test_to_a: .: (0.001636) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.001411) test_close: .: (0.000624) test_dbclass: .: (0.000587) test_dbclass_eq: .: (0.000997) test_dbclass_nil: .: (0.000814) test_each: .: (0.000954) test_each_entry: .: (0.001328) test_ended_pos: .: (0.000900) test_entry_pos_flag: .: (0.000659) test_entry_raw: .: (0.001142) test_eof?: .: (0.001299) test_next_entry: .: (0.001746) test_path: .: (0.000716) test_pos: .: (0.000795) test_raw: .: (0.001077) test_rewind: .: (0.000840) test_start_pos: .: (0.000851) test_start_pos_ended_pos_not_recorded: .: (0.000959) test_to_io: .: (0.000661) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.001226) test_simpleformat2: .: (0.000883) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000930) test_eof_false_after_prefetch: .: (0.000907) test_eof_false_first: .: (0.000611) test_eof_true: .: (0.000771) test_getc: .: (0.000676) test_getc_after_prefetch: .: (0.000632) test_gets: .: (0.000673) test_gets_equal_prefetch_gets: .: (0.000688) test_gets_paragraph_mode: .: (0.000774) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000981) test_gets_paragraph_mode_within_buffer: .: (0.001215) test_gets_rs: .: (0.000917) test_gets_rs_equal_prefetch_gets: .: (0.000819) test_gets_rs_within_buffer: .: (0.001076) test_pos: .: (0.000598) test_pos=: .: (0.000704) test_prefetch_buffer: .: (0.000601) test_prefetch_gets: .: (0.000755) test_prefetch_gets_with_arg: .: (0.000768) test_rewind: .: (0.000591) test_skip_spaces: .: (0.000738) test_to_io: .: (0.000685) test_ungetc: .: (0.000618) test_ungetc_after_prefetch: .: (0.000643) test_ungets: .: (0.001183) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000927) test_self_open_file: .: (0.000697) test_self_open_file_with_block: .: (0.000740) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000925) test_parse_file_open_arg_int_perm: .: (0.000517) test_parse_file_open_arg_int_perm_opt: .: (0.000609) test_parse_file_open_arg_integer: .: (0.000516) test_parse_file_open_arg_nil: .: (0.000510) test_parse_file_open_arg_opt: .: (0.000616) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000576) test_parse_file_open_arg_str: .: (0.000605) test_parse_file_open_arg_str_opt: .: (0.000587) test_parse_file_open_arg_str_perm: .: (0.000571) test_parse_file_open_arg_str_perm_opt: .: (0.000591) test_parse_file_open_arg_str_with_enc: .: (0.000944) test_parse_file_open_arg_str_with_ext_enc: .: (0.000635) test_parse_file_open_mode_integer: .: (0.000513) test_parse_file_open_mode_nil: .: (0.000559) test_parse_file_open_mode_str: .: (0.000471) test_parse_file_open_mode_str_with_enc: .: (0.000486) test_parse_file_open_mode_str_with_ext_enc: .: (0.000477) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000876) test_entry: .: (0.000562) test_entry_ended_pos: .: (0.000575) test_entry_pos_flag: .: (0.000575) test_entry_start_pos: .: (0.000533) test_get_entry: .: (0.000564) test_rewind: .: (0.000502) test_skip_leader: .: (0.000518) test_stream: .: (0.000499) test_stream_pos: .: (0.000868) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000751) test_delimiter_overrun: .: (0.000492) test_entry: .: (0.000542) test_entry_ended_pos: .: (0.000557) test_entry_ended_pos_default_nil: .: (0.000512) test_entry_start_pos: .: (0.000566) test_entry_start_pos_default_nil: .: (0.000511) test_get_entry: .: (0.000828) test_get_parsed_entry: .: (0.000805) test_header: .: (0.000457) test_skip_leader: .: (0.000970) test_skip_leader_without_header: .: (0.000599) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000954) test_entry_ended_pos: .: (0.001089) test_entry_start_pos: .: (0.000785) test_flag_to_fetch_header: .: (0.000751) test_get_entry: .: (0.000990) test_get_parsed_entry: .: (0.001405) test_rewind: .: (0.000795) test_skip_leader: .: (0.000560) Bio::TestGCGMsf: test_alignment: .: (0.002708) test_checksum: .: (0.000782) test_compcheck: .: (0.001149) test_date: .: (0.000829) test_description: .: (0.000776) test_entry_id: .: (0.000773) test_gap_length_weight: .: (0.000818) test_gap_weight: .: (0.000786) test_heading: .: (0.000809) test_length: .: (0.001108) test_seq_type: .: (0.000789) test_symbol_comparison_table: .: (0.000839) test_validate_checksum: .: (0.004435) Bio::TestGFF: test_record_class: .: (0.008476) test_records: .: (0.001130) Bio::TestGFF2: test_const_version: .: (0.001606) test_gff_version: .: (0.002154) test_metadata: .: (0.001236) test_metadata_size: .: (0.001206) test_records_size: .: (0.001218) test_to_s: .: (0.002626) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000883) test_attributes_case2: .: (0.000648) test_attributes_incompatible_backslash_semicolon: .: (0.000855) Bio::TestGFF2MetaData: test_data: .: (0.001498) test_directive: .: (0.000502) test_parse: .: (0.000586) Bio::TestGFF2Record: test_attribute: .: (0.001348) test_attribute_nonexistent: .: (0.001007) test_attributes: .: (0.001065) test_attributes_to_hash: .: (0.001690) test_comment_only?: .: (0.001020) test_delete_attribute: .: (0.001072) test_delete_attribute_multiple: .: (0.001118) test_delete_attribute_multiple2: .: (0.001156) test_delete_attribute_multiple_nil: .: (0.001062) test_delete_attribute_nil: .: (0.001559) test_delete_attribute_nonexistent: .: (0.001104) test_delete_attributes: .: (0.001209) test_delete_attributes_multiple: .: (0.001096) test_delete_attributes_nonexistent: .: (0.001097) test_end: .: (0.000926) test_eqeq: .: (0.002501) test_eqeq_false: .: (0.001819) test_feature: .: (0.000980) test_frame: .: (0.001463) test_get_attribute: .: (0.001139) test_get_attribute_nonexistent: .: (0.001037) test_get_attributes: .: (0.001312) test_get_attributes_nonexistent: .: (0.001015) test_replace_attributes: .: (0.001603) test_replace_attributes_multiple_multiple_over: .: (0.001179) test_replace_attributes_multiple_multiple_same: .: (0.001333) test_replace_attributes_multiple_multiple_two: .: (0.001152) test_replace_attributes_multiple_single: .: (0.001079) test_replace_attributes_nonexistent: .: (0.001688) test_replace_attributes_nonexistent_multiple: .: (0.001136) test_replace_attributes_single_multiple: .: (0.001122) test_score: .: (0.000958) test_self_parse: .: (0.001830) test_seqname: .: (0.001522) test_set_attribute: .: (0.000982) test_set_attribute_multiple: .: (0.001228) test_set_attribute_nonexistent: .: (0.001084) test_sort_attributes_by_tag!: .: (0.001304) test_sort_attributes_by_tag_bang_test2: .: (0.001714) test_sort_attributes_by_tag_bang_with_block: .: (0.001191) test_source: .: (0.000935) test_start: .: (0.000900) test_strand: .: (0.000895) test_to_s: .: (0.001273) Bio::TestGFF2RecordEmpty: test_comment: .: (0.001402) test_comment_eq: .: (0.000533) test_comment_only?: .: (0.000534) test_comment_only_false: .: (0.000541) test_to_s: .: (0.000553) test_to_s_not_empty: .: (0.000757) Bio::TestGFF3: test_const_version: .: (0.002116) test_gff_version: .: (0.002200) test_records: .: (0.002425) test_sequence_regions: .: (0.002126) test_sequences: .: (0.001977) test_to_s: .: (0.003403) Bio::TestGFF3MetaData: test_data: .: (0.000756) test_directive: .: (0.000496) test_parse: .: (0.000543) Bio::TestGFF3Record: test_attributes: .: (0.002058) test_end: .: (0.000933) test_feature: .: (0.000930) test_frame: .: (0.000898) test_id: .: (0.000920) test_score: .: (0.000887) test_seqname: .: (0.001620) test_source: .: (0.000886) test_start: .: (0.000860) test_strand: .: (0.000856) test_to_s: .: (0.001274) test_to_s_attr_order_changed: .: (0.001712) Bio::TestGFF3RecordEscape: test_escape: .: (0.017177) test_escape_attribute: .: (0.000857) test_escape_seqid: .: (0.000719) test_unescape: .: (0.000759) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.018523) test_eqeq: .: (0.000897) test_new_from_sequences_na: .: (0.016451) test_new_from_sequences_na_aa: .: (0.001147) test_new_from_sequences_na_aa_boundary_gap: .: (0.001628) test_new_from_sequences_na_aa_example: .: (0.015159) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.001088) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.001069) test_process_sequences_na: .: (0.000895) test_process_sequences_na_aa: .: (0.016972) test_process_sequences_na_aa_reverse_frameshift: .: (0.000918) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000867) test_process_sequences_na_aa_tooshort: .: (0.011798) test_process_sequences_na_tooshort: .: (0.001015) test_to_s: .: (0.017493) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.001005) test_attributes_one: .: (0.000691) test_attributes_with_escaping: .: (0.000777) test_id_multiple: .: (0.001043) test_id_multiple2: .: (0.001041) test_id_replace: .: (0.000758) test_id_set: .: (0.001525) test_initialize_9: .: (0.000520) test_phase: .: (0.000699) test_score: .: (0.000637) test_to_s_void: .: (0.000596) Bio::TestGFF3RecordTarget: test_end: .: (0.000908) test_parse: .: (0.000775) test_start: .: (0.000634) test_strand: .: (0.000627) test_target_id: .: (0.000581) test_to_s: .: (0.000765) Bio::TestGFF3SequenceRegion: test_end: .: (0.000963) test_parse: .: (0.000794) test_seqid: .: (0.000574) test_start: .: (0.000550) test_to_s: .: (0.000735) Bio::TestGFFRecord: test_attributes: .: (0.000969) test_comment: .: (0.000616) test_end: .: (0.000613) test_feature: .: (0.000628) test_frame: .: (0.001107) test_score: .: (0.000655) test_seqname: .: (0.000665) test_source: .: (0.000645) test_start: .: (0.000606) test_strand: .: (0.000656) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000853) Bio::TestGeneAssociation: test_aspect: .: (0.000881) test_assigned_by: .: (0.000612) test_date: .: (0.000580) test_db: .: (0.000578) test_db_object_id: .: (0.000580) test_db_object_name: .: (0.000585) test_db_object_symbol: .: (0.000572) test_db_object_synonym: .: (0.000605) test_db_object_type: .: (0.000576) test_db_reference: .: (0.000605) test_evidence: .: (0.000690) test_goid: .: (0.000689) test_parser: .: (0.001636) test_qualifier: .: (0.000617) test_taxon: .: (0.001196) test_to_str: .: (0.000600) test_with: .: (0.000616) Bio::TestGenscanReport: test_date_run: .: (0.002610) test_gccontent: .: (0.002499) test_genscan_version: .: (0.002116) test_isochore: .: (0.002697) test_length: .: (0.002165) test_matrix: .: (0.002037) test_predictions_size: .: (0.002485) test_query_name: .: (0.002037) test_time: .: (0.002608) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.002433) test_donor_score: .: (0.002112) test_exon_type: .: (0.002509) test_exon_type_long: .: (0.002099) test_first: .: (0.002687) test_initiation_score: .: (0.002026) test_last: .: (0.002044) test_number: .: (0.002696) test_p_value: .: (0.002197) test_phase: .: (0.002179) test_range: .: (0.002610) test_score: .: (0.001962) test_strand: .: (0.002573) test_t_score: .: (0.002159) test_termination_score: .: (0.002028) Bio::TestGenscanReportGene: test_aaseq: .: (0.002479) test_naseq: .: (0.002118) test_number: .: (0.002411) test_polyA: .: (0.002176) test_promoter: .: (0.002985) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.002778) test_reports_ary_contents: .: (0.002162) Bio::TestHMMERReportConstants: test_rs: .: (0.000869) Bio::TestHMMERReportHit: test_accession: .: (0.003172) test_append_hsp: .: (0.002162) test_bit_score: .: (0.002142) test_definition: .: (0.002503) test_description: .: (0.002145) test_each: .: (0.002270) test_each_hsp: .: (0.002344) test_entry_id: .: (0.002441) test_evalue: .: (0.002005) test_hit: .: (0.002165) test_hit_id: .: (0.002513) test_hsps: .: (0.002191) test_num: .: (0.002125) test_score: .: (0.002133) test_target_def: .: (0.002437) test_target_id: .: (0.002178) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.002492) test_each: .: (0.002496) test_each_hit: .: (0.002171) test_histogram: .: (0.002099) test_hits: .: (0.002122) test_hsps: .: (0.002627) test_parameter: .: (0.002271) test_program: .: (0.002207) test_query_info: .: (0.002068) test_statistical_detail: .: (0.002546) test_total_seq_searched: .: (0.002053) test_whole_seq_top_hits: .: (0.002029) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.002720) test_histogram: .: (0.002994) test_statistical_detail: .: (0.002433) test_total_seq_searched: .: (0.002247) test_whole_seq_top_hit: .: (0.002369) Bio::TestHMMERReportHsp: test_accession: .: (0.002414) test_bit_score: .: (0.002036) test_csline: .: (0.002048) test_domain: .: (0.002545) test_evalue: .: (0.002072) test_flatseq: .: (0.002056) test_hmm_f: .: (0.002031) test_hmm_t: .: (0.002244) test_hmmseq: .: (0.002055) test_hsp: .: (0.007579) test_midline: .: (0.002167) test_query_frame: .: (0.002053) test_query_from: .: (0.002134) test_query_seq: .: (0.002724) test_query_to: .: (0.002051) test_rfline: .: (0.002085) test_score: .: (0.002522) test_seq_f: .: (0.002119) test_seq_ft: .: (0.002175) test_seq_t: .: (0.001977) test_set_alignment: .: (0.002659) test_targat_to: .: (0.002205) test_target_frame: .: (0.001983) test_target_from: .: (0.002738) test_target_seq: .: (0.002286) Bio::TestHetatmFinder: test_each_hetatm: .: (0.001624) test_find_hetatm: .: (0.000910) test_hetatms: .: (0.001909) Bio::TestHeterogen: test_addAtom: .: (0.001174) test_each: .: (0.000886) test_each_hetatm: .: (0.000796) test_get_residue_id_from_atom: .: (0.000845) test_het_atom: .: (0.000691) test_iCode: .: (0.001405) test_inspect: .: (0.000929) test_resSeq: .: (0.000754) test_sort: .: (0.000802) test_square_bracket: .: (0.000746) test_to_s: .: (0.000971) test_update_resudue_id: .: (0.000756) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.001000) test_find_heterogen: .: (0.000628) test_heterogens: .: (0.000864) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.001001) test_match_description: .: (0.000726) test_match_evalue: .: (0.000696) test_match_ipr_description: .: (0.000809) test_match_ipr_id: .: (0.000695) test_match_match_end: .: (0.000736) test_match_match_start: .: (0.000692) test_match_method: .: (0.000771) test_matches_size: .: (0.001414) test_query_id: .: (0.000705) test_query_length: .: (0.000675) Bio::TestIprscanRawReport: test_entry_id: .: (0.006892) test_match_accession: .: (0.006580) test_match_crc64: .: (0.006998) test_match_date: .: (0.006710) test_match_description: .: (0.006892) test_match_evalue: .: (0.006643) test_match_go_terms: .: (0.006554) test_match_ipr_description: .: (0.006673) test_match_ipr_id: .: (0.011224) test_match_match_end: .: (0.006927) test_match_match_start: .: (0.006787) test_match_method: .: (0.006308) test_match_query_id: .: (0.006266) test_match_query_length: .: (0.006529) test_match_status: .: (0.006785) test_obj: .: (0.006983) test_query_id: .: (0.006449) test_query_length: .: (0.006456) test_self_reports_in_raw: .: (0.016091) Bio::TestIprscanReport: test_output_raw: .: (0.002074) test_to_raw: .: (0.001685) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.002666) test_match_accession: .: (0.001563) test_match_date: .: (0.001552) test_match_description: .: (0.001671) test_match_evalue: .: (0.002107) test_match_go_terms: .: (0.001593) test_match_ipr_description: .: (0.001621) test_match_ipr_id: .: (0.001544) test_match_match_end: .: (0.002069) test_match_match_start: .: (0.001603) test_match_method: .: (0.001550) test_match_status: .: (0.001562) test_matches_size: .: (0.002021) test_query_id: .: (0.001606) test_query_length: .: (0.001518) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.002033) test_to_hash_match?: .: (0.002645) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.003884) Bio::TestKeggCompound: test_comment: .: (0.002113) test_dblinks_as_hash: .: (0.001251) test_dblinks_as_strings: .: (0.001022) test_entry_id: .: (0.001015) test_enzymes: .: (0.001738) test_formula: .: (0.001061) test_kcf: .: (0.000924) test_mass: .: (0.001655) test_name: .: (0.001046) test_names: .: (0.001098) test_pathways_as_hash: .: (0.001558) test_pathways_as_strings: .: (0.001253) test_reactions: .: (0.002436) test_remark: .: (0.001010) test_rpairs: .: (0.000999) Bio::TestKeggEnzyme: test_all_reac: .: (0.001896) test_classes: .: (0.001404) test_cofactors: .: (0.001366) test_comment: .: (0.002111) test_dblinks_as_hash: .: (0.001622) test_dblinks_as_strings: .: (0.001361) test_diseases: .: (0.001413) test_entry: .: (0.001558) test_entry_id: .: (0.001529) test_genes: .: (0.147714) test_genes_as_hash: .: (0.039779) test_genes_as_strings: .: (0.011544) test_inhibitors: .: (0.001407) test_iubmb_reactions: .: (0.001504) test_kegg_reactions: .: (0.001442) test_motifs: .: (0.001485) test_name: .: (0.001749) test_names: .: (0.002421) test_obsolete?: .: (0.001390) test_orthologs_as_hash: .: (0.001443) test_orthologs_as_strings: .: (0.001511) test_pathways_as_hash: .: (0.001820) test_pathways_as_strings: .: (0.002194) test_products: .: (0.001422) test_reaction: .: (0.001367) test_structures: .: (0.001978) test_substrates: .: (0.001617) test_sysname: .: (0.002476) Bio::TestKeggGenesDblinks: test_data: .: (0.001046) test_dblinks_0: .: (0.000652) test_dblinks_1: .: (0.000630) test_dblinks_2: .: (0.000650) Bio::TestKeggGenesStructure: test_data: .: (0.000954) test_ids: .: (0.000753) test_ids_in_array: .: (0.000708) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.024277) test_graphics__size: .: (0.030027) test_id: .: (0.023860) test_link: .: (0.023605) test_name: .: (0.025063) test_reaction: .: (0.024625) test_type: .: (0.022381) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.021646) test_graphics__size: .: (0.021285) test_id: .: (0.021251) test_link: .: (0.020863) test_name: .: (0.021091) test_reaction: .: (0.021291) test_type: .: (0.021420) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.022062) test_category: .: (0.021475) test_entry_id: .: (0.023723) test_fgcolor=: .: (0.022484) test_height=: .: (0.021686) test_label=: .: (0.022009) test_shape=: .: (0.022125) test_width=: .: (0.022205) test_x=: .: (0.021904) test_y=: .: (0.021389) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.021554) test_graphics__size: .: (0.021092) test_id: .: (0.021024) test_link: .: (0.020742) test_name: .: (0.020741) test_reaction: .: (0.021152) test_type: .: (0.020776) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.002986) test_graphics=: .: (0.000626) test_id=: .: (0.000628) test_link=: .: (0.000645) test_name=: .: (0.000670) test_reaction=: .: (0.000666) test_type=: .: (0.000619) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000981) test_category=: .: (0.000717) test_entry_id=: .: (0.000683) test_fgcolor=: .: (0.001126) test_height=: .: (0.000703) test_label=: .: (0.000741) test_pathway=: .: (0.000625) test_shape=: .: (0.000749) test_width=: .: (0.000660) test_x=: .: (0.000658) test_y=: .: (0.000704) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.022701) test_coords: .: (0.021422) test_fgcolor: .: (0.021286) test_height: .: (0.021369) test_name: .: (0.021595) test_type: .: (0.021503) test_width: .: (0.023590) test_x: .: (0.021116) test_y: .: (0.020679) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.021237) test_coords: .: (0.020868) test_fgcolor: .: (0.020935) test_height: .: (0.020906) test_name: .: (0.020437) test_type: .: (0.024250) test_width: .: (0.021616) test_x: .: (0.021917) test_y: .: (0.021899) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000898) test_coords=: .: (0.000586) test_fgcolor=: .: (0.000589) test_height=: .: (0.000579) test_name=: .: (0.000589) test_type=: .: (0.000586) test_width=: .: (0.000579) test_x=: .: (0.000600) test_y=: .: (0.000581) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.022283) test_entries__size: .: (0.021152) test_image: .: (0.021213) test_link: .: (0.021228) test_name: .: (0.020952) test_number: .: (0.020974) test_org: .: (0.021166) test_reactions=: .: (0.022129) test_reactions__size: .: (0.020842) test_relations=: .: (0.020924) test_relations__size: .: (0.023828) test_title: .: (0.021763) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.043143) test_name: .: (0.042472) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000992) test_initialize_0: .: (0.000534) test_initialize_1: .: (0.000535) test_initialize_2: .: (0.000640) test_name=: .: (0.000610) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.021697) test_name: .: (0.021350) test_products: .: (0.021091) test_substrates: .: (0.020940) test_type: .: (0.020621) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.001028) test_name=: .: (0.000623) test_products=: .: (0.000659) test_substraces=: .: (0.000604) test_type=: .: (0.000615) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000961) test_entry_id=: .: (0.000671) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.021198) test_entry2: .: (0.021834) test_name: .: (0.020775) test_type: .: (0.023770) test_value: .: (0.021697) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000838) test_node1=: .: (0.000670) test_node2=: .: (0.000657) test_rel=: .: (0.000704) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.001399) test_entry2=: .: (0.000643) test_name=: .: (0.000609) test_type=: .: (0.000620) test_value=: .: (0.000643) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.044506) test_name: .: (0.042113) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000912) test_initialize_0: .: (0.000518) test_initialize_1: .: (0.000513) test_initialize_2: .: (0.000519) test_name=: .: (0.000637) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000930) test_initialize_0: .: (0.000507) test_initialize_1: .: (0.000577) test_initialize_2: .: (0.000551) test_name=: .: (0.000876) Bio::TestKeggModule: test_compounds: .: (0.001424) test_compounds_as_hash: .: (0.001038) test_compounds_as_strings: .: (0.000896) test_definition: .: (0.000899) test_entry_id: .: (0.000856) test_keggclass: .: (0.000864) test_name: .: (0.000828) test_new: .: (0.000803) test_orthologs: .: (0.001322) test_orthologs_as_array: .: (0.001158) test_orthologs_as_hash: .: (0.001040) test_orthologs_as_strings: .: (0.000905) test_pathways: .: (0.000829) test_pathways_as_hash: .: (0.000897) test_pathways_as_strings: .: (0.000834) test_reactions: .: (0.001048) test_reactions_as_hash: .: (0.001378) test_reactions_as_strings: .: (0.000993) Bio::TestKeggOrthology: test_dblinks: .: (0.001708) test_dblinks_as_hash: .: (0.001329) test_dblinks_as_strings: .: (0.001213) test_definition: .: (0.001309) test_entry_id: .: (0.001232) test_genes_as_hash: .: (0.031488) test_genes_as_strings: .: (0.010210) test_keggclass: .: (0.001516) test_keggclasses: .: (0.001768) test_modules: .: (0.001196) test_modules_as_hash: .: (0.001227) test_modules_as_strings: .: (0.001168) test_name: .: (0.001283) test_names: .: (0.001269) test_pathways_as_strings: .: (0.001256) test_pathways_in_keggclass: .: (0.001535) test_references: .: (0.001869) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.001235) test_compounds_as_strings: .: (0.000852) test_dblinks_as_hash: .: (0.000851) test_dblinks_as_strings: .: (0.000916) test_description: .: (0.000923) test_diseases_as_hash: .: (0.000844) test_diseases_as_strings: .: (0.000834) test_entry_id: .: (0.000931) test_enzymes_as_strings: .: (0.000829) test_genes_as_hash: .: (0.001177) test_genes_as_strings: .: (0.000844) test_keggclass: .: (0.000952) test_ko_pathway: .: (0.000911) test_modules_as_hash: .: (0.001045) test_modules_as_strings: .: (0.000922) test_name: .: (0.000952) test_organism: .: (0.000956) test_orthologs_as_hash: .: (0.001273) test_orthologs_as_strings: .: (0.000968) test_pathways_as_hash: .: (0.000892) test_pathways_as_strings: .: (0.000870) test_reactions_as_hash: .: (0.000886) test_reactions_as_strings: .: (0.000855) test_references: .: (0.000871) test_rel_pathways_as_hash: .: (0.000982) test_rel_pathways_as_strings: .: (0.000924) Bio::TestKeggReaction: test_definition: .: (0.001421) test_entry_id: .: (0.001231) test_enzymes: .: (0.001034) test_equation: .: (0.001072) test_name: .: (0.001083) test_orthologs_as_hash: .: (0.001060) test_orthologs_as_strings: .: (0.000986) test_pathways_as_hash: .: (0.001078) test_pathways_as_strings: .: (0.000887) test_rpairs_as_hash: .: (0.001185) test_rpairs_as_strings: .: (0.001031) test_rpairs_as_tokens: .: (0.001131) Bio::TestLasergene: test_methods: .: (0.018501) Bio::TestLocations: test_complement: .: (0.001002) test_hat: .: (0.000715) test_normal: .: (0.000732) test_replace_single_base: .: (0.000593) test_should_not_modify_argument: .: (0.000680) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.009915) test_locations_to_s: .: (0.004625) Bio::TestMEDLINE: test_authors: .: (0.002146) test_authors_with_last_name_all_caps: .: (0.000616) test_authors_with_suffix: .: (0.000595) Bio::TestMEDLINE_20146148: test_ab: .: (0.001871) test_ad: .: (0.001304) test_au: .: (0.001275) test_authors: .: (0.001331) test_doi: .: (0.001483) test_dp: .: (0.001321) test_ip: .: (0.001254) test_mh: .: (0.001405) test_pages: .: (0.001281) test_pg: .: (0.001593) test_pii: .: (0.001303) test_pmid: .: (0.001292) test_pt: .: (0.001295) test_reference: .: (0.002237) test_self_new: .: (0.001378) test_so: .: (0.001381) test_ta: .: (0.001344) test_ti: .: (0.001444) test_ui: .: (0.001276) test_vi: .: (0.008527) test_year: .: (0.001475) Bio::TestMapSimple: test_attributes: .: (0.001236) Bio::TestMapping: test_add_mapping_as_map: .: (0.001131) test_add_mapping_as_marker: .: (0.000796) test_contains_marker?: .: (0.000695) test_mapped_to?: .: (0.001154) test_mapping_location_comparison: .: (0.001164) test_mappings_as_map_each: .: (0.000642) test_mappings_as_marker_each: .: (0.000793) test_mappings_on: .: (0.000776) test_multiple_mappings_between_same_marker_and_map: .: (0.001296) test_positions_on: .: (0.000799) test_raise_error_kind_of: .: (0.001870) Bio::TestMast: test_check_options_with_empty_opts: .: (0.001260) test_check_options_with_invalid_opts: .: (0.000910) test_check_options_with_valid_opts: .: (0.000846) test_command_to_be_run: .: (0.000845) test_config_defaults: .: (0.000763) test_minimal_config: .: (0.000800) test_more_config: .: (0.000686) test_run: .: (0.000574) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.001523) test_report_has_motifs: .: (0.001582) Bio::TestModel: test_addChain: .: (0.000950) test_comp: .: (0.000655) test_each: .: (0.000686) test_each_chain: .: (0.000593) test_inspect: .: (0.000566) test_rehash: .: (0.000530) test_square_brace: .: (0.000601) test_to_s: .: (0.000580) Bio::TestModelFinder: test_find_model: .: (0.000996) Bio::TestMotif: test_creation_and_attributes: .: (0.001342) test_length: .: (0.000563) Bio::TestMyGraph: test_cliquishness: .: (0.001724) Bio::TestNA: test_accessor: .: (0.000890) test_na: .: (0.000523) test_name: .: (0.000541) test_names: .: (0.000507) test_to_re: .: (0.000844) test_weight: .: (0.000563) test_weight_rna: .: (0.000849) Bio::TestNAConstants: test_NAMES: .: (0.000776) test_NAMES_1_to_name: .: (0.000526) test_WEIGHT: .: (0.000570) Bio::TestNATranslate: test_translate: .: (0.001163) test_translate_1: .: (0.000724) test_translate_2: .: (0.000627) test_translate_3: .: (0.000617) test_translate_4: .: (0.000763) test_translate_5: .: (0.000578) test_translate_6: .: (0.000686) Bio::TestNCBIDB: test_fetch: .: (0.001009) test_p_entry2hash: .: (0.000557) test_p_subtag2array: .: (0.000549) test_p_toptag2array: .: (0.000493) Bio::TestNewick: test_reparse: .: (0.003566) test_reparse_before_lazy_parsing: .: (0.001467) test_string_tree: .: (0.002859) Bio::TestNewick2: test_string_tree: .: (0.002194) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000940) test_parse_newick_leaf: .: (0.000796) test_parse_newick_tokenize: .: (0.001168) Bio::TestNexus: test_nexus: .: (0.032955) Bio::TestOSLine: test_period_trancation_O63147: .: (0.001077) test_uncapitalized_letter_Q32725_9POAL: .: (0.000676) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000894) test_load_parameters: .: (0.000596) test_parameters: .: (0.000515) test_set_default_parameters: .: (0.000576) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.004263) test_expected_parameters_set_in_control_file: .: (0.002913) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.001031) test_new_with_parameters: .: (0.000678) test_new_with_two_argument: .: (0.000705) test_new_without_argument: .: (0.000577) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.004554) test_rates_hundred_and_fiftieth_position: .: (0.004162) test_rates_last_position: .: (0.004138) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.025112) test_tree: .: (0.024768) test_tree_length: .: (0.024593) test_tree_log_likelihood: .: (0.024511) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.001857) test_parameters_should_be_loaded_from_control: .: (0.001096) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.004218) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.001010) test_dN_dS: .: (0.000748) test_kappa: .: (0.000759) test_lnL: .: (0.000796) test_m3_classes: .: (0.001017) test_m3_lnL: .: (0.001273) test_m3_to_s: .: (0.000845) test_m3_tree: .: (0.002268) test_omega: .: (0.000775) test_to_s: .: (0.000755) test_tree: .: (0.001897) test_tree_length: .: (0.000737) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.001732) test_p: .: (0.001946) test_position: .: (0.001413) test_probability: .: (0.001423) test_w: .: (0.001876) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.001816) test_graph_omega: .: (0.001680) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.001037) test_footer: .: (0.001201) test_header: .: (0.000778) test_initialize: .: (0.000771) test_models: .: (0.000836) test_nb_sites: .: (0.001985) test_num_codons: .: (0.000813) test_num_sequences: .: (0.000836) test_significant: .: (0.000856) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.001460) test_nb_sites: .: (0.001149) test_significant: .: (0.000827) test_sites: .: (0.004051) Bio::TestPDB: test_accession: .: (0.003198) test_addModel: .: (0.002791) test_authors: .: (0.002593) test_bracket: .: (0.003071) test_classification: .: (0.002340) test_dbref: .: (0.003270) test_definition: .: (0.002314) test_each: .: (0.002833) test_each_model: .: (0.002354) test_entry_id: .: (0.002789) test_helix: .: (0.003247) test_inspect: .: (0.002782) test_jrnl: .: (0.002327) test_keywords: .: (0.002861) test_record: .: (0.002359) test_remark: .: (0.002891) test_seqres: .: (0.003410) test_sheet: .: (0.004150) test_ssbond: .: (0.002354) test_to_s: .: (0.003605) test_turn: .: (0.002334) test_version: .: (0.003072) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.001012) test_U12: .: (0.000754) test_U13: .: (0.000724) test_U22: .: (0.000674) test_U23: .: (0.000879) test_U33: .: (0.000712) test_altLoc: .: (0.000676) test_chainID: .: (0.000727) test_charge: .: (0.000781) test_element: .: (0.000663) test_iCode: .: (0.000709) test_name: .: (0.001305) test_resName: .: (0.000926) test_resSeq: .: (0.000661) test_segID: .: (0.000716) test_serial: .: (0.000741) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000957) test_anisou: .: (0.000553) test_chainID: .: (0.000564) test_charge: .: (0.000617) test_comparable: .: (0.000628) test_do_parse: .: (0.000553) test_element: .: (0.000640) test_iCode: .: (0.000609) test_name: .: (0.000655) test_occupancy: .: (0.000689) test_original_data: .: (0.000553) test_record_name: .: (0.000576) test_resName: .: (0.000657) test_resSeq: .: (0.000550) test_residue: .: (0.000587) test_segID: .: (0.000548) test_serial: .: (0.000573) test_sigatm: .: (0.000547) test_tempFactor: .: (0.000694) test_ter: .: (0.000600) test_to_a: .: (0.000565) test_to_s: .: (0.000692) test_x: .: (0.000742) test_xyz: .: (0.000640) test_y: .: (0.000642) test_z: .: (0.001061) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000949) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000911) test_idcode: .: (0.000636) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.001051) test_chainID2: .: (0.000658) test_icode1: .: (0.000709) test_icode2: .: (0.000697) test_measure: .: (0.000754) test_modNum: .: (0.000709) test_pep1: .: (0.000709) test_pep2: .: (0.001179) test_seqNum1: .: (0.000658) test_seqNum2: .: (0.000627) test_serNum: .: (0.000697) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000903) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000930) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000927) test_alpha: .: (0.000591) test_b: .: (0.000587) test_beta: .: (0.000576) test_c: .: (0.000638) test_gamma: .: (0.000577) test_sGroup: .: (0.000581) test_z: .: (0.000635) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.001482) test_database: .: (0.000702) test_dbAccession: .: (0.000692) test_dbIdCode: .: (0.000694) test_dbseqBegin: .: (0.000698) test_dbseqEnd: .: (0.000701) test_idCode: .: (0.000713) test_idbnsBeg: .: (0.000687) test_insertBegin: .: (0.000762) test_insertEnd: .: (0.000688) test_seqBegin: .: (0.000690) test_seqEnd: .: (0.001175) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000852) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000948) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000895) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000841) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000953) test_depDate: .: (0.000603) test_idCode: .: (0.000609) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000969) test_hetID: .: (0.000710) test_iCode: .: (0.001194) test_numHetAtoms: .: (0.000539) test_seqNum: .: (0.000746) test_text: .: (0.000529) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000806) test_anisou: .: (0.000538) test_chainID: .: (0.000504) test_charge: .: (0.000605) test_comparable: .: (0.000570) test_do_parse: .: (0.000506) test_element: .: (0.000481) test_iCode: .: (0.000729) test_name: .: (0.000591) test_occupancy: .: (0.000611) test_original_data: .: (0.000583) test_record_name: .: (0.000510) test_resName: .: (0.000483) test_resSeq: .: (0.000741) test_residue: .: (0.000482) test_segID: .: (0.000505) test_serial: .: (0.000561) test_sigatm: .: (0.000615) test_tempFactor: .: (0.000571) test_ter: .: (0.000504) test_to_a: .: (0.000653) test_to_s: .: (0.000661) test_x: .: (0.000675) test_xyz: .: (0.000609) test_y: .: (0.001257) test_z: .: (0.000684) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.001177) test_ChainH: .: (0.000806) test_ICode1: .: (0.000829) test_altLoc1: .: (0.000892) test_altLoc2: .: (0.000737) test_altLocH: .: (0.000825) test_chainID2: .: (0.000804) test_iCode2: .: (0.000778) test_iCodeH: .: (0.000722) test_name1: .: (0.001145) test_name2: .: (0.000814) test_nameH: .: (0.000780) test_resName1: .: (0.000781) test_resName2: .: (0.000794) test_resSeq1: .: (0.000811) test_resSeq2: .: (0.000855) test_resSeqH: .: (0.000798) test_sym1: .: (0.000760) test_sym2: .: (0.000782) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.001286) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.001038) test_altLoc2: .: (0.000780) test_chainID1: .: (0.000773) test_chainID2: .: (0.000788) test_iCode1: .: (0.000676) test_iCode2: .: (0.000760) test_name1: .: (0.000779) test_name2: .: (0.000681) test_resName1: .: (0.000801) test_resName2: .: (0.000788) test_resSeq1: .: (0.000684) test_resSeq2: .: (0.001124) test_sym1: .: (0.000696) test_sym2: .: (0.000753) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000816) test_numCoord: .: (0.000477) test_numHelix: .: (0.000441) test_numHet: .: (0.000426) test_numRemark: .: (0.000488) test_numSeq: .: (0.000457) test_numSheet: .: (0.000449) test_numSite: .: (0.000432) test_numTer: .: (0.000421) test_numTurn: .: (0.000421) test_numXform: .: (0.000425) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.001141) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000801) test_comment: .: (0.000484) test_iCode: .: (0.000472) test_idCode: .: (0.000480) test_resName: .: (0.000481) test_seqNum: .: (0.000470) test_stdRes: .: (0.000481) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000775) test_Mn2: .: (0.000418) test_Mn3: .: (0.000407) test_Vn: .: (0.000491) test_iGiven: .: (0.000449) test_serial: .: (0.000460) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.001272) test_Mn2: .: (0.000445) test_Mn3: .: (0.000412) test_Vn: .: (0.000450) test_iGiven: .: (0.000418) test_serial: .: (0.000411) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000715) test_Mn2: .: (0.000429) test_Mn3: .: (0.000413) test_Vn: .: (0.000403) test_iGiven: .: (0.000419) test_serial: .: (0.000491) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000775) test_rIdCode: .: (0.000904) test_repDate: .: (0.000430) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000701) test_On2: .: (0.000444) test_On3: .: (0.000414) test_Tn: .: (0.000394) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000729) test_modId: .: (0.000452) test_modNum: .: (0.000437) test_modType: .: (0.000440) test_record: .: (0.000444) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000679) test_text: .: (0.000441) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000807) test_Sn2: .: (0.000405) test_Sn3: .: (0.000394) test_Un: .: (0.000438) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000693) test_Sn2: .: (0.000420) test_Sn3: .: (0.000404) test_Un: .: (0.000405) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000725) test_Sn2: .: (0.000414) test_Sn3: .: (0.000486) test_Un: .: (0.000402) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.001390) test_conflict: .: (0.000565) test_database: .: (0.000499) test_dbIdCode: .: (0.000500) test_dbRes: .: (0.000519) test_dbSeq: .: (0.000497) test_iCode: .: (0.000540) test_idCode: .: (0.000498) test_resName: .: (0.000494) test_seqNum: .: (0.000496) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000828) test_numRes: .: (0.000514) test_resName: .: (0.000699) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000874) test_curChainId: .: (0.019578) test_curICode: .: (0.000741) test_curResName: .: (0.000610) test_curResSeq: .: (0.000648) test_endChainID: .: (0.000628) test_endICode: .: (0.000641) test_endResName: .: (0.000616) test_endSeqNum: .: (0.000631) test_initChainID: .: (0.000617) test_initICode: .: (0.000623) test_initResName: .: (0.001182) test_initSeqNum: .: (0.000625) test_numStrands: .: (0.000607) test_prevAtom: .: (0.000595) test_prevChainId: .: (0.000617) test_prevICode: .: (0.000615) test_prevResName: .: (0.000605) test_prevResSeq: .: (0.000600) test_sense: .: (0.000667) test_sheetID: .: (0.000618) test_strand: .: (0.001213) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000940) test_chainID: .: (0.000529) test_charge: .: (0.000546) test_element: .: (0.000511) test_iCode: .: (0.000508) test_name: .: (0.000543) test_resName: .: (0.000546) test_resSeq: .: (0.000520) test_segID: .: (0.000519) test_serial: .: (0.000517) test_sigOcc: .: (0.000538) test_sigTemp: .: (0.000559) test_sigX: .: (0.000516) test_sigY: .: (0.000565) test_sigZ: .: (0.000573) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000886) test_SigmaU12: .: (0.000512) test_SigmaU13: .: (0.000516) test_SigmaU22: .: (0.000552) test_SigmaU23: .: (0.000512) test_SigmaU33: .: (0.000538) test_altLoc: .: (0.000519) test_chainID: .: (0.000967) test_charge: .: (0.000532) test_element: .: (0.000514) test_iCode: .: (0.000509) test_name: .: (0.000506) test_resName: .: (0.000570) test_resSeq: .: (0.000542) test_segID: .: (0.000530) test_serial: .: (0.000512) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000921) test_chainID2: .: (0.000544) test_chainID3: .: (0.000586) test_chainID4: .: (0.001017) test_iCode1: .: (0.000592) test_iCode2: .: (0.000542) test_iCode3: .: (0.000537) test_iCode4: .: (0.000542) test_numRes: .: (0.000558) test_resName1: .: (0.000587) test_resName2: .: (0.000554) test_resName3: .: (0.000591) test_resName4: .: (0.000570) test_seq1: .: (0.000548) test_seq2: .: (0.000602) test_seq3: .: (0.001140) test_seq4: .: (0.000542) test_seqNum: .: (0.000541) test_siteID: .: (0.000593) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000848) test_altLoc2: .: (0.000498) test_atom1: .: (0.000483) test_atom2: .: (0.000532) test_chainID1: .: (0.000480) test_chainID2: .: (0.000504) test_iCode1: .: (0.000471) test_iCode2: .: (0.000486) test_resName1: .: (0.000505) test_resName2: .: (0.000474) test_resSeq1: .: (0.000480) test_resSeq2: .: (0.000461) test_sym1: .: (0.000469) test_sym2: .: (0.000470) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000977) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000725) test_sIdCode: .: (0.000445) test_sprsdeDate: .: (0.000429) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000750) test_iCode: .: (0.000440) test_resName: .: (0.000476) test_resSeq: .: (0.000439) test_serial: .: (0.000482) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000721) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000740) test_t1: .: (0.000459) test_t2: .: (0.000435) test_t3: .: (0.000457) test_text: .: (0.000455) Bio::TestPROSITE: test_ac: .: (0.005189) test_cc: .: (0.004559) test_de: .: (0.004329) test_division: .: (0.004560) test_dr: .: (0.038671) test_dt: .: (0.003990) test_false_neg: .: (0.004104) test_false_pos: .: (0.003907) test_false_positive_sequences: .: (0.003912) test_list_falsenegative: .: (0.041308) test_list_falsepositive: .: (0.097771) test_list_potentialhit: .: (0.105535) test_list_truepositive: .: (0.044574) test_list_unknown: .: (0.043859) test_list_xref: .: (0.042691) test_ma: .: (0.004413) test_max_repeat: .: (0.004408) test_name: .: (0.004475) test_nr: .: (0.004217) test_pa: .: (0.004524) test_pa2re: .: (0.004414) test_partial: .: (0.004544) test_pdb_xref: .: (0.004648) test_pdoc_xref: .: (0.003797) test_positive: .: (0.004510) test_positive_hits: .: (0.005174) test_positive_sequences: .: (0.004550) test_release: .: (0.005173) test_ru: .: (0.004109) test_self_pa2re: .: (0.005880) test_site: .: (0.005147) test_skip_flag: .: (0.005049) test_swissprot_release_number: .: (0.004194) test_swissprot_release_sequences: .: (0.005675) test_taxon_range: .: (0.004920) test_total: .: (0.004793) test_total_hits: .: (0.004838) test_total_sequences: .: (0.004910) test_unknown: .: (0.005095) test_unknown_hits: .: (0.004352) test_unknown_sequences: .: (0.004368) Bio::TestPROSITEConst: test_delimiter: .: (0.000902) test_tagsize: .: (0.000507) Bio::TestPTS1: test_function_set: .: (0.001849) test_function_set_number_1: .: (0.000601) test_function_set_number_2: .: (0.000548) test_function_set_number_3: .: (0.000602) test_function_show: .: (0.000524) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000784) Bio::TestPTS1New: test_fungi: .: (0.000807) test_general: .: (0.000534) test_metazoa: .: (0.000565) Bio::TestQualifier: test_qualifier: .: (0.000806) test_value: .: (0.000495) Bio::TestREBASE: test_methods: .: (0.003746) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.002442) test_bit_score: .: (0.002676) test_evalue: .: (0.002152) test_gaps: .: (0.001855) test_hit_from: .: (0.001925) test_hit_to: .: (0.001963) test_hseq: .: (0.009941) test_identity: .: (0.001902) test_midline: .: (0.002004) test_percent_identity: .: (0.001893) test_positive: .: (0.001907) test_qseq: .: (0.003257) test_query_from: .: (0.001953) test_query_to: .: (0.001850) test_score: .: (0.001818) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.002745) test_hits_size: .: (0.003888) test_iterations_size: .: (0.003422) test_program: .: (0.002416) test_query_def: .: (0.003411) test_query_len: .: (0.003373) test_version: .: (0.002553) test_version_date: .: (0.001928) test_version_number: .: (0.001607) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.002363) test_definition: .: (0.001984) test_evalue: .: (0.002841) test_hsps_size: .: (0.001970) test_identity: .: (0.001918) test_lap_at: .: (0.002063) test_len: .: (0.001907) test_midline: .: (0.003235) test_overlap: .: (0.002349) test_query_end: .: (0.001970) test_query_seq: .: (0.002032) test_query_start: .: (0.003038) test_target_def: .: (0.002139) test_target_end: .: (0.001976) test_target_len: .: (0.001883) test_target_seq: .: (0.002000) test_target_start: .: (0.002977) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001738) test_get_entry: .: (0.001660) test_rewind: .: (0.000605) test_skip_leader: .: (0.000878) Bio::TestReference: test_abstract: .: (0.000886) test_affiliations: .: (0.000564) test_authors: .: (0.001185) test_format_bibitem: .: (0.000722) test_format_bibtex: .: (0.000899) test_format_bibtex_with_arguments: .: (0.000849) test_format_cell: .: (0.000596) test_format_current: .: (0.000612) test_format_endnote: .: (0.000664) test_format_general: .: (0.000700) test_format_genome_biol: .: (0.000626) test_format_genome_res: .: (0.000644) test_format_nar: .: (0.000656) test_format_nature: .: (0.001967) test_format_rd: .: (0.000624) test_format_science: .: (0.000751) test_format_trends: .: (0.000594) test_issue: .: (0.000509) test_journal: .: (0.000864) test_mesh: .: (0.000533) test_pages: .: (0.000520) test_pubmed: .: (0.000558) test_pubmed_url: .: (0.000528) test_url: .: (0.000550) test_volume: .: (0.000511) test_year: .: (0.000521) Bio::TestReference_noURL: test_format_endnote: .: (0.001008) test_url: .: (0.000555) Bio::TestReferences: test_append: .: (0.000930) test_each: .: (0.000597) Bio::TestRelation: test_comparison_operator: .: (0.000968) test_uniq: .: (0.000659) Bio::TestResidue: test_addAtom: .: (0.001271) test_each: .: (0.001879) test_each_atom: .: (0.000874) test_get_residue_id_from_atom: .: (0.000760) test_het_atom: .: (0.000673) test_iCode: .: (0.000753) test_inspect: .: (0.001084) test_resSeq: .: (0.000684) test_sort: .: (0.000791) test_square_bracket: .: (0.000743) test_to_s: .: (0.001335) test_update_resudue_id: .: (0.000719) Bio::TestResidueFinder: test_each_residue: .: (0.001033) test_find_residue: .: (0.000684) test_residues: .: (0.000692) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.359529) test_cut_from_bio_sequence_na: .: (0.086878) test_cut_without_permutations: .: (0.063631) test_view_ranges: .: (0.069384) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.004220) test_cuts_after_remove_incomplete_cuts: .: (0.002569) test_strands_for_display: .: (0.008625) test_strands_for_display_current: .: (0.002105) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.001826) test_fragments_for_display_1: .: (0.002659) test_fragments_for_display_10: .: (0.003498) test_fragments_for_display_2: .: (0.002727) test_fragments_for_display_3: .: (0.004454) test_fragments_for_display_4: .: (0.003115) test_fragments_for_display_5: .: (0.002175) test_fragments_for_display_6: .: (0.002461) test_fragments_for_display_7: .: (0.002221) test_fragments_for_display_8: .: (0.001995) test_fragments_for_display_9: .: (0.002536) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.001328) test_obj_3: .: (0.001089) test_obj_7: .: (0.000965) test_obj_z: .: (0.000950) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.001627) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.001044) test_bracket_eq: .: (0.000707) test_concat: .: (0.000647) test_delete: .: (0.000617) test_dup: .: (0.000737) test_each: .: (0.000752) test_eqeq: .: (0.000614) test_eqeq_false: .: (0.000601) test_eqeq_other: .: (0.000538) test_eqeq_self: .: (0.000589) test_include?: .: (0.000876) test_internal_data: .: (0.000548) test_internal_data_eq: .: (0.000634) test_length: .: (0.000529) test_ltlt: .: (0.000585) test_ltlt_larger: .: (0.000590) test_ltlt_middle: .: (0.000610) test_plus: .: (0.000660) test_plus_error: .: (0.000682) test_push: .: (0.000694) test_reverse_each: .: (0.000743) test_self_bracket: .: (0.000542) test_self_new: .: (0.000618) test_size: .: (0.000548) test_sort!: .: (0.000545) test_to_a: .: (0.000956) test_uniq!: .: (0.000549) test_unshift: .: (0.000690) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.014042) test_complement: .: (0.012331) test_complement_with_cut_symbols: .: (0.013201) test_cut_locations: .: (0.012442) test_cut_locations_in_enzyme_notation: .: (0.012374) test_primary: .: (0.012103) test_primary_with_cut_symbols: .: (0.013311) test_to_re: .: (0.012590) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.003494) test_align_with_cuts: .: (0.002627) test_argument_error: .: (0.003661) test_ds: .: (0.003092) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.001549) test_complement: .: (0.000874) test_contents: .: (0.000867) test_primary: .: (0.000870) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.001423) test_complement: .: (0.001188) test_contents: .: (0.000830) test_primary: .: (0.000802) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000994) test_contents: .: (0.000727) test_primary: .: (0.000753) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.001118) test_complement_to_array_index: .: (0.001035) test_complement_to_array_index_class: .: (0.001270) test_contents: .: (0.000768) test_primary: .: (0.000741) test_primary_to_array_index: .: (0.001030) test_primary_to_array_index_class: .: (0.000954) test_to_array_index: .: (0.001620) test_to_array_index_class: .: (0.001498) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.001680) test_rebase: .: (0.000675) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.003218) test_creation_with_no_cuts: .: (0.001697) test_cut_locations: .: (0.001751) test_cut_locations_in_enzyme_notation: .: (0.001748) test_orientation: .: (0.001658) test_pattern: .: (0.001712) test_pattern_palindromic?: .: (0.002364) test_stripped: .: (0.001648) test_to_re: .: (0.001495) test_with_cut_symbols: .: (0.002082) test_with_spaces: .: (0.001800) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.002804) test_creation_with_no_cuts: .: (0.009606) test_cut_locations: .: (0.001814) test_cut_locations_in_enzyme_notation: .: (0.001892) test_orientation: .: (0.001599) test_pattern: .: (0.001779) test_pattern_palindromic?: .: (0.002066) test_stripped: .: (0.001693) test_to_re: .: (0.001457) test_with_cut_symbols: .: (0.001732) test_with_spaces: .: (0.002367) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.001732) test_initialize_with_pattern: .: (0.001294) test_max: .: (0.000662) test_min: .: (0.000756) test_to_array_index: .: (0.001116) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.001018) test_bracket_eq: .: (0.000659) test_concat: .: (0.000578) test_delete: .: (0.000586) test_dup: .: (0.000674) test_each: .: (0.000748) test_eqeq: .: (0.000541) test_eqeq_false: .: (0.000519) test_eqeq_other: .: (0.000544) test_eqeq_self: .: (0.000514) test_include?: .: (0.000632) test_internal_data_hash: .: (0.000532) test_internal_data_hash_eq: .: (0.000844) test_length: .: (0.000510) test_ltlt: .: (0.000551) test_ltlt_noeffect: .: (0.000613) test_plus: .: (0.000539) test_plus_error: .: (0.000702) test_private_push_element: .: (0.000556) test_private_push_element_intermediate: .: (0.000585) test_private_push_element_last: .: (0.000616) test_private_push_element_noeffect: .: (0.000560) test_private_sorted_keys: .: (0.000542) test_private_unshift_element: .: (0.000574) test_private_unshift_element_first: .: (0.000588) test_private_unshift_element_intermediate: .: (0.000602) test_private_unshift_element_noeffect: .: (0.000847) test_push: .: (0.000633) test_reverse_each: .: (0.000786) test_self_bracket: .: (0.000530) test_self_new: .: (0.000616) test_size: .: (0.000533) test_sort!: .: (0.000533) test_to_a: .: (0.000529) test_uniq!: .: (0.000521) test_unshift: .: (0.000599) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000964) test_left_padding: .: (0.000651) test_right_padding: .: (0.000648) test_strip_padding: .: (0.000954) Bio::TestSOFT: test_dataset: .: (0.021486) test_series: .: (0.020896) Bio::TestSOSUIReport: test_entry_id: .: (0.001440) test_prediction: .: (0.000677) test_tmh: .: (0.000711) test_tmhs: .: (0.000738) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000770) test_rs: .: (0.000492) Bio::TestSOSUITMH: test_grade: .: (0.000972) test_range: .: (0.000688) test_sequence: .: (0.000700) Bio::TestSampleGraph: test_bellman_ford: .: (0.001937) test_bfs_shortest_path: .: (0.000853) test_breadth_first_search: .: (0.000832) test_depth_first_search: .: (0.001136) test_dijkstra: .: (0.000936) test_dump_list: .: (0.000918) test_dump_matrix: .: (0.001213) test_extract_subgraph_by_label: .: (0.000890) test_extract_subgraph_by_list: .: (0.000886) test_extract_subgraph_retains_disconnected_nodes: .: (0.000723) test_small_world_aka_node_degree_histogram: .: (0.000724) test_to_matrix: .: (0.001333) test_to_matrix_fixed_index: .: (0.001024) test_undirected_cliquishness: .: (0.001127) Bio::TestScf_version_2: test_complement: .: (0.030651) test_seq: .: (0.029005) test_to_biosequence: .: (0.029292) Bio::TestScf_version_3: test_complement: .: (0.096361) test_seq: .: (0.095419) test_to_biosequence: .: (0.095752) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000916) test_AA_new_sequence_all_legal_symbols: .: (0.000552) test_AA_new_sequence_removes_whitespace: .: (0.000533) test_AA_new_sequence_upcases_symbols: .: (0.000553) test_DNA_new_blank_sequence: .: (0.000524) test_DNA_new_sequence_downcases_symbols: .: (0.000555) test_DNA_new_sequence_removes_whitespace: .: (0.000822) test_NA_randomize_with_counts: .: (0.002515) test_NA_randomize_with_counts_and_block: .: (0.003205) test_RNA_new_sequence: .: (0.000532) test_ambiguous_dna_sequence_complement: .: (0.000598) test_ambiguous_rna_sequence_complement: .: (0.000544) test_amino_acid_codes: .: (0.000989) test_amino_acid_molecular_weight: .: (0.000904) test_amino_acid_names: .: (0.000644) test_amino_acid_randomize_can_be_chained: .: (0.003808) test_amino_acid_randomize_has_same_composition: .: (0.001984) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.002376) test_dna_composition: .: (0.000640) test_dna_gc_percent: .: (0.000699) test_dna_molecular_weight: .: (0.000751) test_dna_pikachu: .: (0.000557) test_dna_sequence_complement: .: (0.000563) test_dna_sequence_translate: .: (0.001680) test_dna_to_re: .: (0.000722) test_element_reference_operator_with_one_argument: .: (0.000528) test_element_reference_operator_with_two_arguments: .: (0.000525) test_invalid_nucleic_acid_illegal_bases: .: (0.000634) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000718) test_nucleic_acid_names: .: (0.000573) test_randomize_dna_can_be_chained: .: (0.001339) test_randomize_dna_retains_composition: .: (0.001032) test_randomize_dna_with_block: .: (0.001491) test_rna_composition: .: (0.000635) test_rna_gc_percent: .: (0.000652) test_rna_molecular_weight: .: (0.000800) test_rna_pikachu: .: (0.000547) test_rna_sequence_complement: .: (0.000575) test_rna_sequence_translate: .: (0.001223) test_rna_to_re: .: (0.000778) test_total: .: (0.000596) test_two_consecutive_dna_randomizations_not_equal: .: (0.001392) test_valid_dna_sequence_illegal_bases: .: (0.000564) Bio::TestSequenceAA: test_codes: .: (0.000912) test_molecular_weight: .: (0.000746) test_names: .: (0.000593) test_to_re: .: (0.000752) test_to_s: .: (0.000512) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.001047) Bio::TestSequenceAANew: test_new: .: (0.000842) test_new_n: .: (0.000525) test_new_r: .: (0.000522) test_new_t: .: (0.000538) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000977) test_concat: .: (0.000527) test_push: .: (0.000506) test_seq: .: (0.000510) test_splicing: .: (0.000776) test_sum: .: (0.000538) test_to_s: .: (0.000493) test_to_str: .: (0.000551) test_total: .: (0.000544) test_window_search: .: (0.001219) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000767) test_normalize_A: .: (0.000540) test_normalize_a: .: (0.000525) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.013382) test_randomize_with_block: .: (0.013644) test_randomize_with_hash: .: (0.004190) test_randomize_with_hash_block: .: (0.016086) 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' =============================================================================== : (0.004524) 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' =============================================================================== : (0.003549) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.001542) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000757) test_subseq_returns_subsequence: .: (0.000524) test_to_s_returns_self_as_string: .: (0.000594) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000889) test_window_search_with_width_3_step_two_with_residual: .: (0.000579) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000903) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000815) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.001057) test_na_self_randomize: .: (0.001270) Bio::TestSequenceDBLink: test_database: .: (0.000783) test_id: .: (0.000515) test_secondary_ids: .: (0.000500) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000883) test_parse_uniprot_DR_line: .: (0.000647) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.003353) test_output_width_35: .: (0.001151) test_output_width_nil: .: (0.001148) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.002227) test_output_after_adding_sequence: .: (0.001216) test_output_after_truncating_sequence: .: (0.000839) test_output_from_error_probabilities: .: (0.010788) test_output_width45: .: (0.001466) test_output_with_converting_score_phred2solexa: .: (0.002395) test_output_with_converting_score_solexa2phred: .: (0.001579) test_output_with_default_score: .: (0.001065) Bio::TestSequenceMasker: test_mask: .: (0.001092) test_mask_with_enumerator: .: (0.000811) test_mask_with_enumerator_empty_mask_char: .: (0.000757) test_mask_with_enumerator_excess: .: (0.002309) test_mask_with_enumerator_longer_mask_char: .: (0.000745) test_mask_with_enumerator_shorter: .: (0.000868) test_mask_with_error_probability: .: (0.000754) test_mask_with_quality_score: .: (0.000678) Bio::TestSequenceNA: test_at_content: .: (0.001496) test_at_skew: .: (0.001126) test_codon_usage: .: (0.000675) test_complement: .: (0.000574) test_dna: .: (0.000556) test_dna!: .: (0.000535) test_forward_complement: .: (0.000693) test_gc_content: .: (0.001097) test_gc_percent: .: (0.000820) test_gc_skew: .: (0.001409) test_iliegal_bases: .: (0.000552) test_molecular_weight: .: (0.000738) test_names: .: (0.001145) test_reverse_complement: .: (0.000690) test_rna: .: (0.000587) test_rna!: .: (0.000525) test_splicing: .: (0.000725) test_to_re: .: (0.000771) test_to_s: .: (0.000515) Bio::TestSequenceNACommon: test_composition: .: (0.000960) test_concat: .: (0.000528) test_push: .: (0.000560) test_seq: .: (0.000550) test_splicing: .: (0.000818) test_sum: .: (0.000540) test_to_s: .: (0.000543) test_to_str: .: (0.000548) test_total: .: (0.000549) test_window_search: .: (0.001093) Bio::TestSequenceNANew: test_new: .: (0.000800) test_new_n: .: (0.000534) test_new_r: .: (0.000530) test_new_t: .: (0.000560) Bio::TestSequenceNATranslation: test_translate: .: (0.001370) test_translate_0: .: (0.003343) test_translate_1: .: (0.000938) test_translate_2: .: (0.000903) test_translate_3: .: (0.000908) test_translate_4: .: (0.000989) test_translate_5: .: (0.000959) test_translate_6: .: (0.000989) test_translate_7: .: (0.001895) test_translate_given_codon_table: .: (0.256214) test_translate_n1: .: (0.002003) test_translate_n2: .: (0.001698) test_translate_n3: .: (0.001699) test_translate_unknown_o: .: (0.001837) test_translate_unknown_x: .: (0.000981) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000857) test_convert_scores_from_phred_to_solexa: .: (0.001611) test_convert_scores_from_solexa_to_phred: .: (0.001348) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000805) test_convert_scores_from_phred: .: (0.000513) test_convert_scores_from_phred_to_solexa: .: (0.001544) test_convert_scores_from_solexa: .: (0.001354) test_convert_scores_from_solexa_to_phred: .: (0.000839) test_convert_scores_to_phred: .: (0.000498) test_convert_scores_to_solexa: .: (0.002114) test_p2q: .: (0.000846) test_phred_p2q: .: (0.000778) test_phred_q2p: .: (0.017379) test_q2p: .: (0.015919) test_quality_score_type: .: (0.000513) test_self_convert_scores_to_solexa: .: (0.001570) test_self_p2q: .: (0.000758) test_self_q2p: .: (0.016072) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000855) test_convert_scores_from_phred: .: (0.001559) test_convert_scores_from_phred_to_solexa: .: (0.001878) test_convert_scores_from_solexa: .: (0.000499) test_convert_scores_from_solexa_to_phred: .: (0.000812) test_convert_scores_to_phred: .: (0.001199) test_convert_scores_to_solexa: .: (0.000489) test_p2q: .: (0.001090) test_q2p: .: (0.017405) test_quality_score_type: .: (0.000569) test_self_convert_scores_to_phred: .: (0.000858) test_self_p2q: .: (0.000919) test_self_q2p: .: (0.017822) test_solexa_p2q: .: (0.000925) test_solexa_q2p: .: (0.020430) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000968) test_center: .: (0.000610) test_chomp: .: (0.000844) test_chop: .: (0.000722) test_delete: .: (0.000561) test_delete_prefix: .: (0.000557) test_delete_suffix: .: (0.000580) test_downcase: .: (0.000557) test_each_char: .: (0.000823) test_each_char_enum: .: (0.000697) test_each_grapheme_cluster: .: (0.001181) test_each_grapheme_cluster_enum: .: (0.000707) test_each_line: .: (0.000765) test_each_line_enum: .: (0.000916) test_gsub: .: (0.000624) test_gsub_with_block: .: (0.001629) test_ljust: .: (0.000619) test_lstrip: .: (0.000556) test_multiply: .: (0.000618) test_next: .: (0.000575) test_reverse: .: (0.000562) test_rjust: .: (0.000587) test_rstrip: .: (0.000568) test_slice: .: (0.000611) test_slice2: .: (0.000817) test_split: .: (0.000674) test_squeeze: .: (0.000592) test_strip: .: (0.000558) test_sub: .: (0.000658) test_sub_with_block: .: (0.000952) test_succ: .: (0.000554) test_swapcase: .: (0.000597) test_tr: .: (0.000574) test_tr_s: .: (0.000572) test_upcase: .: (0.000551) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.001210) test_partition_nomatch: .: (0.000648) test_partition_sep_TSeq: .: (0.000660) test_partition_sep_regexp: .: (0.000703) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000998) test_rpartition_nomatch: .: (0.000662) test_rpartition_sep_TSeq: .: (0.000655) test_rpartition_sep_regexp: .: (0.000726) Bio::TestShRNA: test_blocK_it: .: (0.075106) test_blocK_it_: .: (0.074476) test_blocK_it_BLOCK_IT: .: (0.079037) test_blocK_it_BLOCK_iT: .: (0.074881) test_blocK_it_piGene: .: (0.074305) test_bottom_strand: .: (0.075872) test_bottom_strand_class: .: (0.075550) test_bottom_strand_nil: .: (0.073864) test_design: .: (0.076874) test_design_BLOCK_IT: .: (0.076541) test_report: .: (0.074166) test_report_before_design: .: (0.076068) test_top_strand: .: (0.076718) test_top_strand_class: .: (0.075304) test_top_strand_nil: .: (0.076552) Bio::TestShRNANew: test_new: .: (0.002219) Bio::TestSiRNA: test_antisense_size: .: (0.000858) test_design: .: (0.076107) test_design_reynolds: .: (0.093296) test_design_uitei: .: (0.077758) test_max_gc_percent: .: (0.001121) test_min_gc_percent: .: (0.000555) test_reynolds: .: (0.093049) test_reynolds?: .: (0.000675) test_uitei: .: (0.073837) test_uitei?: .: (0.000620) Bio::TestSiRNANew: test_new: .: (0.001837) Bio::TestSiRNAPair: test_antisense: .: (0.079291) test_gc_percent: .: (0.074454) test_report: .: (0.074859) test_rule: .: (0.077693) test_sense: .: (0.074429) test_start: .: (0.074448) test_stop: .: (0.078354) test_target: .: (0.075188) Bio::TestSiRNAPairNew: test_new: .: (0.001401) Bio::TestSim4Report: test_all_hits: .: (0.001398) test_each: .: (0.001398) test_each_hit: .: (0.000971) test_hits: .: (0.000874) test_num_hits: .: (0.000751) test_query_def: .: (0.000783) test_query_id: .: (0.000781) test_query_len: .: (0.000769) test_seq1: .: (0.000940) Bio::TestSim4Report2: test_all_hits: .: (0.001167) test_each: .: (0.001364) test_each_hit: .: (0.001031) test_hits: .: (0.000844) test_num_hits: .: (0.000760) test_query_def: .: (0.000749) test_query_id: .: (0.000745) test_query_len: .: (0.000780) test_seq1: .: (0.000888) Bio::TestSim4Report4: test_all_hits: .: (0.001197) test_each: .: (0.001373) test_each_hit: .: (0.000996) test_hits: .: (0.000850) test_num_hits: .: (0.000808) test_query_def: .: (0.000794) test_query_id: .: (0.000770) test_query_len: .: (0.000772) test_seq1: .: (0.000991) Bio::TestSim4ReportHit: test_align: .: (0.001289) test_complement?: .: (0.000902) test_definition: .: (0.000781) test_each: .: (0.001245) test_exons: .: (0.001147) test_hit_id: .: (0.000740) test_hsps: .: (0.001180) test_introns: .: (0.001538) test_len: .: (0.000910) test_query_def: .: (0.000757) test_query_id: .: (0.000754) test_query_len: .: (0.000831) test_segmentpairs: .: (0.001221) test_seq1: .: (0.000880) test_seq2: .: (0.000880) test_target_def: .: (0.000759) test_target_id: .: (0.001279) test_target_len: .: (0.000896) Bio::TestSim4ReportHit2: test_align: .: (0.001297) test_complement?: .: (0.000773) test_definition: .: (0.000751) test_each: .: (0.001204) test_exons: .: (0.001151) test_hit_id: .: (0.000746) test_hsps: .: (0.001675) test_introns: .: (0.001287) test_len: .: (0.000748) test_query_def: .: (0.000754) test_query_id: .: (0.000770) test_query_len: .: (0.000768) test_segmentpairs: .: (0.001157) test_seq1: .: (0.000953) test_seq2: .: (0.000918) test_target_def: .: (0.000752) test_target_id: .: (0.000737) test_target_len: .: (0.000926) Bio::TestSim4ReportHit4: test_align: .: (0.001437) test_complement?: .: (0.000779) test_definition: .: (0.000821) test_each: .: (0.001463) test_exons: .: (0.001443) test_hit_id: .: (0.001367) test_hsps: .: (0.001587) test_introns: .: (0.001378) test_len: .: (0.000807) test_query_def: .: (0.000780) test_query_id: .: (0.000762) test_query_len: .: (0.000805) test_segmentpairs: .: (0.001909) test_seq1: .: (0.001050) test_seq2: .: (0.000918) test_target_def: .: (0.000778) test_target_id: .: (0.000826) test_target_len: .: (0.000793) Bio::TestSim4ReportSegment: test_from: .: (0.000809) test_self_new: .: (0.000599) test_seq: .: (0.000525) test_to: .: (0.000502) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.001344) test_direction: .: (0.001070) test_hit_from: .: (0.001040) test_hit_to: .: (0.000994) test_hseq: .: (0.000998) test_midline: .: (0.001511) test_percent_identity: .: (0.001171) test_qseq: .: (0.000999) test_query_from: .: (0.001041) test_query_to: .: (0.001012) test_seq1: .: (0.001117) test_seq2: .: (0.001105) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.001939) test_direction: .: (0.001043) test_hit_from: .: (0.000994) test_hit_to: .: (0.000984) test_hseq: .: (0.000984) test_midline: .: (0.001046) test_percent_identity: .: (0.001022) test_qseq: .: (0.001560) test_query_from: .: (0.001116) test_query_to: .: (0.000981) test_seq1: .: (0.001115) test_seq2: .: (0.001088) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.001461) test_direction: .: (0.001718) test_hit_from: .: (0.001344) test_hit_to: .: (0.001170) test_hseq: .: (0.001180) test_midline: .: (0.001176) test_percent_identity: .: (0.001191) test_qseq: .: (0.001676) test_query_from: .: (0.001271) test_query_to: .: (0.001185) test_seq1: .: (0.001385) test_seq2: .: (0.001311) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.002335) test_direction: .: (0.001228) test_hit_from: .: (0.001232) test_hit_to: .: (0.001211) test_hseq: .: (0.001197) test_midline: .: (0.001614) test_percent_identity: .: (0.001314) test_qseq: .: (0.001200) test_query_from: .: (0.001170) test_query_to: .: (0.001153) test_seq1: .: (0.001452) test_seq2: .: (0.006224) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.001507) test_direction: .: (0.001256) test_hit_from: .: (0.001220) test_hit_to: .: (0.001939) test_hseq: .: (0.001373) test_midline: .: (0.001180) test_percent_identity: .: (0.001184) test_qseq: .: (0.001272) test_query_from: .: (0.001815) test_query_to: .: (0.001374) test_seq1: .: (0.001321) test_seq2: .: (0.001388) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.002295) test_direction: .: (0.001053) test_hit_from: .: (0.001002) test_hit_to: .: (0.000980) test_hseq: .: (0.000989) test_midline: .: (0.001064) test_percent_identity: .: (0.001602) test_qseq: .: (0.001224) test_query_from: .: (0.001031) test_query_to: .: (0.001013) test_seq1: .: (0.001159) test_seq2: .: (0.001101) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.002164) test_direction: .: (0.001044) test_hit_from: .: (0.001030) test_hit_to: .: (0.000992) test_hseq: .: (0.001049) test_midline: .: (0.001028) test_percent_identity: .: (0.001703) test_qseq: .: (0.001275) test_query_from: .: (0.001026) test_query_to: .: (0.001082) test_seq1: .: (0.001155) test_seq2: .: (0.001146) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.001836) test_entry_id: .: (0.000551) test_filename: .: (0.000544) test_len: .: (0.000546) test_self_new: .: (0.000612) test_self_parse: .: (0.000664) Bio::TestTMHMMReport: test_entry_id: .: (0.001518) test_exp_aas_in_tmhs: .: (0.001112) test_exp_first_60aa: .: (0.001669) test_helix: .: (0.001176) test_predicted_tmhs: .: (0.001082) test_query_len: .: (0.001094) test_tmhs: .: (0.001825) test_to_s: .: (0.001514) test_total_prob_of_N_in: .: (0.001119) Bio::TestTMHMMReport_reports: test_reports: .: (0.000836) Bio::TestTMHMMTMH: test_entry_id: .: (0.001427) test_pos: .: (0.001654) test_range: .: (0.001119) test_status: .: (0.001094) test_version: .: (0.001095) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.001197) test_cutoff: .: (0.000870) test_entry_id: .: (0.001301) test_length: .: (0.000825) test_loc: .: (0.000841) test_name: .: (0.000877) test_networks: .: (0.000832) test_prediction: .: (0.000880) test_query_len: .: (0.000869) test_query_sequences: .: (0.000844) test_rc: .: (0.000818) test_version: .: (0.001343) Bio::TestTargetPReportConst: test_delimiter: .: (0.000750) test_rs: .: (0.000505) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000746) test_togows_access_wait: .: (2.009410) Bio::TestTogoWSREST: test_debug: .: (0.001512) test_debug_default: .: (0.000738) test_internal_http: .: (0.000773) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000983) test_entry: .: (0.000545) test_entry_database_list: .: (0.000492) test_new: .: (0.000766) test_new_with_uri_object: .: (0.000810) test_new_with_uri_string: .: (0.000789) test_retrieve: .: (0.000469) test_search: .: (0.000445) test_search_database_list: .: (0.000471) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.001224) test_prepare_return_value: .: (0.000807) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.002073) Bio::TestTree: test_get_edge_distance: .: (0.000857) test_get_edge_distance_string: .: (0.000640) test_get_node_name: .: (0.000496) test_initialize: .: (0.000551) test_options: .: (0.000515) test_root: .: (0.000458) test_root=: .: (0.000501) Bio::TestTree2: test_add_edge: .: (0.001110) test_add_node: .: (0.000910) test_adjacency_matrix: .: (0.001523) test_adjacency_matrix_with_block: .: (0.000853) test_adjacent_nodes: .: (0.000873) test_adjacent_nodes_nonexistent: .: (0.000666) test_ancestors: .: (0.000724) test_children: .: (0.000718) test_clear: .: (0.000724) test_clear_node: .: (0.000846) test_clear_node_nonexistent: .: (0.000861) test_collect_edge!: .: (0.001587) test_collect_node!: .: (0.001084) test_concat: .: (0.001123) test_descendents: .: (0.000770) test_distance_matrix: .: (0.001693) test_each_edge: .: (0.000883) test_each_node: .: (0.000806) test_each_out_edge: .: (0.001277) test_each_out_edge_chimpanzee: .: (0.000746) test_each_out_edge_human: .: (0.000722) test_each_out_edge_mammals: .: (0.000832) test_each_out_edge_nonexistent: .: (0.000697) test_each_out_edge_primates: .: (0.001029) test_each_out_edge_rat: .: (0.000747) test_each_out_edge_rodents: .: (0.000930) test_edges: .: (0.001207) test_get_edge: .: (0.001318) test_get_edge_indirect: .: (0.000644) test_get_edge_merged: .: (0.000698) test_get_edge_nonexistent: .: (0.000623) test_get_node_bootstrap: .: (0.000663) test_get_node_bootstrap_string=: .: (0.000637) test_get_node_by_name: .: (0.000941) test_get_node_by_name_noexistent: .: (0.000646) test_include?: .: (0.001294) test_include_nonexistent: .: (0.000651) test_insert_node: .: (0.001199) test_leaves: .: (0.000783) test_leaves_noargs: .: (0.000667) test_lowest_common_ancestor: .: (0.000757) test_nodes: .: (0.000653) test_number_of_edges: .: (0.000717) test_number_of_nodes: .: (0.000629) test_out_degree: .: (0.000806) test_out_degree_nonexistent: .: (0.000684) test_out_edges: .: (0.000814) test_out_edges_mammals: .: (0.000861) test_out_edges_nonexistent: .: (0.000712) test_out_edges_primates: .: (0.000969) test_out_edges_rodents: .: (0.000925) test_parent: .: (0.000791) test_path: .: (0.000721) test_remove_edge: .: (0.000777) test_remove_edge_if: .: (0.001429) test_remove_edge_if_nothing_removed: .: (0.000830) test_remove_edge_nonexistent: .: (0.001158) test_remove_node: .: (0.000851) test_remove_node_if: .: (0.000742) test_remove_node_if_false: .: (0.000750) test_remove_node_nonexistent: .: (0.000770) test_remove_nonsense_nodes: .: (0.000766) test_subtree: .: (0.000882) test_subtree_with_all_paths: .: (0.001256) test_total_distance: .: (0.001255) Bio::TestTreeEdge: test_distance: .: (0.000762) test_distance=: .: (0.000599) test_distance_string: .: (0.000466) test_distance_string=: .: (0.000573) test_initialize: .: (0.000569) test_inspect: .: (0.000503) test_to_s: .: (0.000450) Bio::TestTreeNode: test_bootstrap: .: (0.000714) test_bootstrap=: .: (0.000575) test_bootstrap_string: .: (0.000439) test_bootstrap_string=: .: (0.000628) test_initialize: .: (0.000516) test_inspect: .: (0.000539) test_name: .: (0.000465) test_to_s: .: (0.000494) Bio::TestUniProt: test_gene_name: .: (0.013418) Bio::TestUniProtKB: test_ac: .: (0.013303) test_accession: .: (0.013177) test_cc: .: (0.016813) test_cc_alternative_products: .: (0.017245) test_cc_database: .: (0.016988) test_cc_mass_spectrometry: .: (0.026743) test_de: .: (0.013990) test_dr: .: (0.019671) test_dr_with_key: .: (0.017969) test_dr_with_key_empty: .: (0.018227) test_dt: .: (0.013618) test_dt_annotation: .: (0.013260) test_dt_created: .: (0.013661) test_dt_sequence: .: (0.013210) test_entry: .: (0.020318) test_ft: .: (0.155188) test_gene_name: .: (0.014003) test_gene_names: .: (0.013564) test_gn: .: (0.013805) test_gn_old_parser: .: (0.013902) test_gn_uniprot_parser: .: (0.013727) test_id_line: .: (0.013303) test_id_line_data_class: .: (0.012484) test_id_line_entry_name: .: (0.013308) test_id_line_molecule_type: .: (0.012698) test_id_line_sequence_length: .: (0.012796) test_kw: .: (0.012610) test_molecule: .: (0.013206) test_oc: .: (0.015572) test_og_1: .: (0.013738) test_og_2: .: (0.013624) test_og_3: .: (0.013193) test_og_4: .: (0.013598) test_og_5: .: (0.013304) test_og_6: .: (0.012968) test_os: .: (0.012914) test_os_access: .: (0.013526) test_os_access2: .: (0.012488) test_ox: .: (0.012950) test_protein_name: .: (0.013468) test_ref: .: (0.032284) test_seq: .: (0.014500) test_sequence_length: .: (0.013679) test_sq: .: (0.013201) test_sq_crc64: .: (0.013565) test_sq_len: .: (0.013523) test_sq_mw: .: (0.013312) test_synonyms: .: (0.012805) Bio::TestUniProtKB_CC: test_allergen: .: (0.001701) test_alternative_products_access_as_hash: .: (0.001150) test_alternative_products_ai: .: (0.001119) test_alternative_products_apu: .: (0.001619) test_alternative_products_as: .: (0.001148) test_alternative_products_rf: .: (0.000534) test_biophysicochemical_properties: .: (0.001547) test_biotechnology: .: (0.001582) test_catalytic_activity: .: (0.000859) test_caution: .: (0.000906) test_cofactor: .: (0.000926) test_developmental_stage: .: (0.000912) test_disease: .: (0.001143) test_domain: .: (0.001249) test_enzyme_regulation: .: (0.000858) test_function: .: (0.000994) test_induction: .: (0.000734) test_interaction: .: (0.001770) test_mass_spectrometry: .: (0.001078) test_miscellaneous: .: (0.000769) test_pathway: .: (0.000875) test_pharmaceutical: .: (0.000780) test_polymorphism: .: (0.001025) test_ptm: .: (0.000773) test_rna_editing: .: (0.000936) test_similarity: .: (0.000744) test_subcellular_location: .: (0.000894) test_subunit: .: (0.000695) test_tissue_specificity: .: (0.001491) test_toxic_dose: .: (0.000746) test_web_resource: .: (0.001082) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.001423) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.001623) test_protein_name: .: (0.001183) test_synonyms: .: (0.001985) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000872) test_entry: .: (0.000537) test_entry_id: .: (0.000586) test_entry_name: .: (0.000586) test_id_line: .: (0.000582) test_molecule: .: (0.000520) test_sequence_length: .: (0.000570) Bio::TestUniProtKB_P03589: test_ac: .: (0.002443) test_accession: .: (0.001694) test_cc: .: (0.002175) test_cc_alternative_products: .: (0.002730) test_cc_database: .: (0.002169) test_cc_mass_spectrometry: .: (0.002715) test_de: .: (0.001738) test_dr: .: (0.002450) test_dr_with_key: .: (0.002949) test_dr_with_key_empty: .: (0.002367) test_dt: .: (0.002200) test_dt_annotation: .: (0.001567) test_dt_created: .: (0.001541) test_dt_sequence: .: (0.002204) test_entry: .: (0.001726) test_ft: .: (0.002757) test_gene_name: .: (0.001740) test_gene_names: .: (0.001684) test_gn: .: (0.001651) test_gn_old_parser: .: (0.002360) test_gn_uniprot_parser: .: (0.001744) test_id_line: .: (0.002078) test_id_line_data_class: .: (0.001722) test_id_line_entry_name: .: (0.001541) test_id_line_sequence_length: .: (0.001549) test_kw: .: (0.002259) test_oc: .: (0.001758) test_oh: .: (0.002593) test_os: .: (0.002310) test_os_access: .: (0.001587) test_os_access2: .: (0.001627) test_ox: .: (0.002309) test_protein_name: .: (0.001920) test_protein_name_after_calling_de: .: (0.001725) test_ref: .: (0.002176) test_seq: .: (0.002517) test_sequence_length: .: (0.006303) test_sq: .: (0.001722) test_sq_crc64: .: (0.001751) test_sq_len: .: (0.002718) test_sq_mw: .: (0.001743) test_synonyms: .: (0.001835) Bio::TestUniProtKB_P28907: test_ac: .: (0.006310) test_accession: .: (0.005193) test_cc: .: (0.006719) test_cc_alternative_products: .: (0.007654) test_cc_database: .: (0.006682) test_cc_mass_spectrometry: .: (0.007113) test_de: .: (0.005403) test_dr: .: (0.012921) test_dr_with_key: .: (0.012872) test_dr_with_key_empty: .: (0.012416) test_dt: .: (0.004990) test_dt_annotation: .: (0.004983) test_dt_created: .: (0.005019) test_dt_sequence: .: (0.005236) test_entry: .: (0.004916) test_ft: .: (0.009728) test_gene_name: .: (0.005355) test_gene_names: .: (0.005206) test_gn: .: (0.005502) test_gn_old_parser: .: (0.005276) test_gn_uniprot_parser: .: (0.005351) test_id_line: .: (0.005101) test_id_line_data_class: .: (0.005095) test_id_line_entry_name: .: (0.005150) test_id_line_sequence_length: .: (0.005593) test_kw: .: (0.005479) test_oc: .: (0.005112) test_os: .: (0.005121) test_os_access: .: (0.005312) test_os_access2: .: (0.008928) test_ox: .: (0.005952) test_protein_name: .: (0.005499) test_protein_name_after_calling_de: .: (0.005537) test_ref: .: (0.008609) test_seq: .: (0.006452) test_sequence_length: .: (0.005234) test_sq: .: (0.005407) test_sq_crc64: .: (0.005472) test_sq_len: .: (0.006031) test_sq_mw: .: (0.005723) test_synonyms: .: (0.005768) test_synonyms_after_calling_de: .: (0.006448) Bio::TestUniProtKB_P49144: test_ac: .: (0.002725) test_accession: .: (0.003285) test_cc: .: (0.003617) test_cc_alternative_products: .: (0.004368) test_cc_database: .: (0.004179) test_cc_mass_spectrometry: .: (0.003462) test_de: .: (0.003178) test_dr: .: (0.004566) test_dr_with_key: .: (0.004464) test_dr_with_key_empty: .: (0.004338) test_dt: .: (0.002394) test_dt_annotation: .: (0.002971) test_dt_created: .: (0.002338) test_dt_sequence: .: (0.002330) test_entry: .: (0.002680) test_ft: .: (0.006043) test_gene_name: .: (0.002505) test_gene_names: .: (0.002522) test_gn: .: (0.002543) test_gn_old_parser: .: (0.003051) test_gn_uniprot_parser: .: (0.002460) test_id_line: .: (0.002443) test_id_line_data_class: .: (0.002405) test_id_line_entry_name: .: (0.003045) test_id_line_sequence_length: .: (0.002363) test_kw: .: (0.003190) test_oc: .: (0.002470) test_os: .: (0.003103) test_os_access: .: (0.002463) test_os_access2: .: (0.003078) test_ox: .: (0.002525) test_protein_name: .: (0.003164) test_protein_name_after_calling_de: .: (0.002569) test_ref: .: (0.003524) test_seq: .: (0.003271) test_sequence_length: .: (0.002378) test_sq: .: (0.003003) test_sq_crc64: .: (0.002388) test_sq_len: .: (0.003177) test_sq_mw: .: (0.002468) test_synonyms: .: (0.003417) test_synonyms_after_calling_de: .: (0.002701) Bio::TestUniProtKB_Ref: test_RA: .: (0.001754) test_RC: .: (0.001154) test_RG: .: (0.001040) test_RL: .: (0.005328) test_RN: .: (0.001193) test_RP: .: (0.001111) test_RT: .: (0.001130) test_RX: .: (0.001112) test_ref: .: (0.001841) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.001062) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.001606) test_alternative_products_with_ft: .: (0.002981) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.001228) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.001142) test_RL_lines: .: (0.000701) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.002515) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.001008) test_RG_line: .: (0.000729) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.001754) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.001085) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000910) test_RL_line: .: (0.001309) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.002235) test_RP_line: .: (0.000990) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000701) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.001122) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.001553) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000863) test_CC_interaction_isoform: .: (0.000848) test_CC_interaction_no_gene_name: .: (0.000810) test_CC_interaction_self_association: .: (0.000935) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.001076) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.001137) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.002180) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.001234) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.001110) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000984) test_DT_line: .: (0.000840) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.011284) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.002145) test_CC_web_resource: .: (0.000542) test_FT_VER_SEQ: .: (0.000827) test_OH_line_exception: .: (0.001748) test_OH_lines: .: (0.001269) Bio::TestUtils: test_centreOfGravity: .: (0.001691) test_dihedral_angle: .: (0.002033) test_distance: .: (0.001294) test_geometricCentre: .: (0.001146) test_rad2deg: .: (0.000824) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.001011) test_dijkstra_on_weighted_graph: .: (0.000691) Finished in 43.876422224 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 89.82 tests/s, 492.31 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_armhf.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.5-1_armhf.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/5016/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/5016/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/5016 and its subdirectories I: Current time: Thu May 9 22:29:12 +14 2024 I: pbuilder-time-stamp: 1715243352