I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 6 03:20:27 +14 2024 I: pbuilder-time-stamp: 1733404827 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/27617/tmp/hooks/D01_modify_environment starting debug: Running on ff64a. 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 Dec 5 13:21 /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/27617/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/27617/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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.32(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=6 ' 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=a62bbc3c650f48cd9b0b95c474c5ae43 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=27617 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.nRzEcwY4/pbuilderrc_aWbj --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.nRzEcwY4/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' SUDO_GID=114 SUDO_UID=109 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 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27617/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 ... 19684 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libb-hooks-op-check-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{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} libgssapi-krb5-2{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{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} libnsl2{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librole-tiny-perl{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-quote-perl{a} libtimedate-perl{a} libtirpc-common{a} libtirpc3t64{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} python3.12{a} python3.12-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} tzdata{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato gnupg-utils gpg-wks-client krb5-locales 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, 139 newly installed, 0 to remove and 0 not upgraded. Need to get 43.4 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.7-3 [800 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.7-3 [1808 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.6-1 [26.7 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 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 12 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1819 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-2 [1348 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 47 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libassuan9 armhf 3.0.1-2 [53.7 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf gpgconf armhf 2.2.45-2 [104 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libksba8 armhf 1.6.7-2+b1 [115 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libnpth0t64 armhf 1.6-3.1+b1 [17.1 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf dirmngr armhf 2.2.45-2 [322 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf gnupg-l10n all 2.2.45-2 [705 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf gpg armhf 2.2.45-2 [463 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf pinentry-curses armhf 1.2.1-4+b1 [76.1 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf gpg-agent armhf 2.2.45-2 [210 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf gpgsm armhf 2.2.45-2 [218 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf gnupg all 2.2.45-2 [376 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libfile-dirlist-perl all 0.05-3 [7600 B] Get: 70 http://deb.debian.org/debian trixie/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libfile-touch-perl all 0.12-2 [8816 B] Get: 73 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libipc-run-perl all 20231003.0-2 [101 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libclass-xsaccessor-perl armhf 1.19-4+b4 [35.1 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libb-hooks-op-check-perl armhf 0.22-3+b2 [10.3 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libdevel-callchecker-perl armhf 0.009-1+b1 [16.0 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libparams-classify-perl armhf 0.015-2+b4 [21.2 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libimport-into-perl all 1.002005-2 [11.3 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libmoo-perl all 2.005005-1 [58.0 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libhttp-date-perl all 6.06-1 [10.7 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libfile-listing-perl all 6.16-1 [12.4 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf liburi-perl all 5.30-1 [105 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libhtml-parser-perl armhf 3.83-1+b1 [96.4 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libhtml-tree-perl all 5.07-3 [211 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libclone-perl armhf 0.47-1+b1 [13.3 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libhttp-message-perl all 7.00-2 [79.8 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf perl-openssl-defaults armhf 7+b2 [6708 B] Get: 101 http://deb.debian.org/debian trixie/main armhf libnet-ssleay-perl armhf 1.94-2 [319 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libnet-http-perl all 6.23-1 [23.9 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libwww-perl all 6.77-1 [183 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf wdiff armhf 1.2.2-6 [118 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf devscripts all 2.24.5 [1080 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf sgml-data all 2.0.11+nmu1 [179 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf docbook all 4.5-11 [126 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libosp5 armhf 1.5.2-15 [883 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf opensp armhf 1.5.2-15 [434 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf docbook-to-man armhf 1:2.0.0-47 [69.1 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf rubygems-integration all 1.18 [6704 B] Get: 118 http://deb.debian.org/debian trixie/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libruby armhf 1:3.1+nmu1 [4664 B] Get: 122 http://deb.debian.org/debian trixie/main armhf ruby-sdbm armhf 1.0.0-5+b5 [13.3 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20240808-1 [77.9 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-1+b2 [45.4 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libruby3.1t64 armhf 3.1.2-8.4 [5081 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf ruby3.1 armhf 3.1.2-8.4 [664 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf ruby-rubygems all 3.4.20-1 [309 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf ruby armhf 1:3.1+nmu1 [5584 B] Get: 130 http://deb.debian.org/debian trixie/main armhf rake all 13.2.1-1 [65.2 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf gem2deb-test-runner armhf 2.2.5 [17.9 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf ruby3.1-dev armhf 3.1.2-8.4 [1003 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf ruby-all-dev armhf 1:3.1+nmu1 [5676 B] Get: 136 http://deb.debian.org/debian trixie/main armhf gem2deb armhf 2.2.5 [48.0 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf ruby-libxml armhf 5.0.3-1+b1 [72.1 kB] Fetched 43.4 MB in 2s (17.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19684 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.7-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_armhf.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:armhf (3.12.7-3) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20004 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_armhf.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_armhf.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21066 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_armhf.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_armhf.deb ... Unpacking openssl (3.3.2-2) ... 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+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../012-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. 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Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../027-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../028-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libassuan9:armhf. Preparing to unpack .../033-libassuan9_3.0.1-2_armhf.deb ... Unpacking libassuan9:armhf (3.0.1-2) ... Selecting previously unselected package gpgconf. Preparing to unpack .../034-gpgconf_2.2.45-2_armhf.deb ... Unpacking gpgconf (2.2.45-2) ... Selecting previously unselected package libksba8:armhf. Preparing to unpack .../035-libksba8_1.6.7-2+b1_armhf.deb ... Unpacking libksba8:armhf (1.6.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../036-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../037-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../038-libldap-2.5-0_2.5.18+dfsg-3+b1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnpth0t64:armhf. Preparing to unpack .../039-libnpth0t64_1.6-3.1+b1_armhf.deb ... Unpacking libnpth0t64:armhf (1.6-3.1+b1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../040-dirmngr_2.2.45-2_armhf.deb ... Unpacking dirmngr (2.2.45-2) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../041-gnupg-l10n_2.2.45-2_all.deb ... Unpacking gnupg-l10n (2.2.45-2) ... Selecting previously unselected package gpg. Preparing to unpack .../042-gpg_2.2.45-2_armhf.deb ... Unpacking gpg (2.2.45-2) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../043-pinentry-curses_1.2.1-4+b1_armhf.deb ... Unpacking pinentry-curses (1.2.1-4+b1) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../044-gpg-agent_2.2.45-2_armhf.deb ... Unpacking gpg-agent (2.2.45-2) ... Selecting previously unselected package gpgsm. Preparing to unpack .../045-gpgsm_2.2.45-2_armhf.deb ... Unpacking gpgsm (2.2.45-2) ... Selecting previously unselected package gnupg. Preparing to unpack .../046-gnupg_2.2.45-2_all.deb ... Unpacking gnupg (2.2.45-2) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../047-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../048-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../049-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../050-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../051-libio-pty-perl_1%3a1.20-1+b2_armhf.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../052-libipc-run-perl_20231003.0-2_all.deb ... Unpacking libipc-run-perl (20231003.0-2) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../053-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../054-libclass-xsaccessor-perl_1.19-4+b4_armhf.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b4) ... Selecting previously unselected package libb-hooks-op-check-perl:armhf. Preparing to unpack .../055-libb-hooks-op-check-perl_0.22-3+b2_armhf.deb ... Unpacking libb-hooks-op-check-perl:armhf (0.22-3+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../056-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:armhf. Preparing to unpack .../057-libdevel-callchecker-perl_0.009-1+b1_armhf.deb ... Unpacking libdevel-callchecker-perl:armhf (0.009-1+b1) ... Selecting previously unselected package libparams-classify-perl:armhf. Preparing to unpack .../058-libparams-classify-perl_0.015-2+b4_armhf.deb ... Unpacking libparams-classify-perl:armhf (0.015-2+b4) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../059-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../060-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../061-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../062-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../063-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../064-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../065-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. 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Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:armhf. Preparing to unpack .../078-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 .../079-libnet-ssleay-perl_1.94-2_armhf.deb ... Unpacking libnet-ssleay-perl:armhf (1.94-2) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../080-libio-socket-ssl-perl_2.089-1_all.deb ... Unpacking libio-socket-ssl-perl (2.089-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../081-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../082-liblwp-protocol-https-perl_6.14-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.14-1) ... 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Preparing to unpack .../089-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package sgml-data. Preparing to unpack .../090-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../091-docbook_4.5-11_all.deb ... Unpacking docbook (4.5-11) ... Selecting previously unselected package libosp5. Preparing to unpack .../092-libosp5_1.5.2-15_armhf.deb ... Unpacking libosp5 (1.5.2-15) ... Selecting previously unselected package opensp. Preparing to unpack .../093-opensp_1.5.2-15_armhf.deb ... Unpacking opensp (1.5.2-15) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../094-docbook-to-man_1%3a2.0.0-47_armhf.deb ... Unpacking docbook-to-man (1:2.0.0-47) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../095-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../096-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../097-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../098-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../099-libruby_1%3a3.1+nmu1_armhf.deb ... Unpacking libruby:armhf (1:3.1+nmu1) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../100-ruby-sdbm_1.0.0-5+b5_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b5) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../101-libedit2_3.1-20240808-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20240808-1) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../102-libncurses6_6.5-2+b1_armhf.deb ... Unpacking libncurses6:armhf (6.5-2+b1) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../103-libyaml-0-2_0.2.5-1+b2_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1+b2) ... Selecting previously unselected package libruby3.1t64:armhf. Preparing to unpack .../104-libruby3.1t64_3.1.2-8.4_armhf.deb ... Unpacking libruby3.1t64:armhf (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../105-ruby3.1_3.1.2-8.4_armhf.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../106-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../107-ruby_1%3a3.1+nmu1_armhf.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package rake. Preparing to unpack .../108-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../109-gem2deb-test-runner_2.2.5_armhf.deb ... Unpacking gem2deb-test-runner (2.2.5) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../110-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../111-libgmp-dev_2%3a6.3.0+dfsg-2+b2_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package ruby3.1-dev:armhf. Preparing to unpack .../112-ruby3.1-dev_3.1.2-8.4_armhf.deb ... Unpacking ruby3.1-dev:armhf (3.1.2-8.4) ... Selecting previously unselected package ruby-all-dev:armhf. Preparing to unpack .../113-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 .../114-gem2deb_2.2.5_armhf.deb ... Unpacking gem2deb (2.2.5) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../115-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 .../116-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 .../117-ruby-libxml_5.0.3-1+b1_armhf.deb ... Unpacking ruby-libxml:armhf (5.0.3-1+b1) ... Setting up libksba8:armhf (1.6.7-2+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up wdiff (1.2.2-6) ... Setting up libfile-which-perl (1.27-2) ... Setting up libnpth0t64:armhf (1.6-3.1+b1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libclone-perl:armhf (0.47-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libedit2:armhf (3.1-20240808-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:armhf (7+b2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up libosp5 (1.5.2-15) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 5 13:22:30 UTC 2024. Universal Time is now: Thu Dec 5 13:22:30 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+b2) ... Setting up gnupg-l10n (2.2.45-2) ... Setting up libncurses6:armhf (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.22.5-2) ... Setting up libb-hooks-op-check-perl:armhf (0.22-3+b2) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... 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 (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libassuan9:armhf (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liburi-perl (5.30-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:armhf (1.94-2) ... 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 (1.2.1-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.4.7-8) ... Setting up libnet-http-perl (6.23-1) ... Setting up opensp (1.5.2-15) ... Setting up libdevel-callchecker-perl:armhf (0.009-1+b1) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... 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 libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libhtml-parser-perl:armhf (3.83-1+b1) ... Setting up gpgconf (2.2.45-2) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.45-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.45-2) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:armhf (0.015-2+b4) ... Setting up gpgsm (2.2.45-2) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.45-2) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up gnupg (2.2.45-2) ... Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libruby:armhf (1:3.1+nmu1) ... Setting up libwww-perl (6.77-1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby (1:3.1+nmu1) ... Setting up devscripts (2.24.5) ... Setting up rdtool (0.6.38-4.1) ... Setting up ruby-sdbm:armhf (1.0.0-5+b5) ... Setting up libruby3.1t64:armhf (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby3.1-dev:armhf (3.1.2-8.4) ... Setting up ruby-libxml:armhf (5.0.3-1+b1) ... Setting up gem2deb-test-runner (2.2.5) ... Setting up ruby-all-dev:armhf (1:3.1+nmu1) ... Setting up gem2deb (2.2.5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-47) ... 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/27617/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/27617/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 ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 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/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 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/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 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/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 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/build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.5/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.5/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.5.gemspec /usr/bin/ruby3.1 /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/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.003690) test_dbs: .: (0.001486) test_go_ids: .: (0.001216) test_go_terms: .: (0.001051) test_parser: .: (0.002223) test_set_date: .: (0.001140) test_set_desc: .: (0.001165) test_to_str: .: (0.001200) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.003577) test_mktmpdir_without_block: .: (0.003427) test_remove_entry_secure: .: (0.001911) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.015722) test_call_command_fork: .: (0.000720) test_call_command_open3: .: (0.015057) test_call_command_popen: .: (0.014106) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.014866) test_call_command_fork: .: (0.000747) test_call_command_open3: .: (0.014592) test_call_command_popen: .: (0.015257) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.015299) test_call_command_fork: .: (0.000665) test_call_command_open3: .: (0.014606) test_call_command_popen: .: (0.014384) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.009082) test_call_command_fork_chdir: .: (0.001507) test_call_command_popen_chdir: .: (0.008156) test_query_command_chdir: .: (0.008499) test_query_command_fork_chdir: .: (0.001378) test_query_command_popen_chdir: .: (0.008029) Bio::FuncTestCommandQuery: test_query_command: .: (0.022532) test_query_command_fork: .: (0.011570) test_query_command_open3: .: (0.022996) test_query_command_popen: .: (0.021583) Bio::FuncTestCommandTmpdir: test_close!: .: (0.003783) test_initialize: .: (0.001839) test_path: .: (0.001734) test_path_after_close: .: (0.002429) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.073924) test_output_fasta: .: (0.059992) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.001758) test_accession: .: (0.001018) test_accessions: .: (0.000885) test_comment: .: (0.000861) test_common_name: .: (0.001110) test_definition: .: (0.001214) test_features: .: (0.001747) test_gi: .: (0.000918) test_keywords: .: (0.001157) test_locus: .: (0.000624) test_nid: .: (0.000851) test_organism: .: (0.000968) test_origin: .: (0.000994) test_references: .: (0.003095) test_segment: .: (0.001105) test_source: .: (0.001651) test_taxonomy: .: (0.001091) test_version: .: (0.001135) test_versions: .: (0.000894) Bio::TestAA: test_13: .: (0.001130) test_1n: .: (0.000481) test_name2one: .: (0.000684) test_name2three: .: (0.000699) test_one2name: .: (0.000519) test_one2three: .: (0.000461) test_three2name: .: (0.000455) test_three2one: .: (0.000611) test_to_1_1: .: (0.000449) test_to_1_3: .: (0.000597) test_to_1_name: .: (0.000639) test_to_3_1: .: (0.000463) test_to_3_3: .: (0.000471) test_to_3_name: .: (0.000631) test_to_re: .: (0.000680) Bio::TestAAConstants: test_bio_aminoacid: .: (0.001306) Bio::TestAAindex: test_api: .: (0.000991) test_auto_aax1: .: (0.002459) test_auto_aax2: .: (0.002806) Bio::TestAAindex1: test_author: .: (0.003042) test_comment: .: (0.002122) test_correlation_coefficient: .: (0.004722) test_dblinks: .: (0.002115) test_definition: .: (0.002045) test_entry_id: .: (0.001983) test_index: .: (0.003158) test_journal: .: (0.002448) test_title: .: (0.002182) Bio::TestAAindex2: test_access_A_R: .: (0.009845) test_access_R_A: .: (0.008045) test_author: .: (0.002209) test_cols: .: (0.002122) test_comment: .: (0.002087) test_dblinks: .: (0.002103) test_definition: .: (0.002122) test_entry_id: .: (0.002321) test_journal: .: (0.002387) test_matrix: .: (0.007855) test_matrix_1_2: .: (0.004584) test_matrix_2_2: .: (0.004283) test_matrix_A_R: .: (0.004546) test_matrix_R_A: .: (0.004291) test_matrix_determinant: .: (0.025963) test_matrix_rank: .: (0.025609) test_matrix_transpose: .: (0.004989) test_rows: .: (0.001159) test_title: .: (0.035667) Bio::TestAAindexConstant: test_delimiter: .: (0.001182) test_tagsize: .: (0.000495) Bio::TestAbif: test_complement: .: (0.059452) test_seq: .: (0.045488) test_to_biosequence: .: (0.048256) Bio::TestActsLikeMap: test_mixin: .: (0.002010) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.001971) Bio::TestActsLikeMarker: test_mixin: .: (0.001406) Bio::TestAlignment: test_add_seq_no_key: .: (0.001624) test_add_seq_using_seq_with_aaseq_method: .: (0.000816) test_add_seq_using_seq_with_definition_method: .: (0.000618) test_add_seq_using_seq_with_entry_id_method: .: (0.000662) test_add_seq_using_seq_with_naseq_method: .: (0.001833) test_add_seq_using_seq_with_seq_method: .: (0.000831) test_consensus_iupac_gap_modes: .: (0.002428) test_consensus_iupac_missing_char: .: (0.001122) test_consensus_iupac_missing_char_option: .: (0.001250) test_consensus_iupac_no_gaps: .: (0.001635) test_consensus_iupac_of_ambiguous_bases: .: (0.002467) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.032939) test_consensus_opt_gap_mode: .: (0.003834) test_consensus_opt_missing_char: .: (0.001559) test_consensus_string_no_gaps: .: (0.001487) test_consensus_threshold_four_sequences: .: (0.003153) test_consensus_threshold_two_sequences: .: (0.002316) test_convert_match: .: (0.001847) test_convert_unmatch: .: (0.001010) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000995) test_convert_unmatch_different_match_char: .: (0.000855) test_convert_unmatch_multiple_sequences: .: (0.002034) test_default_gap_char: .: (0.000553) test_default_gap_regexp_matches_default_gap_char: .: (0.000553) test_default_missing_char: .: (0.000494) test_each_site_equal_length: .: (0.000983) test_each_site_unequal_length: .: (0.001096) test_equals: .: (0.001187) test_match_line_protein: .: (0.002752) test_normalizebang_extends_sequences_with_gaps: .: (0.000921) test_seq_length_is_max_seq_length: .: (0.004560) test_seq_length_when_one_sequence: .: (0.000644) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000580) test_seqclass_when_seqclass_set: .: (0.000570) test_seqclass_when_sequence_used: .: (0.000547) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000566) test_set_and_get_gap_char: .: (0.000591) test_store_cannot_override_key: .: (0.000602) test_store_with_default_keys_and_user_defined_keys: .: (0.000631) test_store_with_nil_key_uses_next_number_for_key: .: (0.000593) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.001395) test_alignment_concat: .: (0.000827) test_alignment_length: .: (0.000488) test_alignment_lstrip!: .: (0.000982) test_alignment_lstrip_nil: .: (0.000715) test_alignment_normalize!: .: (0.000564) test_alignment_rstrip!: .: (0.001023) test_alignment_rstrip_nil: .: (0.000768) test_alignment_site: .: (0.000950) test_alignment_slice: .: (0.000566) test_alignment_strip!: .: (0.001282) test_alignment_strip_nil: .: (0.000755) test_alignment_subseq: .: (0.000776) test_alignment_window: .: (0.000582) test_collect_each_site: .: (0.000829) test_consensus_each_site_default: .: (0.001023) test_consensus_each_site_gap_mode_1: .: (0.000916) test_consensus_each_site_gap_mode_minus1: .: (0.001016) test_consensus_iupac: .: (0.003417) test_consensus_string_default: .: (0.000977) test_consensus_string_half: .: (0.000825) test_convert_match: .: (0.000678) test_convert_unmatch: .: (0.000681) test_each_seq: .: (0.000761) test_each_site: .: (0.001092) test_each_site_step: .: (0.000810) test_each_window: .: (0.001060) test_match_line: .: (0.006382) test_match_line_amino: .: (0.007867) test_match_line_nuc: .: (0.001124) test_private_alignment_site: .: (0.000613) test_remove_all_gaps!: .: (0.001691) test_seqclass: .: (0.000627) test_seqclass=: .: (0.000727) test_seqclass_default: .: (0.000457) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.019836) test_determine_seq_method: .: (0.012425) test_entries: .: (0.002392) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.001582) test_avoid_same_name_numbering: .: (0.000835) test_clustal_have_same_name_true: .: (0.000621) test_have_same_name_false: .: (0.000629) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.002806) test_gap_char_default: .: (0.000688) test_gap_char_never_nil: .: (0.000551) test_gap_regexp: .: (0.000592) test_gap_regexp=: .: (0.000605) test_gap_regexp_never_nil: .: (0.000536) test_get_all_property_default: .: (0.000600) test_get_all_property_nodefault: .: (0.000640) test_is_gap_default_false: .: (0.000612) test_is_gap_default_true: .: (0.000594) test_is_gap_nodefault_false: .: (0.000679) test_is_gap_nodefault_true: .: (0.000682) test_missing_char=: .: (0.000579) test_missing_char_default: .: (0.000559) test_missing_char_never_nil: .: (0.000750) test_seqclass=: .: (0.001867) test_seqclass_default: .: (0.000669) test_seqclass_never_nil: .: (0.000631) test_set_all_property: .: (0.000674) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.003672) test_consensus_string_50percent: .: (0.000655) test_consensus_string_50percent_nil: .: (0.000611) test_consensus_string_default: .: (0.000530) test_consensus_string_default_nil: .: (0.000537) test_has_gap_false: .: (0.000554) test_has_gap_true: .: (0.000499) test_match_line_amino_100percent: .: (0.000690) test_match_line_amino_missing: .: (0.002072) test_match_line_amino_strong: .: (0.000820) test_match_line_amino_weak: .: (0.001029) test_match_line_nuc_100percent: .: (0.000711) test_match_line_nuc_missing: .: (0.000722) test_remove_gaps!: .: (0.000555) test_remove_gaps_bang_not_removed: .: (0.000467) Bio::TestAtomFinder: test_atoms: .: (0.105132) test_each_atom: .: (0.001369) test_find_atom: .: (0.001175) Bio::TestBioFastaDefline: test_acc_version: .: (0.002678) test_accession: .: (0.002560) test_accessions: .: (0.002479) test_description: .: (0.001968) test_descriptions: .: (0.001896) test_entry_id: .: (0.001869) test_get: .: (0.002223) test_get_all_by_type: .: (0.001954) test_get_by_type: .: (0.001813) test_gi: .: (0.001704) test_id_strings: .: (0.003617) test_locus: .: (0.001556) test_method_missing: .: (0.002055) test_to_s: .: (0.001839) test_words: .: (0.004110) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.005632) test_goid2term: .: (0.001973) test_parse_goids: .: (0.001928) Bio::TestBioGenBank: test_basecount: .: (0.002447) test_circular: .: (0.001280) test_classification: .: (0.001847) test_date: .: (0.001185) test_date_modified: .: (0.003531) test_division: .: (0.001234) test_each_cds_feature: .: (0.004319) test_each_cds_qualifiers: .: (0.004472) test_each_gene: .: (0.004535) test_entry_id: .: (0.001533) test_length: .: (0.001485) test_locus_circular: .: (0.001760) test_locus_class: .: (0.001951) test_locus_date: .: (0.001637) test_locus_division: .: (0.001679) test_locus_entry_id: .: (0.001612) test_locus_length: .: (0.001704) test_locus_natype: .: (0.001718) test_locus_strand: .: (0.001717) test_natype: .: (0.001642) test_seq: .: (0.001924) test_seq_len: .: (0.001759) test_strand: .: (0.001713) test_strandedness: .: (0.001426) test_to_biosequence: .: (0.011946) Bio::TestBioGenPept: test_circular: .: (0.002441) test_date: .: (0.001154) test_dbsource: .: (0.027619) test_division: .: (0.001429) test_entry_id: .: (0.001151) test_length: .: (0.001089) test_locus: .: (0.001275) test_seq: .: (0.001337) test_seq_len: .: (0.001355) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.002674) test_aaseq: .: (0.001606) test_chromosome: .: (0.002280) test_codon_usage: .: (0.002020) test_cu_list: .: (0.001153) test_dblinks_as_hash: .: (0.001500) test_dblinks_as_strings: .: (0.001213) test_definition: .: (0.001324) test_division: .: (0.001152) test_eclinks: .: (0.001317) test_entry: .: (0.002032) test_entry_id: .: (0.001230) test_gbposition: .: (0.001397) test_gene: .: (0.001280) test_genes: .: (0.001316) test_keggclass: .: (0.001392) test_keggclasses: .: (0.001429) test_locations: .: (0.001847) test_motifs_as_hash: .: (0.001596) test_motifs_as_strings: .: (0.002238) test_name: .: (0.001276) test_names_as_array: .: (0.001440) test_new: .: (0.001217) test_ntlen: .: (0.001821) test_ntseq: .: (0.001971) test_organism: .: (0.001220) test_orthologs_as_hash: .: (0.001275) test_orthologs_as_strings: .: (0.001205) test_pathway: .: (0.002347) test_pathway_after_pathways_as_strings: .: (0.002088) test_pathway_before_pathways_as_strings: .: (0.001859) test_pathways_as_hash: .: (0.001379) test_pathways_as_strings: .: (0.001307) test_position: .: (0.001299) test_structure: .: (0.001401) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.008891) test_comment: .: (0.002728) test_data_source: .: (0.002201) test_definition: .: (0.002114) test_disease: .: (0.002213) test_entry_id: .: (0.002089) test_lineage: .: (0.002852) test_nalen: .: (0.002264) test_name: .: (0.002139) test_new: .: (0.002148) test_num_gene: .: (0.002645) test_num_rna: .: (0.002442) test_original_databases: .: (0.002262) test_original_db: .: (0.002357) test_plasmids: .: (0.002129) test_references: .: (0.016891) test_statistics: .: (0.003054) test_taxid: .: (0.002726) test_taxonomy: .: (0.002640) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.003297) test_comment: .: (0.001611) test_data_source: .: (0.002231) test_definition: .: (0.001570) test_disease: .: (0.001497) test_entry_id: .: (0.001487) test_lineage: .: (0.001572) test_nalen: .: (0.001287) test_name: .: (0.001278) test_new: .: (0.001313) test_num_gene: .: (0.002012) test_num_rna: .: (0.001527) test_original_databases: .: (0.001255) test_original_db: .: (0.001340) test_plasmids: .: (0.001895) test_references: .: (0.002114) test_statistics: .: (0.001420) test_taxid: .: (0.002347) test_taxonomy: .: (0.001568) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.002618) test_compounds_as_strings: .: (0.001212) test_dblinks_as_hash: .: (0.001131) test_dblinks_as_strings: .: (0.001063) test_description: .: (0.001243) test_diseases_as_hash: .: (0.001023) test_diseases_as_strings: .: (0.000960) test_entry_id: .: (0.002516) test_enzymes_as_strings: .: (0.001789) test_genes_as_hash: .: (0.001205) test_genes_as_strings: .: (0.001084) test_keggclass: .: (0.001259) test_ko_pathway: .: (0.001189) test_modules_as_hash: .: (0.001091) test_modules_as_strings: .: (0.001147) test_name: .: (0.001237) test_new: .: (0.001181) test_organism: .: (0.001112) test_orthologs_as_hash: .: (0.002459) test_orthologs_as_strings: .: (0.001723) test_pathways_as_hash: .: (0.001258) test_pathways_as_strings: .: (0.001058) test_reactions_as_hash: .: (0.001156) test_reactions_as_strings: .: (0.001109) test_references: .: (0.001103) test_rel_pathways_as_hash: .: (0.001334) test_rel_pathways_as_strings: .: (0.001106) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.003607) test_compounds_as_strings: .: (0.003092) test_dblinks_as_hash: .: (0.001359) test_dblinks_as_strings: .: (0.001346) test_description: .: (0.001263) test_diseases_as_hash: .: (0.001346) test_diseases_as_strings: .: (0.001319) test_entry_id: .: (0.001334) test_enzymes_as_strings: .: (0.001152) test_genes_as_hash: .: (0.002417) test_genes_as_strings: .: (0.001800) test_keggclass: .: (0.001322) test_ko_pathway: .: (0.001370) test_modules_as_hash: .: (0.001399) test_modules_as_strings: .: (0.001277) test_name: .: (0.001343) test_new: .: (0.001271) test_organism: .: (0.001528) test_orthologs_as_hash: .: (0.001925) test_orthologs_as_strings: .: (0.001359) test_pathways_as_hash: .: (0.001356) test_pathways_as_strings: .: (0.001243) test_reactions_as_hash: .: (0.001101) test_reactions_as_strings: .: (0.001064) test_references: .: (0.001170) test_rel_pathways_as_hash: .: (0.001408) test_rel_pathways_as_strings: .: (0.001420) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.002375) test_compounds_as_strings: .: (0.001524) test_dblinks_as_hash: .: (0.000984) test_dblinks_as_strings: .: (0.000950) test_description: .: (0.001273) test_diseases_as_hash: .: (0.001071) test_diseases_as_strings: .: (0.001001) test_entry_id: .: (0.001136) test_enzymes_as_strings: .: (0.001091) test_genes_as_hash: .: (0.000955) test_genes_as_strings: .: (0.000931) test_keggclass: .: (0.001066) test_ko_pathway: .: (0.000973) test_modules_as_hash: .: (0.000977) test_modules_as_strings: .: (0.002142) test_name: .: (0.001495) test_new: .: (0.001001) test_organism: .: (0.001044) test_orthologs_as_hash: .: (0.001539) test_orthologs_as_strings: .: (0.001191) test_pathways_as_hash: .: (0.001047) test_pathways_as_strings: .: (0.001030) test_reactions_as_hash: .: (0.000953) test_reactions_as_strings: .: (0.001019) test_references: .: (0.001163) test_rel_pathways_as_hash: .: (0.002601) test_rel_pathways_as_strings: .: (0.001169) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.002456) test_compounds_as_strings: .: (0.001220) test_dblinks_as_hash: .: (0.001284) test_dblinks_as_strings: .: (0.001370) test_description: .: (0.002029) test_diseases_as_hash: .: (0.001275) test_diseases_as_strings: .: (0.002027) test_entry_id: .: (0.001566) test_enzymes_as_strings: .: (0.001121) test_genes_as_hash: .: (0.001079) test_genes_as_strings: .: (0.001191) test_keggclass: .: (0.001289) test_ko_pathway: .: (0.001476) test_modules_as_hash: .: (0.001785) test_modules_as_strings: .: (0.002120) test_name: .: (0.001438) test_new: .: (0.001189) test_organism: .: (0.001432) test_orthologs_as_hash: .: (0.001218) test_orthologs_as_strings: .: (0.001341) test_pathways_as_hash: .: (0.001221) test_pathways_as_strings: .: (0.001134) test_reactions_as_hash: .: (0.001149) test_reactions_as_strings: .: (0.001675) test_references: .: (0.004359) test_rel_pathways_as_hash: .: (0.001613) test_rel_pathways_as_strings: .: (0.001232) Bio::TestBioKeggDRUG: test_activity: .: (0.002562) test_comment: .: (0.002137) test_dblinks_as_hash: .: (0.001760) test_dblinks_as_strings: .: (0.001375) test_entry_id: .: (0.001310) test_formula: .: (0.001324) test_kcf: .: (0.001289) test_mass: .: (0.001345) test_name: .: (0.001512) test_names: .: (0.002271) test_pathways_as_hash: .: (0.001524) test_pathways_as_strings: .: (0.001279) test_products: .: (0.001501) test_remark: .: (0.001501) Bio::TestBioKeggGLYCAN: test_comment: .: (0.002674) test_composition: .: (0.001489) test_compounds: .: (0.001315) test_dblinks_as_hash: .: (0.002864) test_dblinks_as_strings: .: (0.001850) test_entry_id: .: (0.001359) test_enzymes: .: (0.001403) test_kcf: .: (0.001124) test_keggclass: .: (0.001367) test_mass: .: (0.001415) test_name: .: (0.001430) test_orthologs_as_hash: .: (0.002514) test_orthologs_as_strings: .: (0.001535) test_pathways_as_hash: .: (0.001452) test_pathways_as_strings: .: (0.001176) test_reactions: .: (0.001236) test_references: .: (0.001592) test_remark: .: (0.001301) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.002278) test_composition: .: (0.002279) test_compounds: .: (0.001232) test_dblinks_as_hash: .: (0.001287) test_dblinks_as_strings: .: (0.001088) test_entry_id: .: (0.001220) test_enzymes: .: (0.001261) test_kcf: .: (0.001059) test_keggclass: .: (0.001056) test_mass: .: (0.001152) test_name: .: (0.001034) test_orthologs_as_hash: .: (0.000983) test_orthologs_as_strings: .: (0.002037) test_pathways_as_hash: .: (0.001005) test_pathways_as_strings: .: (0.000893) test_reactions: .: (0.001065) test_references: .: (0.000928) test_remark: .: (0.001095) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.003497) test_compounds_as_strings: .: (0.001860) test_dblinks_as_hash: .: (0.002336) test_dblinks_as_strings: .: (0.001426) test_description: .: (0.001322) test_diseases_as_hash: .: (0.001468) test_diseases_as_strings: .: (0.001345) test_entry_id: .: (0.001497) test_enzymes_as_strings: .: (0.001191) test_genes_as_hash: .: (0.001194) test_genes_as_strings: .: (0.001483) test_keggclass: .: (0.001325) test_ko_pathway: .: (0.002397) test_modules_as_hash: .: (0.001682) test_modules_as_strings: .: (0.001490) test_name: .: (0.001295) test_new: .: (0.001183) test_organism: .: (0.001325) test_orthologs_as_hash: .: (0.001140) test_orthologs_as_strings: .: (0.001095) test_pathways_as_hash: .: (0.001223) test_pathways_as_strings: .: (0.002003) test_reactions_as_hash: .: (0.002908) test_reactions_as_strings: .: (0.002101) test_references: .: (0.016069) test_rel_pathways_as_hash: .: (0.002366) test_rel_pathways_as_strings: .: (0.001706) Bio::TestBioLITDB: test_author: .: (0.002526) test_entry_id: .: (0.001119) test_field: .: (0.001150) test_journal: .: (0.001187) test_keyword: .: (0.002589) test_reference: .: (0.002223) test_title: .: (0.001325) test_volume: .: (0.001041) Bio::TestBioNBRF: test_aalen: .: (0.002138) test_aaseq: .: (0.000867) test_entry: .: (0.000732) test_length: .: (0.000776) test_nalen: .: (0.001117) test_naseq: .: (0.000932) test_seq: .: (0.002361) test_seq_class: .: (0.000825) test_to_nbrf: .: (0.000903) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.001862) test_to_newick_format_leaf: .: (0.001610) test_to_newick_format_leaf_NHX: .: (0.001037) Bio::TestBl2seqReport: test_db_len: .: (0.004822) test_db_num: .: (0.003865) test_new: .: (0.002132) test_undefed_methods: .: (0.006076) test_undefed_methods_for_iteration: .: (0.006074) Bio::TestBl2seqReportConstants: test_rs: .: (0.001131) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.003399) test_hits: .: (0.002278) Bio::TestBlast: test_blast_reports_format0: .: (0.031689) test_blast_reports_format0_with_block: .: (0.004338) test_blast_reports_format7: .: (0.092918) test_blast_reports_format7_with_block: .: (0.087356) test_blast_reports_format7_with_parser: .: (0.087887) test_blast_reports_format7_with_parser_with_block: .: (0.101388) test_blast_reports_format8: .: (0.005282) test_blast_reports_format8_with_block: .: (0.003174) test_blast_reports_format8_with_parser: .: (0.001602) test_blast_reports_format8_with_parser_with_block: .: (0.001294) test_blast_reports_xml: .: (0.084933) test_blast_reports_xml_with_block: .: (0.085548) test_blastll: .: (0.000981) test_db: .: (0.000804) test_exec_genomenet: .: (0.000729) test_exec_local: .: (0.000697) test_exec_ncbi: .: (0.001440) test_filter: .: (0.000801) test_format: .: (0.000809) test_make_command_line: .: (0.002876) test_make_command_line_2: .: (0.002233) test_matrix: .: (0.000795) test_new: .: (0.001960) test_new_opt_string: .: (0.001511) test_option: .: (0.000940) test_option_set: .: (0.001365) test_option_set_m0: .: (0.001417) test_options: .: (0.000904) test_output: .: (0.000806) test_parse_result: .: (0.152798) test_parser: .: (0.001081) test_program: .: (0.001066) test_query: .: (0.000894) test_self_local: .: (0.001617) test_self_remote: .: (0.027103) test_server: .: (0.001089) Bio::TestBlastNCBIOptions: test_add_options: .: (0.002328) test_delete: .: (0.002318) test_equal_equal: .: (0.002412) test_get: .: (0.002404) test_make_command_line_options: .: (0.018218) test_normalize!: .: (0.001303) test_parse: .: (0.001343) test_set: .: (0.019891) Bio::TestBlastReport: test_db: .: (0.129621) test_db_len: .: (0.089750) test_db_num: .: (0.088414) test_each_hit: .: (0.087135) test_each_iteration: .: (0.089025) test_eff_space: .: (0.087144) test_entrez_query: .: (0.085870) test_entropy: .: (0.084019) test_expect: .: (0.086201) test_filter: .: (0.086358) test_gap_extend: .: (0.081707) test_gap_open: .: (0.084716) test_hits: .: (0.085153) test_hsp_len: .: (0.085512) test_inclusion: .: (0.088476) test_iterations: .: (0.086615) test_kappa: .: (0.085514) test_lambda: .: (0.085258) test_matrix: .: (0.081960) test_message: .: (0.089998) test_parameters: .: (0.083476) test_pattern: .: (0.084015) test_program: .: (0.084029) test_query_def: .: (0.083421) test_query_id: .: (0.087618) test_query_len: .: (0.084698) test_reference: .: (0.082914) test_sc_match: .: (0.084223) test_sc_mismatch: .: (0.082777) test_statistics: .: (0.088481) test_version: .: (0.083928) Bio::TestBlastReportDefault: test_db: .: (0.003623) test_db_len: .: (0.002641) test_db_num: .: (0.002788) test_each_hit: .: (0.002697) test_each_iteration: .: (0.002345) test_eff_space: .: (0.003707) test_entropy: .: (0.002918) test_expect: .: (0.003141) test_gap_extend: .: (0.002984) test_gap_open: .: (0.002887) test_gapped_entropy: .: (0.002487) test_gapped_kappa: .: (0.002499) test_gapped_lambda: .: (0.002879) test_hits: .: (0.002436) test_iterations: .: (0.002321) test_kappa: .: (0.002500) test_lambda: .: (0.002486) test_matrix: .: (0.003035) test_message: .: (0.002458) test_pattern: .: (0.002352) test_program: .: (0.002497) test_query_def: .: (0.002554) test_query_len: .: (0.002477) test_reference: .: (0.002655) test_sc_match: .: (0.003002) test_sc_mismatch: .: (0.003014) test_version: .: (0.002434) Bio::TestBlastReportHit: test_Hit_accession: .: (0.082911) test_Hit_bit_score: .: (0.083030) test_Hit_definition: .: (0.090913) test_Hit_evalue: .: (0.083238) test_Hit_hit_id: .: (0.086412) test_Hit_hsps: .: (0.085555) test_Hit_identity: .: (0.083843) test_Hit_lap_at: .: (0.088985) test_Hit_len: .: (0.084681) test_Hit_midline: .: (0.084085) test_Hit_num: .: (0.083749) test_Hit_overlap: .: (0.086902) test_Hit_query_def: .: (0.086313) test_Hit_query_end: .: (0.083994) test_Hit_query_id: .: (0.084631) test_Hit_query_len: .: (0.084619) test_Hit_query_seq: .: (0.089626) test_Hit_query_start: .: (0.086623) test_Hit_taeget_def: .: (0.086537) test_Hit_target_end: .: (0.082863) test_Hit_target_id: .: (0.085096) test_Hit_target_len: .: (0.090359) test_Hit_target_seq: .: (0.085868) test_Hit_target_start: .: (0.081575) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.003912) test_Hit_definition: .: (0.002823) test_Hit_evalue: .: (0.002713) test_Hit_hsps: .: (0.002580) test_Hit_identity: .: (0.003128) test_Hit_lap_at: .: (0.003734) test_Hit_len: .: (0.002680) test_Hit_midline: .: (0.003647) test_Hit_overlap: .: (0.002698) test_Hit_query_end: .: (0.003592) test_Hit_query_seq: .: (0.004348) test_Hit_query_start: .: (0.003567) test_Hit_taeget_def: .: (0.002651) test_Hit_target_end: .: (0.003576) test_Hit_target_id: .: (0.002708) test_Hit_target_len: .: (0.002747) test_Hit_target_seq: .: (0.004353) test_Hit_target_start: .: (0.003589) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.268685) test_Hit_bit_score: .: (0.256387) test_Hit_definition: .: (0.251607) test_Hit_evalue: .: (0.257746) test_Hit_hit_id: .: (0.247718) test_Hit_hsps: .: (0.259020) test_Hit_identity: .: (0.260998) test_Hit_lap_at: .: (0.264340) test_Hit_len: .: (0.257830) test_Hit_midline: .: (0.262147) test_Hit_num: .: (0.254621) test_Hit_overlap: .: (0.245692) test_Hit_query_def: .: (0.255506) test_Hit_query_end: .: (0.266359) test_Hit_query_id: .: (0.244921) test_Hit_query_len: .: (0.244182) test_Hit_query_seq: .: (0.266885) test_Hit_query_start: .: (0.267463) test_Hit_taeget_def: .: (0.246439) test_Hit_target_end: .: (0.259663) test_Hit_target_id: .: (0.260561) test_Hit_target_len: .: (0.241890) test_Hit_target_seq: .: (0.248266) test_Hit_target_start: .: (0.250823) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.246892) test_Hit_bit_score: .: (0.256814) test_Hit_definition: .: (0.248448) test_Hit_evalue: .: (0.247232) test_Hit_hit_id: .: (0.248340) test_Hit_hsps: .: (0.255824) test_Hit_identity: .: (0.257158) test_Hit_lap_at: .: (0.248416) test_Hit_len: .: (0.254169) test_Hit_midline: .: (0.258190) test_Hit_num: .: (0.253171) test_Hit_overlap: .: (0.250421) test_Hit_query_def: .: (0.255054) test_Hit_query_end: .: (0.254379) test_Hit_query_id: .: (0.248659) test_Hit_query_len: .: (0.252770) test_Hit_query_seq: .: (0.257101) test_Hit_query_start: .: (0.247097) test_Hit_taeget_def: .: (0.254296) test_Hit_target_end: .: (0.258533) test_Hit_target_id: .: (0.252386) test_Hit_target_len: .: (0.254805) test_Hit_target_seq: .: (0.254307) test_Hit_target_start: .: (0.258710) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.085921) test_Hit_bit_score: .: (0.086180) test_Hit_definition: .: (0.085965) test_Hit_evalue: .: (0.089778) test_Hit_hit_id: .: (0.086267) test_Hit_hsps: .: (0.085502) test_Hit_identity: .: (0.087059) test_Hit_lap_at: .: (0.084123) test_Hit_len: .: (0.088632) test_Hit_midline: .: (0.084794) test_Hit_num: .: (0.084174) test_Hit_overlap: .: (0.084137) test_Hit_query_def: .: (0.090176) test_Hit_query_end: .: (0.088709) test_Hit_query_id: .: (0.088969) test_Hit_query_len: .: (0.088097) test_Hit_query_seq: .: (0.086336) test_Hit_query_start: .: (0.085727) test_Hit_taeget_def: .: (0.083744) test_Hit_target_end: .: (0.084383) test_Hit_target_id: .: (0.082354) test_Hit_target_len: .: (0.088464) test_Hit_target_seq: .: (0.084830) test_Hit_target_start: .: (0.084118) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.002125) test_Hit_bit_score: .: (0.000874) test_Hit_definition: .: (0.000715) test_Hit_evalue: .: (0.000707) test_Hit_hit_id: .: (0.000873) test_Hit_hsps: .: (0.000751) test_Hit_identity: .: (0.000683) test_Hit_lap_at: .: (0.000732) test_Hit_len: .: (0.000788) test_Hit_midline: .: (0.000893) test_Hit_num: .: (0.001336) test_Hit_overlap: .: (0.000946) test_Hit_query_def: .: (0.000787) test_Hit_query_end: .: (0.000693) test_Hit_query_id: .: (0.000702) test_Hit_query_len: .: (0.000689) test_Hit_query_seq: .: (0.000838) test_Hit_query_start: .: (0.000894) test_Hit_taeget_def: .: (0.000719) test_Hit_target_end: .: (0.000703) test_Hit_target_id: .: (0.000727) test_Hit_target_len: .: (0.000689) test_Hit_target_seq: .: (0.000675) test_Hit_target_start: .: (0.000686) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.083746) test_Hsp_bit_score: .: (0.089459) test_Hsp_density: .: (0.085111) test_Hsp_evalue: .: (0.084168) test_Hsp_gaps: .: (0.085370) test_Hsp_hit_frame: .: (0.087509) test_Hsp_hit_from: .: (0.086510) test_Hsp_hit_to: .: (0.082984) test_Hsp_hseq: .: (0.083922) test_Hsp_identity: .: (0.083588) test_Hsp_midline: .: (0.088418) test_Hsp_mismatch_count: .: (0.083142) test_Hsp_num: .: (0.083702) test_Hsp_pattern_from: .: (0.083930) test_Hsp_pattern_to: .: (0.088475) test_Hsp_percent_identity: .: (0.083751) test_Hsp_positive: .: (0.084036) test_Hsp_qseq: .: (0.084059) test_Hsp_query_frame: .: (0.084104) test_Hsp_query_from: .: (0.088144) test_Hsp_query_to: .: (0.085157) test_Hsp_score: .: (0.084286) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.003655) test_Hsp_bit_score: .: (0.002727) test_Hsp_evalue: .: (0.003263) test_Hsp_gaps: .: (0.002876) test_Hsp_hit_frame: .: (0.002671) test_Hsp_hit_from: .: (0.003497) test_Hsp_hit_to: .: (0.003500) test_Hsp_hseq: .: (0.003552) test_Hsp_identity: .: (0.002583) test_Hsp_midline: .: (0.004378) test_Hsp_percent_identity: .: (0.002752) test_Hsp_positive: .: (0.002741) test_Hsp_qseq: .: (0.003579) test_Hsp_query_frame: .: (0.002690) test_Hsp_query_from: .: (0.003503) test_Hsp_query_to: .: (0.003407) test_Hsp_score: .: (0.003622) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.256202) test_Hsp_bit_score: .: (0.258454) test_Hsp_density: .: (0.250290) test_Hsp_evalue: .: (0.259401) test_Hsp_gaps: .: (0.256685) test_Hsp_hit_frame: .: (0.258295) test_Hsp_hit_from: .: (0.252566) test_Hsp_hit_to: .: (0.257233) test_Hsp_hseq: .: (0.260066) test_Hsp_identity: .: (0.252417) test_Hsp_midline: .: (0.258441) test_Hsp_mismatch_count: .: (0.259156) test_Hsp_num: .: (0.255770) test_Hsp_pattern_from: .: (0.249645) test_Hsp_pattern_to: .: (0.256817) test_Hsp_percent_identity: .: (0.256951) test_Hsp_positive: .: (0.254742) test_Hsp_qseq: .: (0.252255) test_Hsp_query_frame: .: (0.252559) test_Hsp_query_from: .: (0.260570) test_Hsp_query_to: .: (0.259200) test_Hsp_score: .: (0.251451) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.258553) test_Hsp_bit_score: .: (0.258381) test_Hsp_density: .: (0.262577) test_Hsp_evalue: .: (0.254753) test_Hsp_gaps: .: (0.255167) test_Hsp_hit_frame: .: (0.257599) test_Hsp_hit_from: .: (0.252549) test_Hsp_hit_to: .: (0.253022) test_Hsp_hseq: .: (0.257725) test_Hsp_identity: .: (0.258766) test_Hsp_midline: .: (0.250158) test_Hsp_mismatch_count: .: (0.257054) test_Hsp_num: .: (0.258917) test_Hsp_pattern_from: .: (0.259378) test_Hsp_pattern_to: .: (0.251348) test_Hsp_percent_identity: .: (0.256486) test_Hsp_positive: .: (0.260366) test_Hsp_qseq: .: (0.258856) test_Hsp_query_frame: .: (0.249771) test_Hsp_query_from: .: (0.259671) test_Hsp_query_to: .: (0.448298) test_Hsp_score: .: (0.265674) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.094226) test_Hsp_bit_score: .: (0.089234) test_Hsp_density: .: (0.088455) test_Hsp_evalue: .: (0.083517) test_Hsp_gaps: .: (0.083668) test_Hsp_hit_frame: .: (0.088268) test_Hsp_hit_from: .: (0.084863) test_Hsp_hit_to: .: (0.082895) test_Hsp_hseq: .: (0.083968) test_Hsp_identity: .: (0.082448) test_Hsp_midline: .: (0.087749) test_Hsp_mismatch_count: .: (0.084062) test_Hsp_num: .: (0.083718) test_Hsp_pattern_from: .: (0.083667) test_Hsp_pattern_to: .: (0.086311) test_Hsp_percent_identity: .: (0.086441) test_Hsp_positive: .: (0.084727) test_Hsp_qseq: .: (0.082598) test_Hsp_query_frame: .: (0.083773) test_Hsp_query_from: .: (0.087614) test_Hsp_query_to: .: (0.085730) test_Hsp_score: .: (0.085396) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.002029) test_Hsp_bit_score: .: (0.000907) test_Hsp_density: .: (0.000917) test_Hsp_evalue: .: (0.000943) test_Hsp_gaps: .: (0.000883) test_Hsp_hit_frame: .: (0.000792) test_Hsp_hit_from: .: (0.000977) test_Hsp_hit_to: .: (0.000896) test_Hsp_hseq: .: (0.000865) test_Hsp_identity: .: (0.001677) test_Hsp_midline: .: (0.001221) test_Hsp_mismatch_count: .: (0.000897) test_Hsp_num: .: (0.000896) test_Hsp_pattern_from: .: (0.000858) test_Hsp_pattern_to: .: (0.000853) test_Hsp_percent_identity: .: (0.000838) test_Hsp_positive: .: (0.000929) test_Hsp_qseq: .: (0.000855) test_Hsp_query_frame: .: (0.000845) test_Hsp_query_from: .: (0.000866) test_Hsp_query_to: .: (0.000907) test_Hsp_score: .: (0.000884) Bio::TestBlastReportIteration: test_hits: .: (0.085923) test_message: .: (0.084916) test_num: .: (0.088530) test_statistics: .: (0.085575) Bio::TestBlastReportIterationDefault: test_hits: .: (0.003639) test_message: .: (0.002483) test_num: .: (0.002545) Bio::TestBlastReportIterationMulti: test_each: .: (0.253665) test_hits: .: (0.251301) test_message: .: (0.259859) test_num: .: (0.250060) test_query_def: .: (0.254379) test_query_id: .: (0.259228) test_query_len: .: (0.247641) test_statistics: .: (0.252758) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.260714) test_hits: .: (0.248523) test_message: .: (0.266702) test_num: .: (0.260003) test_query_def: .: (0.247991) test_query_id: .: (0.252745) test_query_len: .: (0.256587) test_statistics: .: (0.247155) Bio::TestBlastReportIterationREXML: test_hits: .: (0.090955) test_message: .: (0.086739) test_num: .: (0.085685) test_statistics: .: (0.083788) Bio::TestBlastReportIterationTabular: test_hits: .: (0.001929) test_message: .: (0.000880) test_num: .: (0.000807) test_statistics: .: (0.000852) Bio::TestBlastReportMulti: test_db: .: (0.252812) test_db_len: .: (0.250153) test_db_num: .: (0.255916) test_each_hit: .: (0.253992) test_each_iteration: .: (0.251315) test_eff_space: .: (0.248061) test_entropy: .: (0.254868) test_expect: .: (0.255203) test_filter: .: (0.247497) test_gap_extend: .: (0.251527) test_gap_open: .: (0.250499) test_hits: .: (0.245765) test_hsp_len: .: (0.250156) test_iterations: .: (0.255610) test_kappa: .: (0.243150) test_lambda: .: (0.253868) test_matrix: .: (0.255968) test_message: .: (0.245736) test_parameters: .: (0.255001) test_pattern: .: (0.257008) test_program: .: (0.255175) test_query_def: .: (0.247993) test_query_id: .: (0.253588) test_query_len: .: (0.252673) test_reference: .: (0.244630) test_reports: .: (0.252435) test_statistics: .: (0.257753) test_version: .: (0.248541) Bio::TestBlastReportMultiREXML: test_db: .: (0.252673) test_db_len: .: (0.248380) test_db_num: .: (0.251165) test_each_hit: .: (0.250330) test_each_iteration: .: (0.256420) test_eff_space: .: (0.257445) test_entropy: .: (0.252896) test_expect: .: (0.252248) test_filter: .: (0.256984) test_gap_extend: .: (0.257663) test_gap_open: .: (0.249672) test_hits: .: (0.255906) test_hsp_len: .: (0.249225) test_iterations: .: (0.246201) test_kappa: .: (0.248173) test_lambda: .: (0.256225) test_matrix: .: (0.255241) test_message: .: (0.252214) test_parameters: .: (0.253672) test_pattern: .: (0.255013) test_program: .: (0.255506) test_query_def: .: (0.247764) test_query_id: .: (0.254865) test_query_len: .: (0.253615) test_reference: .: (0.255127) test_reports: .: (0.248119) test_statistics: .: (0.255170) test_version: .: (0.255078) Bio::TestBlastReportREXML: test_db: .: (0.083767) test_db_len: .: (0.085698) test_db_num: .: (0.088578) test_each_hit: .: (0.083503) test_each_iteration: .: (0.084366) test_eff_space: .: (0.084738) test_entrez_query: .: (0.088950) test_entropy: .: (0.084108) test_expect: .: (0.084211) test_filter: .: (0.084818) test_gap_extend: .: (0.087739) test_gap_open: .: (0.084273) test_hits: .: (0.083106) test_hsp_len: .: (0.082612) test_inclusion: .: (0.087411) test_iterations: .: (0.084530) test_kappa: .: (0.084354) test_lambda: .: (0.084851) test_matrix: .: (0.087877) test_message: .: (0.086341) test_parameters: .: (0.080922) test_pattern: .: (0.079721) test_program: .: (0.079909) test_query_def: .: (0.083959) test_query_id: .: (0.080172) test_query_len: .: (0.079633) test_reference: .: (0.080123) test_sc_match: .: (0.084356) test_sc_mismatch: .: (0.082080) test_statistics: .: (0.079384) test_version: .: (0.080746) Bio::TestBlastReportTabular: test_db: .: (0.001623) test_db_len: .: (0.000751) test_db_num: .: (0.000753) test_each_hit: .: (0.000703) test_each_iteration: .: (0.000673) test_eff_space: .: (0.000674) test_entrez_query: .: (0.000857) test_entropy: .: (0.000778) test_expect: .: (0.000692) test_filter: .: (0.000670) test_gap_extend: .: (0.000843) test_gap_open: .: (0.000728) test_hits: .: (0.000715) test_hsp_len: .: (0.000671) test_inclusion: .: (0.000781) test_iterations: .: (0.001061) test_kappa: .: (0.000703) test_lambda: .: (0.000788) test_matrix: .: (0.000703) test_message: .: (0.000703) test_parameters: .: (0.000688) test_pattern: .: (0.000848) test_program: .: (0.000836) test_query_def: .: (0.000751) test_query_id: .: (0.000700) test_query_len: .: (0.000730) test_reference: .: (0.000824) test_sc_match: .: (0.000755) test_sc_mismatch: .: (0.001418) test_statistics: .: (0.001090) test_version: .: (0.000692) Bio::TestChain: test_aaseq: .: (0.001632) test_addLigand: .: (0.000581) test_addResidue: .: (0.000547) test_atom_seq: .: (0.000598) test_comp: .: (0.000686) test_each: .: (0.000633) test_each_heterogen: .: (0.000581) test_each_residue: .: (0.000599) test_get_heterogen_by_id: .: (0.000725) test_get_residue_by_id: .: (0.000589) test_inspect: .: (0.000708) test_rehash: .: (0.000573) test_rehash_heterogens: .: (0.000516) test_rehash_residues: .: (0.000539) test_square_brace: .: (0.000585) test_to_s: .: (0.000626) Bio::TestChainFinder: test_chains: .: (0.001279) test_each_chain: .: (0.000740) test_find_chain: .: (0.000586) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.056895) test_header: .: (0.004796) test_match_line: .: (0.003327) test_sequence0: .: (0.003278) test_sequence1: .: (0.004070) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.057298) test_header: .: (0.005917) test_match_line: .: (0.004839) test_sequence0: .: (0.004582) test_sequence1: .: (0.005413) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.066650) test_header: .: (0.005052) test_match_line: .: (0.003273) test_sequence0: .: (0.003242) test_sequence1: .: (0.003310) Bio::TestCodonTable: test_Tables: .: (0.001223) test_accessor: .: (0.000692) test_definition: .: (0.000443) test_each: .: (0.000533) test_revtrans: .: (0.000940) test_self_accessor: .: (0.000480) test_self_copy: .: (0.004061) test_set_accessor: .: (0.547823) test_start: .: (0.000517) test_start_codon?: .: (0.000546) test_stop: .: (0.000447) test_stop_codon?: .: (0.000526) test_table: .: (0.000431) Bio::TestCodonTableConstants: test_Definitions: .: (0.001050) test_Starts: .: (0.000526) test_Tables: .: (0.000424) test_stops: .: (0.000496) Bio::TestColorScheme: test_buried: .: (0.005213) Bio::TestCommand: test_command_constants: .: (0.001175) test_escape_shell: .: (0.000705) test_escape_shell_unix: .: (0.000588) test_escape_shell_windows: .: (0.000594) test_make_cgi_params_by_array_of_array: .: (0.001644) test_make_cgi_params_by_array_of_hash: .: (0.002110) test_make_cgi_params_by_array_of_string: .: (0.000885) test_make_cgi_params_by_hash_in_string: .: (0.002362) test_make_cgi_params_by_hash_in_symbol: .: (0.002366) test_make_cgi_params_by_string: .: (0.000691) test_make_command_line: .: (0.000600) test_make_command_line_unix: .: (0.000587) test_make_command_line_windows: .: (0.000568) test_safe_command_line_array: .: (0.000608) test_safe_command_line_array_passthrough: .: (0.000645) Bio::TestContingencyTable: test_lite_example: .: (1.122563) Bio::TestDB: test_entry_id: .: (0.001286) test_exists: .: (0.000461) test_fetch: .: (0.000714) test_get: .: (0.000441) test_open: .: (0.000432) test_tags: .: (0.000433) Bio::TestDataType: test_const_like_method: .: (0.002455) test_pdb_achar: .: (0.001017) test_pdb_atom: .: (0.000884) test_pdb_character: .: (0.000873) test_pdb_date: .: (0.000858) test_pdb_idcode: .: (0.000901) test_pdb_integer: .: (0.000443) test_pdb_list: .: (0.000477) test_pdb_lstring: .: (0.000794) test_pdb_real: .: (0.000659) test_pdb_resudue_name: .: (0.000911) test_pdb_slist: .: (0.000484) test_pdb_string: .: (0.000871) test_pdb_stringrj: .: (0.000467) test_pdb_symop: .: (0.001283) test_specification_list: .: (0.000545) Bio::TestEMBL: test_ac: .: (0.003276) test_accession: .: (0.001861) test_cc: .: (0.001702) test_de: .: (0.002263) test_division: .: (0.001994) test_dr: .: (0.001786) test_dt: .: (0.001768) test_dt_created: .: (0.001800) test_dt_iterator: .: (0.001746) test_dt_updated: .: (0.002152) test_each_cds: .: (0.002715) test_each_gene: .: (0.002602) test_entry: .: (0.002148) test_fh: .: (0.002106) test_ft: .: (0.002715) test_ft_accessor: .: (0.002834) test_ft_iterator: .: (0.002871) test_id_line: .: (0.001958) test_id_line_data_class: .: (0.002029) test_id_line_division: .: (0.001885) test_id_line_entry_name: .: (0.001982) test_id_line_iterator: .: (0.002309) test_id_line_molecule_type: .: (0.001938) test_id_line_sequence_length: .: (0.001964) test_kw: .: (0.001901) test_molecule: .: (0.002533) test_oc: .: (0.002189) test_og: .: (0.001806) test_os: .: (0.001937) test_ref: .: (0.002790) test_references: .: (0.003289) test_seq: .: (0.003296) test_sequence_length: .: (0.002412) test_sq: .: (0.001900) test_sq_get: .: (0.001884) test_sv: .: (0.001749) test_version: .: (0.001833) Bio::TestEMBL89: test_ac: .: (0.003534) test_accession: .: (0.001875) test_cc: .: (0.001703) test_de: .: (0.001814) test_division: .: (0.001921) test_dr: .: (0.001635) test_dt: .: (0.001753) test_dt_created: .: (0.001665) test_dt_iterator: .: (0.001686) test_dt_updated: .: (0.001635) test_each_cds: .: (0.002964) test_each_gene: .: (0.002489) test_entry: .: (0.002049) test_fh: .: (0.001761) test_ft: .: (0.002941) test_ft_accessor: .: (0.002533) test_ft_iterator: .: (0.002713) test_id_line: .: (0.002013) test_id_line_data_class: .: (0.002237) test_id_line_division: .: (0.001934) test_id_line_entry_name: .: (0.001846) test_id_line_iterator: .: (0.001903) test_id_line_molecule_type: .: (0.002217) test_id_line_sequence_length: .: (0.001930) test_id_line_sequence_version: .: (0.001833) test_kw: .: (0.010752) test_molecule: .: (0.002252) test_oc: .: (0.002168) test_og: .: (0.001743) test_os: .: (0.001961) test_ref: .: (0.002935) test_references: .: (0.003154) test_seq: .: (0.004109) test_sequence_length: .: (0.002252) test_sq: .: (0.001862) test_sq_get: .: (0.001871) test_sv: .: (0.002884) test_version: .: (0.002264) Bio::TestEMBLAPI: test_ac: .: (0.001510) test_accessions: .: (0.000812) Bio::TestEMBLCommon: test_ac: .: (0.000996) test_accession: .: (0.000509) test_accessions: .: (0.000480) test_de: .: (0.000455) test_definition: .: (0.000465) test_description: .: (0.001089) test_dr: .: (0.000507) test_keywords: .: (0.000439) test_kw: .: (0.000435) test_oc: .: (0.000460) test_og: .: (0.000452) test_os: .: (0.000434) test_ref: .: (0.000456) test_references: .: (0.000440) Bio::TestEMBLDB: test_fetch: .: (0.001391) test_p_entry2hash: .: (0.000444) Bio::TestEMBLToBioSequence: test_classification: .: (0.017866) test_date_created: .: (0.003290) test_date_modified: .: (0.002537) test_definition: .: (0.002109) test_division: .: (0.002264) test_entry_id: .: (0.002618) test_entry_version: .: (0.002034) test_features: .: (0.002999) test_keywords: .: (0.002499) test_molecule_type: .: (0.002183) test_primary_accession: .: (0.002125) test_references: .: (0.004071) test_release_created: .: (0.002262) test_release_modified: .: (0.002072) test_secondary_accessions: .: (0.002055) test_sequence_version: .: (0.003123) test_species: .: (0.002249) test_topology: .: (0.002235) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.018241) test_date_created: .: (0.018344) test_date_modified: .: (0.018451) test_definition: .: (0.017315) test_division: .: (0.016859) test_entry_id: .: (0.015740) test_entry_version: .: (0.016202) test_features: .: (0.095056) test_keywords: .: (0.074678) test_molecule_type: .: (0.070516) test_primary_accession: .: (0.016272) test_references: .: (0.018325) test_release_created: .: (0.016690) test_release_modified: .: (0.017125) test_secondary_accessions: .: (0.015730) test_sequence_version: .: (0.016663) test_species: .: (0.016944) test_topology: .: (0.016104) Bio::TestFasta: test_db: .: (0.001218) test_format: .: (0.000468) test_format_arg_integer: .: (0.000558) test_format_arg_str: .: (0.001684) test_ktup: .: (0.000587) test_matrix: .: (0.000511) test_option: .: (0.000672) test_options: .: (0.000535) test_output: .: (0.000428) test_program: .: (0.000538) test_server: .: (0.000503) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.001166) test_accession: .: (0.000620) test_accessions: .: (0.000599) test_description: .: (0.000544) test_descriptions: .: (0.000541) test_entry_id: .: (0.000534) test_get_all_by_type: .: (0.000542) test_gi: .: (0.000561) test_id_strings: .: (0.001999) test_list_ids: .: (0.000604) test_locus: .: (0.000564) test_words: .: (0.000742) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.001243) test_accession: .: (0.000733) test_accessions: .: (0.000731) test_description: .: (0.000639) test_descriptions: .: (0.000603) test_emb: .: (0.000811) test_entry_id: .: (0.000678) test_get_all_by_type: .: (0.000659) test_get_emb: .: (0.000691) test_gi: .: (0.000701) test_id_strings: .: (0.000918) test_list_ids: .: (0.000663) test_locus: .: (0.001960) test_words: .: (0.000926) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.001219) test_accession: .: (0.000687) test_accessions: .: (0.000620) test_description: .: (0.000554) test_descriptions: .: (0.000550) test_entry_id: .: (0.000546) test_get_all_by_type: .: (0.000600) test_gi: .: (0.000590) test_id_strings: .: (0.000784) test_list_ids: .: (0.000603) test_locus: .: (0.000629) test_sp: .: (0.000645) test_words: .: (0.000760) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.002648) test_accession: .: (0.000921) test_accessions: .: (0.000894) test_description: .: (0.000840) test_descriptions: .: (0.000783) test_entry_id: .: (0.000767) test_get_all_by_type: .: (0.000792) test_gi: .: (0.000830) test_id_strings: .: (0.001451) test_list_ids: .: (0.001914) test_locus: .: (0.000952) test_words: .: (0.001532) Bio::TestFastaDeflineSce: test_acc_version: .: (0.001353) test_accession: .: (0.000753) test_accessions: .: (0.000713) test_description: .: (0.000711) test_descriptions: .: (0.000696) test_entry_id: .: (0.000672) test_get_all_by_type: .: (0.000686) test_gi: .: (0.000738) test_id_strings: .: (0.002215) test_list_ids: .: (0.000777) test_locus: .: (0.000737) test_words: .: (0.001190) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.001184) test_accession: .: (0.000566) test_accessions: .: (0.000542) test_description: .: (0.000511) test_descriptions: .: (0.000509) test_entry_id: .: (0.000539) test_get_all_by_type: .: (0.000518) test_gi: .: (0.000515) test_id_strings: .: (0.001714) test_list_ids: .: (0.000663) test_locus: .: (0.000542) test_words: .: (0.000646) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.001251) test_accession: .: (0.000651) test_accessions: .: (0.000612) test_description: .: (0.000559) test_descriptions: .: (0.000560) test_entry_id: .: (0.000602) test_get: .: (0.000613) test_get_all_by_type: .: (0.000558) test_id_strings: .: (0.000983) test_list_ids: .: (0.001621) test_locus: .: (0.000661) test_sp: .: (0.000636) test_words: .: (0.000974) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.001196) test_accession: .: (0.000637) test_accessions: .: (0.000601) test_description: .: (0.000587) test_descriptions: .: (0.000576) test_entry_id: .: (0.000563) test_get: .: (0.000601) test_get_all_by_type: .: (0.000546) test_id_strings: .: (0.002277) test_list_ids: .: (0.000629) test_locus: .: (0.000613) test_tr: .: (0.000634) test_words: .: (0.001164) Bio::TestFastaFirstName: test_first_name1: .: (0.001215) test_first_name_multi_identifier: .: (0.000571) test_first_name_single_worded_defintion: .: (0.000531) test_no_definition: .: (0.000512) test_space_before_first_name: .: (0.000530) test_tabbed_defintion: .: (0.000549) Bio::TestFastaFormat: test_aalen: .: (0.001225) test_aaseq: .: (0.000634) test_acc_version: .: (0.000888) test_accession: .: (0.000816) test_accessions: .: (0.001811) test_data: .: (0.001012) test_definition: .: (0.000566) test_entry: .: (0.000556) test_entry_id: .: (0.000766) test_entry_overrun: .: (0.000599) test_first_name: .: (0.000603) test_gi: .: (0.000781) test_identifiers: .: (0.000792) test_length: .: (0.000596) test_query: .: (0.000725) test_seq: .: (0.000596) Bio::TestFastaFormatConst: test_delimiter: .: (0.001092) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.001466) test_data: .: (0.000603) test_definition: .: (0.000551) test_entry: .: (0.002090) test_entry_id: .: (0.000937) test_first_name: .: (0.000633) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.001171) test_naseq: .: (0.000532) test_naseq_class: .: (0.000531) Bio::TestFastaFormatSwissProt: test_locus: .: (0.001231) Bio::TestFastaInitialize: test_new_1: .: (0.002438) test_option: .: (0.000540) test_option_backward_compatibility: .: (0.000609) Bio::TestFastaNumericFormat: test_arg: .: (0.001288) test_data: .: (0.000730) test_definition: .: (0.000488) test_each: .: (0.000659) test_entry: .: (0.000480) test_entry_id: .: (0.000545) test_length: .: (0.000662) test_to_biosequence: .: (0.003582) Bio::TestFastaQuery: test_query: .: (0.000861) test_self_local: .: (0.000342) test_self_parser: .: (0.000337) test_self_remote: .: (0.000333) Bio::TestFastacmd: test_database: .: (0.001944) test_fastacmd: .: (0.000429) test_methods: .: (0.000623) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.003453) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.003087) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.004006) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.003086) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.003298) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.004316) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.003430) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.003123) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.003090) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.003027) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.003238) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.016956) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.003497) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.008054) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.007082) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.004135) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.003314) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.002993) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.034724) test_error_probabilities_as_sanger: .: (0.034370) test_error_probabilities_as_solexa: .: (0.034497) test_quality_scores_as_illumina: .: (0.002731) test_quality_scores_as_sanger: .: (0.001673) test_quality_scores_as_solexa: .: (0.003263) test_validate_format: .: (0.003081) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.006141) test_entry_id: .: (0.006614) test_error_probabilities: .: (0.860735) test_nalen: .: (0.006558) test_naseq: .: (0.005571) test_quality_scores: .: (0.011983) test_quality_string: .: (0.004822) test_roundtrip: .: (0.930716) test_seq: .: (0.005874) test_sequence_string: .: (0.004746) test_to_biosequence: .: (0.872674) test_to_biosequence_and_output: .: (0.030588) test_to_s: .: (0.005648) test_validate_format: .: (0.009173) test_validate_format_with_array: .: (0.006894) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.003343) test_mask_20_with_empty_string: .: (0.002083) test_mask_20_with_longer_string: .: (0.002015) test_mask_20_with_x: .: (0.001995) test_mask_60: .: (0.002424) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.047798) test_error_probabilities_as_sanger: .: (0.045760) test_error_probabilities_as_solexa: .: (0.052334) test_quality_scores_as_illumina: .: (0.002153) test_quality_scores_as_sanger: .: (0.001783) test_quality_scores_as_solexa: .: (0.002631) test_validate_format: .: (0.004781) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.035488) test_error_probabilities_as_sanger: .: (0.034238) test_error_probabilities_as_solexa: .: (0.034446) test_quality_scores_as_illumina: .: (0.002402) test_quality_scores_as_sanger: .: (0.002233) test_quality_scores_as_solexa: .: (0.002256) test_validate_format: .: (0.003391) Bio::TestFeature: test_append: .: (0.001217) test_append_nil: .: (0.000568) test_assoc: .: (0.000549) test_each: .: (0.000458) test_feature: .: (0.000517) test_locations: .: (0.000806) test_new: .: (0.000475) test_position: .: (0.000461) test_qualifiers: .: (0.000462) Bio::TestFeatures: test_append: .: (0.001992) test_arg: .: (0.000582) test_each: .: (0.000530) test_features: .: (0.000606) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.005090) test_aaindex2: .: (0.001353) test_blast: .: (0.001044) test_blastxml: .: (0.004741) test_embl: .: (0.001566) test_embl_oldrelease: .: (0.001404) test_fastaformat: .: (0.003315) test_fastanumericformat: .: (0.001483) test_fastq: .: (0.001088) test_genbank: .: (0.001251) test_genpept: .: (0.001295) test_hmmer: .: (0.002300) test_maxml_cluster: .: (0.015194) test_maxml_sequence: .: (0.000721) test_medline: .: (0.000870) test_prosite: .: (0.020909) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.018148) test_transfac: .: (0.008086) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.001422) test_auto_1arg_filename: .: (0.002057) test_auto_1arg_io: .: (0.001852) test_auto_1arg_io_with_block: .: (0.003823) test_auto_1arg_with_block: .: (0.003947) test_auto_2arg_filename_mode: .: (0.009951) test_auto_2arg_filename_mode_with_block: .: (0.003527) test_auto_3arg: .: (0.001792) test_auto_3arg_with_block: .: (0.003389) test_foreach: .: (0.003732) test_new_2arg_class: .: (0.000956) test_new_2arg_nil: .: (0.001759) test_open_0arg: .: (0.000617) test_open_1arg_class: .: (0.000575) test_open_1arg_filename: .: (0.001779) test_open_1arg_io: .: (0.001658) test_open_1arg_io_with_block: .: (0.004281) test_open_1arg_nil: .: (0.000712) test_open_1arg_with_block: .: (0.003359) test_open_2arg_autodetect: .: (0.001709) test_open_2arg_autodetect_io: .: (0.001617) test_open_2arg_autodetect_io_with_block: .: (0.004425) test_open_2arg_autodetect_with_block: .: (0.003642) test_open_2arg_class: .: (0.001037) test_open_2arg_class_io: .: (0.000993) test_open_2arg_class_io_with_block: .: (0.002801) test_open_2arg_class_with_block: .: (0.003440) test_open_2arg_filename_mode: .: (0.002286) test_open_2arg_filename_mode_with_block: .: (0.003763) test_open_3arg: .: (0.004003) test_open_3arg_with_block: .: (0.009472) test_open_4arg: .: (0.008422) test_to_a: .: (0.002990) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.002476) test_close: .: (0.000847) test_dbclass: .: (0.000771) test_dbclass_eq: .: (0.001004) test_dbclass_nil: .: (0.001173) test_each: .: (0.002587) test_each_entry: .: (0.002278) test_ended_pos: .: (0.001504) test_entry_pos_flag: .: (0.000982) test_entry_raw: .: (0.001890) test_eof?: .: (0.001610) test_next_entry: .: (0.002135) test_path: .: (0.000838) test_pos: .: (0.001975) test_raw: .: (0.001873) test_rewind: .: (0.001266) test_start_pos: .: (0.001430) test_start_pos_ended_pos_not_recorded: .: (0.001517) test_to_io: .: (0.000919) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.001553) test_simpleformat2: .: (0.001009) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.001189) test_eof_false_after_prefetch: .: (0.001836) test_eof_false_first: .: (0.000820) test_eof_true: .: (0.001032) test_getc: .: (0.000597) test_getc_after_prefetch: .: (0.000586) test_gets: .: (0.000636) test_gets_equal_prefetch_gets: .: (0.000690) test_gets_paragraph_mode: .: (0.000852) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.002025) test_gets_paragraph_mode_within_buffer: .: (0.002120) test_gets_rs: .: (0.000825) test_gets_rs_equal_prefetch_gets: .: (0.000897) test_gets_rs_within_buffer: .: (0.002367) test_pos: .: (0.000882) test_pos=: .: (0.000705) test_prefetch_buffer: .: (0.000622) test_prefetch_gets: .: (0.000711) test_prefetch_gets_with_arg: .: (0.000911) test_rewind: .: (0.000652) test_skip_spaces: .: (0.000685) test_to_io: .: (0.000636) test_ungetc: .: (0.000710) test_ungetc_after_prefetch: .: (0.000809) test_ungets: .: (0.000945) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.001358) test_self_open_file: .: (0.000739) test_self_open_file_with_block: .: (0.000847) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.002017) test_parse_file_open_arg_int_perm: .: (0.000503) test_parse_file_open_arg_int_perm_opt: .: (0.000511) test_parse_file_open_arg_integer: .: (0.000533) test_parse_file_open_arg_nil: .: (0.000561) test_parse_file_open_arg_opt: .: (0.000657) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000533) test_parse_file_open_arg_str: .: (0.000533) test_parse_file_open_arg_str_opt: .: (0.000567) test_parse_file_open_arg_str_perm: .: (0.000560) test_parse_file_open_arg_str_perm_opt: .: (0.000564) test_parse_file_open_arg_str_with_enc: .: (0.000658) test_parse_file_open_arg_str_with_ext_enc: .: (0.000620) test_parse_file_open_mode_integer: .: (0.000477) test_parse_file_open_mode_nil: .: (0.000620) test_parse_file_open_mode_str: .: (0.000562) test_parse_file_open_mode_str_with_enc: .: (0.000607) test_parse_file_open_mode_str_with_ext_enc: .: (0.001299) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.001107) test_entry: .: (0.000534) test_entry_ended_pos: .: (0.000555) test_entry_pos_flag: .: (0.000608) test_entry_start_pos: .: (0.000521) test_get_entry: .: (0.000649) test_rewind: .: (0.000644) test_skip_leader: .: (0.000747) test_stream: .: (0.000549) test_stream_pos: .: (0.000641) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.001186) test_delimiter_overrun: .: (0.000583) test_entry: .: (0.000833) test_entry_ended_pos: .: (0.000620) test_entry_ended_pos_default_nil: .: (0.001306) test_entry_start_pos: .: (0.000620) test_entry_start_pos_default_nil: .: (0.000601) test_get_entry: .: (0.001197) test_get_parsed_entry: .: (0.001231) test_header: .: (0.000487) test_skip_leader: .: (0.000705) test_skip_leader_without_header: .: (0.000701) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.001580) test_entry_ended_pos: .: (0.001961) test_entry_start_pos: .: (0.001204) test_flag_to_fetch_header: .: (0.001072) test_get_entry: .: (0.001584) test_get_parsed_entry: .: (0.001651) test_rewind: .: (0.001858) test_skip_leader: .: (0.000773) Bio::TestGCGMsf: test_alignment: .: (0.005396) test_checksum: .: (0.001210) test_compcheck: .: (0.001291) test_date: .: (0.002211) test_description: .: (0.001245) test_entry_id: .: (0.001214) test_gap_length_weight: .: (0.001261) test_gap_weight: .: (0.001232) test_heading: .: (0.001194) test_length: .: (0.001226) test_seq_type: .: (0.002394) test_symbol_comparison_table: .: (0.001781) test_validate_checksum: .: (0.009827) Bio::TestGFF: test_record_class: .: (0.002629) test_records: .: (0.003210) Bio::TestGFF2: test_const_version: .: (0.003070) test_gff_version: .: (0.002367) test_metadata: .: (0.003231) test_metadata_size: .: (0.002267) test_records_size: .: (0.002278) test_to_s: .: (0.077610) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.001508) test_attributes_case2: .: (0.000985) test_attributes_incompatible_backslash_semicolon: .: (0.029170) Bio::TestGFF2MetaData: test_data: .: (0.001110) test_directive: .: (0.000489) test_parse: .: (0.000564) Bio::TestGFF2Record: test_attribute: .: (0.034266) test_attribute_nonexistent: .: (0.001525) test_attributes: .: (0.001558) test_attributes_to_hash: .: (0.028101) test_comment_only?: .: (0.001420) test_delete_attribute: .: (0.031387) test_delete_attribute_multiple: .: (0.001789) test_delete_attribute_multiple2: .: (0.010875) test_delete_attribute_multiple_nil: .: (0.001701) test_delete_attribute_nil: .: (0.001639) test_delete_attribute_nonexistent: .: (0.001585) test_delete_attributes: .: (0.001846) test_delete_attributes_multiple: .: (0.001666) test_delete_attributes_nonexistent: .: (0.002854) test_end: .: (0.001658) test_eqeq: .: (0.003444) test_eqeq_false: .: (0.004203) test_feature: .: (0.001481) test_frame: .: (0.001328) test_get_attribute: .: (0.001930) test_get_attribute_nonexistent: .: (0.001346) test_get_attributes: .: (0.002073) test_get_attributes_nonexistent: .: (0.002370) test_replace_attributes: .: (0.001673) test_replace_attributes_multiple_multiple_over: .: (0.001627) test_replace_attributes_multiple_multiple_same: .: (0.001986) test_replace_attributes_multiple_multiple_two: .: (0.001619) test_replace_attributes_multiple_single: .: (0.001786) test_replace_attributes_nonexistent: .: (0.002579) test_replace_attributes_nonexistent_multiple: .: (0.001671) test_replace_attributes_single_multiple: .: (0.001621) test_score: .: (0.001421) test_self_parse: .: (0.004180) test_seqname: .: (0.001367) test_set_attribute: .: (0.001584) test_set_attribute_multiple: .: (0.001969) test_set_attribute_nonexistent: .: (0.001637) test_sort_attributes_by_tag!: .: (0.002888) test_sort_attributes_by_tag_bang_test2: .: (0.002017) test_sort_attributes_by_tag_bang_with_block: .: (0.001874) test_source: .: (0.001328) test_start: .: (0.001368) test_strand: .: (0.001352) test_to_s: .: (0.003156) Bio::TestGFF2RecordEmpty: test_comment: .: (0.001199) test_comment_eq: .: (0.000550) test_comment_only?: .: (0.000553) test_comment_only_false: .: (0.000514) test_to_s: .: (0.000568) test_to_s_not_empty: .: (0.000969) Bio::TestGFF3: test_const_version: .: (0.004981) test_gff_version: .: (0.003305) test_records: .: (0.004929) test_sequence_regions: .: (0.003543) test_sequences: .: (0.004831) test_to_s: .: (0.005812) Bio::TestGFF3MetaData: test_data: .: (0.001590) test_directive: .: (0.000497) test_parse: .: (0.000559) Bio::TestGFF3Record: test_attributes: .: (0.002169) test_end: .: (0.001366) test_feature: .: (0.001384) test_frame: .: (0.002316) test_id: .: (0.001457) test_score: .: (0.001242) test_seqname: .: (0.001229) test_source: .: (0.001270) test_start: .: (0.001238) test_strand: .: (0.001525) test_to_s: .: (0.002121) test_to_s_attr_order_changed: .: (0.002574) Bio::TestGFF3RecordEscape: test_escape: .: (0.001398) test_escape_attribute: .: (0.000851) test_escape_seqid: .: (0.000829) test_unescape: .: (0.001794) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.001942) test_eqeq: .: (0.001182) test_new_from_sequences_na: .: (0.001162) test_new_from_sequences_na_aa: .: (0.001815) test_new_from_sequences_na_aa_boundary_gap: .: (0.002509) test_new_from_sequences_na_aa_example: .: (0.002922) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.001789) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.001555) test_process_sequences_na: .: (0.001243) test_process_sequences_na_aa: .: (0.001183) test_process_sequences_na_aa_reverse_frameshift: .: (0.001131) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.001232) test_process_sequences_na_aa_tooshort: .: (0.001774) test_process_sequences_na_tooshort: .: (0.002836) test_to_s: .: (0.001196) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.001502) test_attributes_one: .: (0.000711) test_attributes_with_escaping: .: (0.000793) test_id_multiple: .: (0.001439) test_id_multiple2: .: (0.001361) test_id_replace: .: (0.000838) test_id_set: .: (0.001065) test_initialize_9: .: (0.000520) test_phase: .: (0.001642) test_score: .: (0.000729) test_to_s_void: .: (0.000663) Bio::TestGFF3RecordTarget: test_end: .: (0.001226) test_parse: .: (0.001048) test_start: .: (0.000612) test_strand: .: (0.000585) test_target_id: .: (0.000598) test_to_s: .: (0.000976) Bio::TestGFF3SequenceRegion: test_end: .: (0.001240) test_parse: .: (0.001039) test_seqid: .: (0.000655) test_start: .: (0.001309) test_to_s: .: (0.000960) Bio::TestGFFRecord: test_attributes: .: (0.001367) test_comment: .: (0.000694) test_end: .: (0.000662) test_feature: .: (0.000650) test_frame: .: (0.000643) test_score: .: (0.000613) test_seqname: .: (0.000612) test_source: .: (0.000606) test_start: .: (0.000630) test_strand: .: (0.001528) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.001120) Bio::TestGeneAssociation: test_aspect: .: (0.001273) test_assigned_by: .: (0.000648) test_date: .: (0.000607) test_db: .: (0.000672) test_db_object_id: .: (0.000670) test_db_object_name: .: (0.000613) test_db_object_symbol: .: (0.000596) test_db_object_synonym: .: (0.000614) test_db_object_type: .: (0.000638) test_db_reference: .: (0.000617) test_evidence: .: (0.001606) test_goid: .: (0.000788) test_parser: .: (0.003482) test_qualifier: .: (0.000674) test_taxon: .: (0.000613) test_to_str: .: (0.000654) test_with: .: (0.000614) Bio::TestGenscanReport: test_date_run: .: (0.006392) test_gccontent: .: (0.003947) test_genscan_version: .: (0.005444) test_isochore: .: (0.003898) test_length: .: (0.003883) test_matrix: .: (0.004842) test_predictions_size: .: (0.003898) test_query_name: .: (0.005083) test_time: .: (0.003927) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.005478) test_donor_score: .: (0.004199) test_exon_type: .: (0.003872) test_exon_type_long: .: (0.005285) test_first: .: (0.003948) test_initiation_score: .: (0.004953) test_last: .: (0.003898) test_number: .: (0.003811) test_p_value: .: (0.005011) test_phase: .: (0.003931) test_range: .: (0.004453) test_score: .: (0.003844) test_strand: .: (0.015914) test_t_score: .: (0.004004) test_termination_score: .: (0.004826) Bio::TestGenscanReportGene: test_aaseq: .: (0.004782) test_naseq: .: (0.004874) test_number: .: (0.003882) test_polyA: .: (0.004717) test_promoter: .: (0.004026) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.004767) test_reports_ary_contents: .: (0.004563) Bio::TestHMMERReportConstants: test_rs: .: (0.001152) Bio::TestHMMERReportHit: test_accession: .: (0.004428) test_append_hsp: .: (0.004443) test_bit_score: .: (0.003973) test_definition: .: (0.003869) test_description: .: (0.003819) test_each: .: (0.004707) test_each_hsp: .: (0.004170) test_entry_id: .: (0.003920) test_evalue: .: (0.004565) test_hit: .: (0.004051) test_hit_id: .: (0.003879) test_hsps: .: (0.003893) test_num: .: (0.004432) test_score: .: (0.003937) test_target_def: .: (0.003854) test_target_id: .: (0.003838) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.004571) test_each: .: (0.003888) test_each_hit: .: (0.003849) test_histogram: .: (0.004521) test_hits: .: (0.004040) test_hsps: .: (0.003857) test_parameter: .: (0.004026) test_program: .: (0.004921) test_query_info: .: (0.004113) test_statistical_detail: .: (0.003853) test_total_seq_searched: .: (0.004475) test_whole_seq_top_hits: .: (0.004049) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.005368) test_histogram: .: (0.005468) test_statistical_detail: .: (0.004751) test_total_seq_searched: .: (0.004415) test_whole_seq_top_hit: .: (0.005373) Bio::TestHMMERReportHsp: test_accession: .: (0.004446) test_bit_score: .: (0.003855) test_csline: .: (0.003834) test_domain: .: (0.004451) test_evalue: .: (0.003989) test_flatseq: .: (0.003812) test_hmm_f: .: (0.003803) test_hmm_t: .: (0.004468) test_hmmseq: .: (0.003975) test_hsp: .: (0.003819) test_midline: .: (0.003816) test_query_frame: .: (0.004851) test_query_from: .: (0.003852) test_query_seq: .: (0.003845) test_query_to: .: (0.004750) test_rfline: .: (0.004262) test_score: .: (0.003840) test_seq_f: .: (0.003841) test_seq_ft: .: (0.004967) test_seq_t: .: (0.004261) test_set_alignment: .: (0.003811) test_targat_to: .: (0.003865) test_target_frame: .: (0.004930) test_target_from: .: (0.004274) test_target_seq: .: (0.003857) Bio::TestHetatmFinder: test_each_hetatm: .: (0.003629) test_find_hetatm: .: (0.001483) test_hetatms: .: (0.001685) Bio::TestHeterogen: test_addAtom: .: (0.001938) test_each: .: (0.001140) test_each_hetatm: .: (0.001128) test_get_residue_id_from_atom: .: (0.001044) test_het_atom: .: (0.000899) test_iCode: .: (0.000817) test_inspect: .: (0.001323) test_resSeq: .: (0.000951) test_sort: .: (0.001041) test_square_bracket: .: (0.000951) test_to_s: .: (0.001412) test_update_resudue_id: .: (0.000988) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.001477) test_find_heterogen: .: (0.000691) test_heterogens: .: (0.000763) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.001575) test_match_description: .: (0.000889) test_match_evalue: .: (0.000852) test_match_ipr_description: .: (0.000908) test_match_ipr_id: .: (0.000871) test_match_match_end: .: (0.002091) test_match_match_start: .: (0.000870) test_match_method: .: (0.000834) test_matches_size: .: (0.000810) test_query_id: .: (0.000878) test_query_length: .: (0.000820) Bio::TestIprscanRawReport: test_entry_id: .: (0.023218) test_match_accession: .: (0.013009) test_match_crc64: .: (0.012498) test_match_date: .: (0.013906) test_match_description: .: (0.013029) test_match_evalue: .: (0.012774) test_match_go_terms: .: (0.012710) test_match_ipr_description: .: (0.012482) test_match_ipr_id: .: (0.013839) test_match_match_end: .: (0.011670) test_match_match_start: .: (0.012070) test_match_method: .: (0.017554) test_match_query_id: .: (0.012411) test_match_query_length: .: (0.012268) test_match_status: .: (0.013040) test_obj: .: (0.012399) test_query_id: .: (0.012361) test_query_length: .: (0.012040) test_self_reports_in_raw: .: (0.060709) Bio::TestIprscanReport: test_output_raw: .: (0.036410) test_to_raw: .: (0.034603) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.003445) test_match_accession: .: (0.035233) test_match_date: .: (0.002816) test_match_description: .: (0.031975) test_match_evalue: .: (0.002839) test_match_go_terms: .: (0.027077) test_match_ipr_description: .: (0.024134) test_match_ipr_id: .: (0.002963) test_match_match_end: .: (0.002728) test_match_match_start: .: (0.002727) test_match_method: .: (0.003672) test_match_status: .: (0.002905) test_matches_size: .: (0.002690) test_query_id: .: (0.002644) test_query_length: .: (0.003605) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.003766) test_to_hash_match?: .: (0.003812) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.008379) Bio::TestKeggCompound: test_comment: .: (0.002987) test_dblinks_as_hash: .: (0.001984) test_dblinks_as_strings: .: (0.002715) test_entry_id: .: (0.001602) test_enzymes: .: (0.003370) test_formula: .: (0.001624) test_kcf: .: (0.001405) test_mass: .: (0.001559) test_name: .: (0.002480) test_names: .: (0.001967) test_pathways_as_hash: .: (0.002776) test_pathways_as_strings: .: (0.001940) test_reactions: .: (0.004509) test_remark: .: (0.001653) test_rpairs: .: (0.001530) Bio::TestKeggEnzyme: test_all_reac: .: (0.004346) test_classes: .: (0.002543) test_cofactors: .: (0.002661) test_comment: .: (0.003629) test_dblinks_as_hash: .: (0.003132) test_dblinks_as_strings: .: (0.002547) test_diseases: .: (0.002661) test_entry: .: (0.003018) test_entry_id: .: (0.003028) test_genes: .: (0.080085) test_genes_as_hash: .: (0.089476) test_genes_as_strings: .: (0.024637) test_inhibitors: .: (0.002591) test_iubmb_reactions: .: (0.002825) test_kegg_reactions: .: (0.002750) test_motifs: .: (0.003744) test_name: .: (0.003050) test_names: .: (0.002947) test_obsolete?: .: (0.002539) test_orthologs_as_hash: .: (0.003095) test_orthologs_as_strings: .: (0.003009) test_pathways_as_hash: .: (0.004540) test_pathways_as_strings: .: (0.003624) test_products: .: (0.003167) test_reaction: .: (0.003240) test_structures: .: (0.004256) test_substrates: .: (0.004110) test_sysname: .: (0.003515) Bio::TestKeggGenesDblinks: test_data: .: (0.001329) test_dblinks_0: .: (0.000820) test_dblinks_1: .: (0.000737) test_dblinks_2: .: (0.000694) Bio::TestKeggGenesStructure: test_data: .: (0.001350) test_ids: .: (0.001053) test_ids_in_array: .: (0.000853) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.051187) test_graphics__size: .: (0.046144) test_id: .: (0.045284) test_link: .: (0.044193) test_name: .: (0.044220) test_reaction: .: (0.043911) test_type: .: (0.043609) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.044240) test_graphics__size: .: (0.043642) test_id: .: (0.043448) test_link: .: (0.046059) test_name: .: (0.051055) test_reaction: .: (0.062863) test_type: .: (0.059361) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.054714) test_category: .: (0.052326) test_entry_id: .: (0.050990) test_fgcolor=: .: (0.052132) test_height=: .: (0.052413) test_label=: .: (0.050819) test_shape=: .: (0.050646) test_width=: .: (0.050127) test_x=: .: (0.050503) test_y=: .: (0.050466) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.050613) test_graphics__size: .: (0.050691) test_id: .: (0.053586) test_link: .: (0.052391) test_name: .: (0.051279) test_reaction: .: (0.050630) test_type: .: (0.050551) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.001428) test_graphics=: .: (0.000705) test_id=: .: (0.001392) test_link=: .: (0.000769) test_name=: .: (0.000751) test_reaction=: .: (0.000722) test_type=: .: (0.000689) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.001558) test_category=: .: (0.000951) test_entry_id=: .: (0.000946) test_fgcolor=: .: (0.000903) test_height=: .: (0.000879) test_label=: .: (0.001018) test_pathway=: .: (0.000755) test_shape=: .: (0.000939) test_width=: .: (0.001036) test_x=: .: (0.000861) test_y=: .: (0.000847) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.050667) test_coords: .: (0.049669) test_fgcolor: .: (0.049077) test_height: .: (0.049938) test_name: .: (0.049397) test_type: .: (0.049338) test_width: .: (0.049088) test_x: .: (0.048182) test_y: .: (0.049264) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.055874) test_coords: .: (0.050995) test_fgcolor: .: (0.050732) test_height: .: (0.051332) test_name: .: (0.050624) test_type: .: (0.050045) test_width: .: (0.050207) test_x: .: (0.049644) test_y: .: (0.049427) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.001441) test_coords=: .: (0.001179) test_fgcolor=: .: (0.000733) test_height=: .: (0.000660) test_name=: .: (0.000669) test_type=: .: (0.000723) test_width=: .: (0.000673) test_x=: .: (0.000742) test_y=: .: (0.000798) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.049864) test_entries__size: .: (0.048797) test_image: .: (0.048999) test_link: .: (0.048659) test_name: .: (0.048925) test_number: .: (0.049134) test_org: .: (0.055140) test_reactions=: .: (0.050929) test_reactions__size: .: (0.051247) test_relations=: .: (0.051524) test_relations__size: .: (0.046662) test_title: .: (0.044193) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.088376) test_name: .: (0.087339) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.001252) test_initialize_0: .: (0.000476) test_initialize_1: .: (0.000514) test_initialize_2: .: (0.000860) test_name=: .: (0.000667) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.044247) test_name: .: (0.043532) test_products: .: (0.043737) test_substrates: .: (0.043756) test_type: .: (0.048930) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.001243) test_name=: .: (0.000727) test_products=: .: (0.000671) test_substraces=: .: (0.000657) test_type=: .: (0.000676) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.002111) test_entry_id=: .: (0.000823) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.045434) test_entry2: .: (0.044432) test_name: .: (0.045559) test_type: .: (0.044328) test_value: .: (0.044223) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.001007) test_node1=: .: (0.000801) test_node2=: .: (0.000830) test_rel=: .: (0.000797) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.001159) test_entry2=: .: (0.000655) test_name=: .: (0.000665) test_type=: .: (0.000653) test_value=: .: (0.001197) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.088188) test_name: .: (0.087030) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.001269) test_initialize_0: .: (0.000461) test_initialize_1: .: (0.000464) test_initialize_2: .: (0.000485) test_name=: .: (0.000711) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.001789) test_initialize_0: .: (0.000458) test_initialize_1: .: (0.000503) test_initialize_2: .: (0.000476) test_name=: .: (0.000662) Bio::TestKeggModule: test_compounds: .: (0.002670) test_compounds_as_hash: .: (0.001404) test_compounds_as_strings: .: (0.001174) test_definition: .: (0.001121) test_entry_id: .: (0.000992) test_keggclass: .: (0.001159) test_name: .: (0.001002) test_new: .: (0.000941) test_orthologs: .: (0.001469) test_orthologs_as_array: .: (0.001525) test_orthologs_as_hash: .: (0.001387) test_orthologs_as_strings: .: (0.001172) test_pathways: .: (0.000969) test_pathways_as_hash: .: (0.001324) test_pathways_as_strings: .: (0.000977) test_reactions: .: (0.001372) test_reactions_as_hash: .: (0.001417) test_reactions_as_strings: .: (0.001122) Bio::TestKeggOrthology: test_dblinks: .: (0.003578) test_dblinks_as_hash: .: (0.002207) test_dblinks_as_strings: .: (0.001959) test_definition: .: (0.002960) test_entry_id: .: (0.002045) test_genes_as_hash: .: (0.063595) test_genes_as_strings: .: (0.021136) test_keggclass: .: (0.002711) test_keggclasses: .: (0.002623) test_modules: .: (0.002298) test_modules_as_hash: .: (0.001985) test_modules_as_strings: .: (0.001989) test_name: .: (0.002021) test_names: .: (0.002006) test_pathways_as_strings: .: (0.002063) test_pathways_in_keggclass: .: (0.002627) test_references: .: (0.003547) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.002279) test_compounds_as_strings: .: (0.001061) test_dblinks_as_hash: .: (0.001061) test_dblinks_as_strings: .: (0.000984) test_description: .: (0.001089) test_diseases_as_hash: .: (0.001060) test_diseases_as_strings: .: (0.000982) test_entry_id: .: (0.002022) test_enzymes_as_strings: .: (0.001034) test_genes_as_hash: .: (0.000977) test_genes_as_strings: .: (0.000980) test_keggclass: .: (0.001124) test_ko_pathway: .: (0.001052) test_modules_as_hash: .: (0.001464) test_modules_as_strings: .: (0.001118) test_name: .: (0.001912) test_organism: .: (0.001322) test_orthologs_as_hash: .: (0.000997) test_orthologs_as_strings: .: (0.000972) test_pathways_as_hash: .: (0.001116) test_pathways_as_strings: .: (0.001017) test_reactions_as_hash: .: (0.000971) test_reactions_as_strings: .: (0.001058) test_references: .: (0.000993) test_rel_pathways_as_hash: .: (0.002039) test_rel_pathways_as_strings: .: (0.001347) Bio::TestKeggReaction: test_definition: .: (0.002507) test_entry_id: .: (0.001248) test_enzymes: .: (0.001185) test_equation: .: (0.001234) test_name: .: (0.001213) test_orthologs_as_hash: .: (0.001379) test_orthologs_as_strings: .: (0.001787) test_pathways_as_hash: .: (0.001337) test_pathways_as_strings: .: (0.001192) test_rpairs_as_hash: .: (0.001392) test_rpairs_as_strings: .: (0.001201) test_rpairs_as_tokens: .: (0.001321) Bio::TestLasergene: test_methods: .: (0.040231) Bio::TestLocations: test_complement: .: (0.001964) test_hat: .: (0.000765) test_normal: .: (0.000669) test_replace_single_base: .: (0.000596) test_should_not_modify_argument: .: (0.000530) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.020767) test_locations_to_s: .: (0.009671) Bio::TestMEDLINE: test_authors: .: (0.003787) test_authors_with_last_name_all_caps: .: (0.000564) test_authors_with_suffix: .: (0.000576) Bio::TestMEDLINE_20146148: test_ab: .: (0.004019) test_ad: .: (0.002135) test_au: .: (0.001923) test_authors: .: (0.002064) test_doi: .: (0.002571) test_dp: .: (0.001992) test_ip: .: (0.002030) test_mh: .: (0.002005) test_pages: .: (0.002669) test_pg: .: (0.002135) test_pii: .: (0.001947) test_pmid: .: (0.001989) test_pt: .: (0.002582) test_reference: .: (0.003175) test_self_new: .: (0.002093) test_so: .: (0.001923) test_ta: .: (0.002598) test_ti: .: (0.002192) test_ui: .: (0.001909) test_vi: .: (0.001926) test_year: .: (0.001853) Bio::TestMapSimple: test_attributes: .: (0.001658) Bio::TestMapping: test_add_mapping_as_map: .: (0.001588) test_add_mapping_as_marker: .: (0.000848) test_contains_marker?: .: (0.000633) test_mapped_to?: .: (0.000605) test_mapping_location_comparison: .: (0.001639) test_mappings_as_map_each: .: (0.000620) test_mappings_as_marker_each: .: (0.000796) test_mappings_on: .: (0.001505) test_multiple_mappings_between_same_marker_and_map: .: (0.001814) test_positions_on: .: (0.000926) test_raise_error_kind_of: .: (0.001921) Bio::TestMast: test_check_options_with_empty_opts: .: (0.001599) test_check_options_with_invalid_opts: .: (0.000964) test_check_options_with_valid_opts: .: (0.000853) test_command_to_be_run: .: (0.000967) test_config_defaults: .: (0.000763) test_minimal_config: .: (0.001358) test_more_config: .: (0.000723) test_run: .: (0.000509) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.002727) test_report_has_motifs: .: (0.001411) Bio::TestModel: test_addChain: .: (0.001075) test_comp: .: (0.000603) test_each: .: (0.000634) test_each_chain: .: (0.000566) test_inspect: .: (0.000496) test_rehash: .: (0.000461) test_square_brace: .: (0.001028) test_to_s: .: (0.000577) Bio::TestModelFinder: test_find_model: .: (0.001138) Bio::TestMotif: test_creation_and_attributes: .: (0.001321) test_length: .: (0.000475) Bio::TestMyGraph: test_cliquishness: .: (0.002608) Bio::TestNA: test_accessor: .: (0.000937) test_na: .: (0.000441) test_name: .: (0.000432) test_names: .: (0.000415) test_to_re: .: (0.001530) test_weight: .: (0.000527) test_weight_rna: .: (0.000501) Bio::TestNAConstants: test_NAMES: .: (0.000936) test_NAMES_1_to_name: .: (0.000427) test_WEIGHT: .: (0.000481) Bio::TestNATranslate: test_translate: .: (0.001364) test_translate_1: .: (0.000776) test_translate_2: .: (0.000519) test_translate_3: .: (0.000498) test_translate_4: .: (0.000740) test_translate_5: .: (0.000524) test_translate_6: .: (0.000522) Bio::TestNCBIDB: test_fetch: .: (0.001608) test_p_entry2hash: .: (0.000394) test_p_subtag2array: .: (0.000412) test_p_toptag2array: .: (0.000382) Bio::TestNewick: test_reparse: .: (0.006626) test_reparse_before_lazy_parsing: .: (0.002233) test_string_tree: .: (0.005019) Bio::TestNewick2: test_string_tree: .: (0.003567) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.001117) test_parse_newick_leaf: .: (0.000981) test_parse_newick_tokenize: .: (0.001865) Bio::TestNexus: test_nexus: .: (0.065000) Bio::TestOSLine: test_period_trancation_O63147: .: (0.001329) test_uncapitalized_letter_Q32725_9POAL: .: (0.001112) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.001114) test_load_parameters: .: (0.000581) test_parameters: .: (0.000439) test_set_default_parameters: .: (0.000564) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.003452) test_expected_parameters_set_in_control_file: .: (0.003492) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.001200) test_new_with_parameters: .: (0.001173) test_new_with_two_argument: .: (0.000724) test_new_without_argument: .: (0.000516) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.011118) test_rates_hundred_and_fiftieth_position: .: (0.007751) test_rates_last_position: .: (0.007582) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.066431) test_tree: .: (0.065425) test_tree_length: .: (0.065612) test_tree_log_likelihood: .: (0.065348) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.002878) test_parameters_should_be_loaded_from_control: .: (0.001508) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.007688) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.002238) test_dN_dS: .: (0.001176) test_kappa: .: (0.001026) test_lnL: .: (0.000946) test_m3_classes: .: (0.001507) test_m3_lnL: .: (0.001165) test_m3_to_s: .: (0.001020) test_m3_tree: .: (0.004697) test_omega: .: (0.001052) test_to_s: .: (0.001012) test_tree: .: (0.004291) test_tree_length: .: (0.001572) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.003000) test_p: .: (0.002113) test_position: .: (0.002090) test_probability: .: (0.002357) test_w: .: (0.002061) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.003514) test_graph_omega: .: (0.002772) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.001700) test_footer: .: (0.000964) test_header: .: (0.000899) test_initialize: .: (0.001100) test_models: .: (0.001053) test_nb_sites: .: (0.003983) test_num_codons: .: (0.001089) test_num_sequences: .: (0.001066) test_significant: .: (0.001023) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.002407) test_nb_sites: .: (0.001619) test_significant: .: (0.001906) test_sites: .: (0.006165) Bio::TestPDB: test_accession: .: (0.006950) test_addModel: .: (0.005492) test_authors: .: (0.004386) test_bracket: .: (0.004278) test_classification: .: (0.005566) test_dbref: .: (0.004819) test_definition: .: (0.005309) test_each: .: (0.004494) test_each_model: .: (0.005254) test_entry_id: .: (0.004388) test_helix: .: (0.005319) test_inspect: .: (0.004449) test_jrnl: .: (0.004962) test_keywords: .: (0.004435) test_record: .: (0.004891) test_remark: .: (0.005399) test_seqres: .: (0.006389) test_sheet: .: (0.008394) test_ssbond: .: (0.005207) test_to_s: .: (0.005761) test_turn: .: (0.005918) test_version: .: (0.004474) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.001417) test_U12: .: (0.000708) test_U13: .: (0.000666) test_U22: .: (0.001532) test_U23: .: (0.000666) test_U33: .: (0.000653) test_altLoc: .: (0.000661) test_chainID: .: (0.000655) test_charge: .: (0.000697) test_element: .: (0.000686) test_iCode: .: (0.000669) test_name: .: (0.000660) test_resName: .: (0.000995) test_resSeq: .: (0.000669) test_segID: .: (0.000657) test_serial: .: (0.000656) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.001123) test_anisou: .: (0.000510) test_chainID: .: (0.001467) test_charge: .: (0.000761) test_comparable: .: (0.000655) test_do_parse: .: (0.000482) test_element: .: (0.000482) test_iCode: .: (0.000475) test_name: .: (0.000486) test_occupancy: .: (0.000775) test_original_data: .: (0.000507) test_record_name: .: (0.000495) test_resName: .: (0.000489) test_resSeq: .: (0.000482) test_residue: .: (0.000533) test_segID: .: (0.000493) test_serial: .: (0.029164) test_sigatm: .: (0.000559) test_tempFactor: .: (0.000770) test_ter: .: (0.000512) test_to_a: .: (0.000535) test_to_s: .: (0.000641) test_x: .: (0.000665) test_xyz: .: (0.000691) test_y: .: (0.000697) test_z: .: (0.000662) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.001167) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.002074) test_idcode: .: (0.000518) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.001271) test_chainID2: .: (0.000652) test_icode1: .: (0.000627) test_icode2: .: (0.000659) test_measure: .: (0.000718) test_modNum: .: (0.000641) test_pep1: .: (0.000629) test_pep2: .: (0.000621) test_seqNum1: .: (0.000675) test_seqNum2: .: (0.000647) test_serNum: .: (0.001845) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.001198) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.001066) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.001174) test_alpha: .: (0.000550) test_b: .: (0.000530) test_beta: .: (0.000540) test_c: .: (0.000538) test_gamma: .: (0.000540) test_sGroup: .: (0.000550) test_z: .: (0.000538) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.002351) test_database: .: (0.000807) test_dbAccession: .: (0.000724) test_dbIdCode: .: (0.000767) test_dbseqBegin: .: (0.000822) test_dbseqEnd: .: (0.000735) test_idCode: .: (0.000718) test_idbnsBeg: .: (0.000739) test_insertBegin: .: (0.000731) test_insertEnd: .: (0.000725) test_seqBegin: .: (0.000721) test_seqEnd: .: (0.000719) Bio::TestPDBRecord::TestDefault: test_text: .: (0.001264) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.001073) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.001039) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000990) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.001070) test_depDate: .: (0.000561) test_idCode: .: (0.000542) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.001192) test_hetID: .: (0.000594) test_iCode: .: (0.001961) test_numHetAtoms: .: (0.000611) test_seqNum: .: (0.000573) test_text: .: (0.000569) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.001143) test_anisou: .: (0.000508) test_chainID: .: (0.000498) test_charge: .: (0.000489) test_comparable: .: (0.000647) test_do_parse: .: (0.000539) test_element: .: (0.000495) test_iCode: .: (0.000487) test_name: .: (0.000482) test_occupancy: .: (0.002181) test_original_data: .: (0.000538) test_record_name: .: (0.000491) test_resName: .: (0.000484) test_resSeq: .: (0.000481) test_residue: .: (0.000522) test_segID: .: (0.000493) test_serial: .: (0.000476) test_sigatm: .: (0.000483) test_tempFactor: .: (0.000662) test_ter: .: (0.000482) test_to_a: .: (0.000515) test_to_s: .: (0.000628) test_x: .: (0.000656) test_xyz: .: (0.001877) test_y: .: (0.000670) test_z: .: (0.000639) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.001587) test_ChainH: .: (0.000832) test_ICode1: .: (0.000812) test_altLoc1: .: (0.000861) test_altLoc2: .: (0.000866) test_altLocH: .: (0.000806) test_chainID2: .: (0.000810) test_iCode2: .: (0.001642) test_iCodeH: .: (0.000817) test_name1: .: (0.000777) test_name2: .: (0.000826) test_nameH: .: (0.000830) test_resName1: .: (0.000795) test_resName2: .: (0.000788) test_resSeq1: .: (0.000827) test_resSeq2: .: (0.000878) test_resSeqH: .: (0.000804) test_sym1: .: (0.000795) test_sym2: .: (0.001640) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.001125) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.001316) test_altLoc2: .: (0.000722) test_chainID1: .: (0.000704) test_chainID2: .: (0.000699) test_iCode1: .: (0.000805) test_iCode2: .: (0.000773) test_name1: .: (0.000706) test_name2: .: (0.000697) test_resName1: .: (0.001811) test_resName2: .: (0.000721) test_resSeq1: .: (0.000694) test_resSeq2: .: (0.000744) test_sym1: .: (0.000686) test_sym2: .: (0.000691) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.001203) test_numCoord: .: (0.000552) test_numHelix: .: (0.000543) test_numHet: .: (0.000541) test_numRemark: .: (0.000547) test_numSeq: .: (0.000571) test_numSheet: .: (0.000547) test_numSite: .: (0.000588) test_numTer: .: (0.000539) test_numTurn: .: (0.000559) test_numXform: .: (0.000533) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.001030) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.001195) test_comment: .: (0.000623) test_iCode: .: (0.000602) test_idCode: .: (0.000611) test_resName: .: (0.000603) test_seqNum: .: (0.000608) test_stdRes: .: (0.000606) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.002207) test_Mn2: .: (0.000556) test_Mn3: .: (0.000498) test_Vn: .: (0.000504) test_iGiven: .: (0.000516) test_serial: .: (0.000496) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.001181) test_Mn2: .: (0.000519) test_Mn3: .: (0.000512) test_Vn: .: (0.000551) test_iGiven: .: (0.000522) test_serial: .: (0.000508) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.001053) test_Mn2: .: (0.001539) test_Mn3: .: (0.000538) test_Vn: .: (0.000500) test_iGiven: .: (0.000509) test_serial: .: (0.000536) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.001212) test_rIdCode: .: (0.000564) test_repDate: .: (0.000544) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.001171) test_On2: .: (0.000508) test_On3: .: (0.000499) test_Tn: .: (0.000489) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.002125) test_modId: .: (0.000596) test_modNum: .: (0.000615) test_modType: .: (0.000554) test_record: .: (0.000554) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.001061) test_text: .: (0.000536) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.001054) test_Sn2: .: (0.000496) test_Sn3: .: (0.000482) test_Un: .: (0.000529) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.001032) test_Sn2: .: (0.000495) test_Sn3: .: (0.001523) test_Un: .: (0.000540) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.001082) test_Sn2: .: (0.000524) test_Sn3: .: (0.000507) test_Un: .: (0.000493) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.001230) test_conflict: .: (0.000706) test_database: .: (0.000660) test_dbIdCode: .: (0.000655) test_dbRes: .: (0.000655) test_dbSeq: .: (0.000646) test_iCode: .: (0.000762) test_idCode: .: (0.000673) test_resName: .: (0.000699) test_seqNum: .: (0.000711) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.001232) test_numRes: .: (0.000644) test_resName: .: (0.000711) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.001376) test_curChainId: .: (0.000853) test_curICode: .: (0.000893) test_curResName: .: (0.000879) test_curResSeq: .: (0.000832) test_endChainID: .: (0.001726) test_endICode: .: (0.000872) test_endResName: .: (0.000822) test_endSeqNum: .: (0.000828) test_initChainID: .: (0.000871) test_initICode: .: (0.000830) test_initResName: .: (0.000825) test_initSeqNum: .: (0.000831) test_numStrands: .: (0.000939) test_prevAtom: .: (0.000872) test_prevChainId: .: (0.000833) test_prevICode: .: (0.000876) test_prevResName: .: (0.000865) test_prevResSeq: .: (0.000871) test_sense: .: (0.000862) test_sheetID: .: (0.000833) test_strand: .: (0.000824) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.001391) test_chainID: .: (0.000688) test_charge: .: (0.000676) test_element: .: (0.000667) test_iCode: .: (0.000696) test_name: .: (0.000682) test_resName: .: (0.000668) test_resSeq: .: (0.000654) test_segID: .: (0.000658) test_serial: .: (0.001854) test_sigOcc: .: (0.000669) test_sigTemp: .: (0.000649) test_sigX: .: (0.000681) test_sigY: .: (0.001161) test_sigZ: .: (0.000663) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.001329) test_SigmaU12: .: (0.000694) test_SigmaU13: .: (0.000676) test_SigmaU22: .: (0.000672) test_SigmaU23: .: (0.000667) test_SigmaU33: .: (0.000670) test_altLoc: .: (0.000673) test_chainID: .: (0.000662) test_charge: .: (0.000666) test_element: .: (0.000689) test_iCode: .: (0.001665) test_name: .: (0.000666) test_resName: .: (0.000689) test_resSeq: .: (0.001066) test_segID: .: (0.000667) test_serial: .: (0.000656) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.001399) test_chainID2: .: (0.000751) test_chainID3: .: (0.000741) test_chainID4: .: (0.000734) test_iCode1: .: (0.000746) test_iCode2: .: (0.001782) test_iCode3: .: (0.000759) test_iCode4: .: (0.000729) test_numRes: .: (0.000721) test_resName1: .: (0.000720) test_resName2: .: (0.000723) test_resName3: .: (0.000774) test_resName4: .: (0.000732) test_seq1: .: (0.000719) test_seq2: .: (0.000715) test_seq3: .: (0.001021) test_seq4: .: (0.000752) test_seqNum: .: (0.001534) test_siteID: .: (0.000784) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.001254) test_altLoc2: .: (0.000627) test_atom1: .: (0.000650) test_atom2: .: (0.000625) test_chainID1: .: (0.000618) test_chainID2: .: (0.000613) test_iCode1: .: (0.000613) test_iCode2: .: (0.000636) test_resName1: .: (0.000611) test_resName2: .: (0.000613) test_resSeq1: .: (0.000614) test_resSeq2: .: (0.001714) test_sym1: .: (0.000653) test_sym2: .: (0.000604) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.001256) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.001125) test_sIdCode: .: (0.000556) test_sprsdeDate: .: (0.000541) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.001093) test_iCode: .: (0.000555) test_resName: .: (0.000554) test_resSeq: .: (0.000541) test_serial: .: (0.000546) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.001045) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.002089) test_t1: .: (0.000562) test_t2: .: (0.000541) test_t3: .: (0.000530) test_text: .: (0.000547) Bio::TestPROSITE: test_ac: .: (0.009659) test_cc: .: (0.008375) test_de: .: (0.008897) test_division: .: (0.008709) test_dr: .: (0.087033) test_dt: .: (0.008179) test_false_neg: .: (0.008701) test_false_pos: .: (0.021448) test_false_positive_sequences: .: (0.035711) test_list_falsenegative: .: (0.265041) test_list_falsepositive: .: (0.095150) test_list_potentialhit: .: (0.093218) test_list_truepositive: .: (0.099954) test_list_unknown: .: (0.093305) test_list_xref: .: (0.092660) test_ma: .: (0.008196) test_max_repeat: .: (0.009370) test_name: .: (0.009004) test_nr: .: (0.009820) test_pa: .: (0.008436) test_pa2re: .: (0.008803) test_partial: .: (0.010375) test_pdb_xref: .: (0.010455) test_pdoc_xref: .: (0.009330) test_positive: .: (0.010228) test_positive_hits: .: (0.009582) test_positive_sequences: .: (0.009978) test_release: .: (0.008866) test_ru: .: (0.009436) test_self_pa2re: .: (0.009142) test_site: .: (0.009421) test_skip_flag: .: (0.009263) test_swissprot_release_number: .: (0.009862) test_swissprot_release_sequences: .: (0.008569) test_taxon_range: .: (0.009176) test_total: .: (0.009711) test_total_hits: .: (0.009128) test_total_sequences: .: (0.020437) test_unknown: .: (0.009360) test_unknown_hits: .: (0.010073) test_unknown_sequences: .: (0.010882) Bio::TestPROSITEConst: test_delimiter: .: (0.001199) test_tagsize: .: (0.000437) Bio::TestPTS1: test_function_set: .: (0.001044) test_function_set_number_1: .: (0.000527) test_function_set_number_2: .: (0.000565) test_function_set_number_3: .: (0.000503) test_function_show: .: (0.000457) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000933) Bio::TestPTS1New: test_fungi: .: (0.001019) test_general: .: (0.000484) test_metazoa: .: (0.002040) Bio::TestQualifier: test_qualifier: .: (0.001035) test_value: .: (0.000420) Bio::TestREBASE: test_methods: .: (0.004432) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.007684) test_bit_score: .: (0.003352) test_evalue: .: (0.003277) test_gaps: .: (0.003418) test_hit_from: .: (0.003598) test_hit_to: .: (0.005456) test_hseq: .: (0.003474) test_identity: .: (0.003240) test_midline: .: (0.003523) test_percent_identity: .: (0.004664) test_positive: .: (0.004041) test_qseq: .: (0.003499) test_query_from: .: (0.003418) test_query_to: .: (0.003331) test_score: .: (0.005006) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.003758) test_hits_size: .: (0.007416) test_iterations_size: .: (0.008593) test_program: .: (0.003475) test_query_def: .: (0.006920) test_query_len: .: (0.006899) test_version: .: (0.002818) test_version_date: .: (0.005800) test_version_number: .: (0.002898) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.004195) test_definition: .: (0.003504) test_evalue: .: (0.003464) test_hsps_size: .: (0.004896) test_identity: .: (0.004223) test_lap_at: .: (0.003774) test_len: .: (0.003420) test_midline: .: (0.005552) test_overlap: .: (0.004690) test_query_end: .: (0.003729) test_query_seq: .: (0.003701) test_query_start: .: (0.003659) test_target_def: .: (0.005049) test_target_end: .: (0.003794) test_target_len: .: (0.003455) test_target_seq: .: (0.003692) test_target_start: .: (0.003644) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.003781) test_get_entry: .: (0.002536) test_rewind: .: (0.000550) test_skip_leader: .: (0.001026) Bio::TestReference: test_abstract: .: (0.001041) test_affiliations: .: (0.000485) test_authors: .: (0.000478) test_format_bibitem: .: (0.000759) test_format_bibtex: .: (0.002222) test_format_bibtex_with_arguments: .: (0.001101) test_format_cell: .: (0.000598) test_format_current: .: (0.000585) test_format_endnote: .: (0.000714) test_format_general: .: (0.000713) test_format_genome_biol: .: (0.000639) test_format_genome_res: .: (0.000759) test_format_nar: .: (0.000645) test_format_nature: .: (0.000748) test_format_rd: .: (0.000650) test_format_science: .: (0.003141) test_format_trends: .: (0.000550) test_issue: .: (0.000522) test_journal: .: (0.002034) test_mesh: .: (0.000512) test_pages: .: (0.000463) test_pubmed: .: (0.000462) test_pubmed_url: .: (0.000489) test_url: .: (0.000454) test_volume: .: (0.000449) test_year: .: (0.000443) Bio::TestReference_noURL: test_format_endnote: .: (0.001331) test_url: .: (0.000473) Bio::TestReferences: test_append: .: (0.003450) test_each: .: (0.000627) Bio::TestRelation: test_comparison_operator: .: (0.001320) test_uniq: .: (0.000673) Bio::TestResidue: test_addAtom: .: (0.001777) test_each: .: (0.001077) test_each_atom: .: (0.003245) test_get_residue_id_from_atom: .: (0.001006) test_het_atom: .: (0.000755) test_iCode: .: (0.000902) test_inspect: .: (0.001184) test_resSeq: .: (0.000821) test_sort: .: (0.000951) test_square_bracket: .: (0.002617) test_to_s: .: (0.002133) test_update_resudue_id: .: (0.000836) Bio::TestResidueFinder: test_each_residue: .: (0.001281) test_find_residue: .: (0.000723) test_residues: .: (0.000766) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.741789) test_cut_from_bio_sequence_na: .: (0.177835) test_cut_without_permutations: .: (0.118426) test_view_ranges: .: (0.127292) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.007242) test_cuts_after_remove_incomplete_cuts: .: (0.004444) test_strands_for_display: .: (0.022682) test_strands_for_display_current: .: (0.004410) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.003107) test_fragments_for_display_1: .: (0.004848) test_fragments_for_display_10: .: (0.006518) test_fragments_for_display_2: .: (0.004942) test_fragments_for_display_3: .: (0.007878) test_fragments_for_display_4: .: (0.005796) test_fragments_for_display_5: .: (0.004360) test_fragments_for_display_6: .: (0.003706) test_fragments_for_display_7: .: (0.003732) test_fragments_for_display_8: .: (0.003955) test_fragments_for_display_9: .: (0.003580) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.002024) test_obj_3: .: (0.001571) test_obj_7: .: (0.001812) test_obj_z: .: (0.001457) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.001901) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.001474) test_bracket_eq: .: (0.000741) test_concat: .: (0.000684) test_delete: .: (0.000635) test_dup: .: (0.001531) test_each: .: (0.000945) test_eqeq: .: (0.000629) test_eqeq_false: .: (0.000585) test_eqeq_other: .: (0.000496) test_eqeq_self: .: (0.000488) test_include?: .: (0.000572) test_internal_data: .: (0.000537) test_internal_data_eq: .: (0.000643) test_length: .: (0.000513) test_ltlt: .: (0.000597) test_ltlt_larger: .: (0.000594) test_ltlt_middle: .: (0.000589) test_plus: .: (0.000702) test_plus_error: .: (0.000705) test_push: .: (0.001160) test_reverse_each: .: (0.000924) test_self_bracket: .: (0.000547) test_self_new: .: (0.000569) test_size: .: (0.000515) test_sort!: .: (0.000491) test_to_a: .: (0.000563) test_uniq!: .: (0.000533) test_unshift: .: (0.000732) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.025784) test_complement: .: (0.023470) test_complement_with_cut_symbols: .: (0.024701) test_cut_locations: .: (0.023428) test_cut_locations_in_enzyme_notation: .: (0.023254) test_primary: .: (0.023121) test_primary_with_cut_symbols: .: (0.024231) test_to_re: .: (0.022622) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.005970) test_align_with_cuts: .: (0.004971) test_argument_error: .: (0.005690) test_ds: .: (0.005164) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.002458) test_complement: .: (0.001143) test_contents: .: (0.001534) test_primary: .: (0.001128) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.001988) test_complement: .: (0.001128) test_contents: .: (0.001123) test_primary: .: (0.001070) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.001393) test_contents: .: (0.001360) test_primary: .: (0.000815) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.001480) test_complement_to_array_index: .: (0.001312) test_complement_to_array_index_class: .: (0.001186) test_contents: .: (0.000907) test_primary: .: (0.000847) test_primary_to_array_index: .: (0.001318) test_primary_to_array_index_class: .: (0.001176) test_to_array_index: .: (0.003225) test_to_array_index_class: .: (0.002336) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.002509) test_rebase: .: (0.000790) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.004814) test_creation_with_no_cuts: .: (0.003285) test_cut_locations: .: (0.002734) test_cut_locations_in_enzyme_notation: .: (0.002697) test_orientation: .: (0.002516) test_pattern: .: (0.003220) test_pattern_palindromic?: .: (0.003175) test_stripped: .: (0.002464) test_to_re: .: (0.002203) test_with_cut_symbols: .: (0.003200) test_with_spaces: .: (0.003019) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.005293) test_creation_with_no_cuts: .: (0.002749) test_cut_locations: .: (0.002722) test_cut_locations_in_enzyme_notation: .: (0.002687) test_orientation: .: (0.002990) test_pattern: .: (0.002772) test_pattern_palindromic?: .: (0.003170) test_stripped: .: (0.003088) test_to_re: .: (0.002188) test_with_cut_symbols: .: (0.002752) test_with_spaces: .: (0.003576) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.002695) test_initialize_with_pattern: .: (0.001966) test_max: .: (0.000801) test_min: .: (0.000756) test_to_array_index: .: (0.000946) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.001859) test_bracket_eq: .: (0.000753) test_concat: .: (0.000566) test_delete: .: (0.000516) test_dup: .: (0.000721) test_each: .: (0.000916) test_eqeq: .: (0.000528) test_eqeq_false: .: (0.000482) test_eqeq_other: .: (0.000447) test_eqeq_self: .: (0.000446) test_include?: .: (0.000517) test_internal_data_hash: .: (0.000464) test_internal_data_hash_eq: .: (0.000555) test_length: .: (0.000447) test_ltlt: .: (0.000525) test_ltlt_noeffect: .: (0.000567) test_plus: .: (0.000505) test_plus_error: .: (0.000653) test_private_push_element: .: (0.000527) test_private_push_element_intermediate: .: (0.000543) test_private_push_element_last: .: (0.000544) test_private_push_element_noeffect: .: (0.000524) test_private_sorted_keys: .: (0.000467) test_private_unshift_element: .: (0.000515) test_private_unshift_element_first: .: (0.000544) test_private_unshift_element_intermediate: .: (0.000568) test_private_unshift_element_noeffect: .: (0.000527) test_push: .: (0.000545) test_reverse_each: .: (0.000905) test_self_bracket: .: (0.000458) test_self_new: .: (0.000568) test_size: .: (0.000469) test_sort!: .: (0.000993) test_to_a: .: (0.000470) test_uniq!: .: (0.000445) test_unshift: .: (0.000574) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.001197) test_left_padding: .: (0.000678) test_right_padding: .: (0.000669) test_strip_padding: .: (0.000695) Bio::TestSOFT: test_dataset: .: (0.059691) test_series: .: (0.042494) Bio::TestSOSUIReport: test_entry_id: .: (0.002186) test_prediction: .: (0.000783) test_tmh: .: (0.000757) test_tmhs: .: (0.000874) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000921) test_rs: .: (0.000504) Bio::TestSOSUITMH: test_grade: .: (0.001330) test_range: .: (0.000769) test_sequence: .: (0.000815) Bio::TestSampleGraph: test_bellman_ford: .: (0.003419) test_bfs_shortest_path: .: (0.001039) test_breadth_first_search: .: (0.000984) test_depth_first_search: .: (0.001709) test_dijkstra: .: (0.001304) test_dump_list: .: (0.001259) test_dump_matrix: .: (0.002465) test_extract_subgraph_by_label: .: (0.001149) test_extract_subgraph_by_list: .: (0.001199) test_extract_subgraph_retains_disconnected_nodes: .: (0.000890) test_small_world_aka_node_degree_histogram: .: (0.000814) test_to_matrix: .: (0.002043) test_to_matrix_fixed_index: .: (0.001407) test_undirected_cliquishness: .: (0.001797) Bio::TestScf_version_2: test_complement: .: (0.064325) test_seq: .: (0.060338) test_to_biosequence: .: (0.060544) Bio::TestScf_version_3: test_complement: .: (0.203246) test_seq: .: (0.198388) test_to_biosequence: .: (0.201026) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.001088) test_AA_new_sequence_all_legal_symbols: .: (0.000496) test_AA_new_sequence_removes_whitespace: .: (0.000469) test_AA_new_sequence_upcases_symbols: .: (0.000525) test_DNA_new_blank_sequence: .: (0.000465) test_DNA_new_sequence_downcases_symbols: .: (0.000473) test_DNA_new_sequence_removes_whitespace: .: (0.000461) test_NA_randomize_with_counts: .: (0.004942) test_NA_randomize_with_counts_and_block: .: (0.005860) test_RNA_new_sequence: .: (0.000499) test_ambiguous_dna_sequence_complement: .: (0.000507) test_ambiguous_rna_sequence_complement: .: (0.000491) test_amino_acid_codes: .: (0.000769) test_amino_acid_molecular_weight: .: (0.000989) test_amino_acid_names: .: (0.000642) test_amino_acid_randomize_can_be_chained: .: (0.007698) test_amino_acid_randomize_has_same_composition: .: (0.003465) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.004384) test_dna_composition: .: (0.000766) test_dna_gc_percent: .: (0.000760) test_dna_molecular_weight: .: (0.000929) test_dna_pikachu: .: (0.000530) test_dna_sequence_complement: .: (0.000508) test_dna_sequence_translate: .: (0.002173) test_dna_to_re: .: (0.000887) test_element_reference_operator_with_one_argument: .: (0.000630) test_element_reference_operator_with_two_arguments: .: (0.000583) test_invalid_nucleic_acid_illegal_bases: .: (0.001529) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000892) test_nucleic_acid_names: .: (0.000631) test_randomize_dna_can_be_chained: .: (0.002128) test_randomize_dna_retains_composition: .: (0.001569) test_randomize_dna_with_block: .: (0.001794) test_rna_composition: .: (0.001588) test_rna_gc_percent: .: (0.000752) test_rna_molecular_weight: .: (0.000909) test_rna_pikachu: .: (0.000499) test_rna_sequence_complement: .: (0.000619) test_rna_sequence_translate: .: (0.001521) test_rna_to_re: .: (0.000813) test_total: .: (0.000550) test_two_consecutive_dna_randomizations_not_equal: .: (0.001462) test_valid_dna_sequence_illegal_bases: .: (0.000476) Bio::TestSequenceAA: test_codes: .: (0.001975) test_molecular_weight: .: (0.001175) test_names: .: (0.000621) test_to_re: .: (0.000778) test_to_s: .: (0.000470) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.001373) Bio::TestSequenceAANew: test_new: .: (0.000949) test_new_n: .: (0.000494) test_new_r: .: (0.000475) test_new_t: .: (0.000516) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.001407) test_concat: .: (0.000483) test_push: .: (0.001187) test_seq: .: (0.000452) test_splicing: .: (0.000916) test_sum: .: (0.000446) test_to_s: .: (0.000411) test_to_str: .: (0.000428) test_total: .: (0.000503) test_window_search: .: (0.001596) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.001006) test_normalize_A: .: (0.000609) test_normalize_a: .: (0.000565) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.006613) test_randomize_with_block: .: (0.025490) test_randomize_with_hash: .: (0.008419) test_randomize_with_hash_block: .: (0.073760) 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' =============================================================================== : (0.028234) 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' =============================================================================== : (0.019496) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.023195) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000634) test_subseq_returns_subsequence: .: (0.000494) test_to_s_returns_self_as_string: .: (0.000644) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.001166) test_window_search_with_width_3_step_two_with_residual: .: (0.000583) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.024593) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.001072) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.019399) test_na_self_randomize: .: (0.001046) Bio::TestSequenceDBLink: test_database: .: (0.001047) test_id: .: (0.000437) test_secondary_ids: .: (0.000445) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.020728) test_parse_uniprot_DR_line: .: (0.000868) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.040227) test_output_width_35: .: (0.002036) test_output_width_nil: .: (0.024474) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.014212) test_output_after_adding_sequence: .: (0.001886) test_output_after_truncating_sequence: .: (0.001258) test_output_from_error_probabilities: .: (0.024058) test_output_width45: .: (0.001727) test_output_with_converting_score_phred2solexa: .: (0.005085) test_output_with_converting_score_solexa2phred: .: (0.002550) test_output_with_default_score: .: (0.002225) Bio::TestSequenceMasker: test_mask: .: (0.001595) test_mask_with_enumerator: .: (0.001079) test_mask_with_enumerator_empty_mask_char: .: (0.000998) test_mask_with_enumerator_excess: .: (0.003665) test_mask_with_enumerator_longer_mask_char: .: (0.000996) test_mask_with_enumerator_shorter: .: (0.001507) test_mask_with_error_probability: .: (0.000997) test_mask_with_quality_score: .: (0.001616) Bio::TestSequenceNA: test_at_content: .: (0.002373) test_at_skew: .: (0.001809) test_codon_usage: .: (0.000753) test_complement: .: (0.000625) test_dna: .: (0.000569) test_dna!: .: (0.000558) test_forward_complement: .: (0.000899) test_gc_content: .: (0.002613) test_gc_percent: .: (0.001194) test_gc_skew: .: (0.002406) test_iliegal_bases: .: (0.000633) test_molecular_weight: .: (0.001005) test_names: .: (0.000813) test_reverse_complement: .: (0.000929) test_rna: .: (0.000566) test_rna!: .: (0.000540) test_splicing: .: (0.001701) test_to_re: .: (0.000981) test_to_s: .: (0.000476) Bio::TestSequenceNACommon: test_composition: .: (0.001464) test_concat: .: (0.000509) test_push: .: (0.000473) test_seq: .: (0.000472) test_splicing: .: (0.000839) test_sum: .: (0.000519) test_to_s: .: (0.000482) test_to_str: .: (0.000463) test_total: .: (0.000547) test_window_search: .: (0.002947) Bio::TestSequenceNANew: test_new: .: (0.001143) test_new_n: .: (0.000536) test_new_r: .: (0.000481) test_new_t: .: (0.000477) Bio::TestSequenceNATranslation: test_translate: .: (0.002194) test_translate_0: .: (0.004869) test_translate_1: .: (0.001474) test_translate_2: .: (0.001311) test_translate_3: .: (0.001256) test_translate_4: .: (0.002358) test_translate_5: .: (0.001373) test_translate_6: .: (0.001487) test_translate_7: .: (0.003126) test_translate_given_codon_table: .: (0.284321) test_translate_n1: .: (0.003371) test_translate_n2: .: (0.003630) test_translate_n3: .: (0.002773) test_translate_unknown_o: .: (0.001483) test_translate_unknown_x: .: (0.001369) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.001159) test_convert_scores_from_phred_to_solexa: .: (0.003256) test_convert_scores_from_solexa_to_phred: .: (0.001234) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.001057) test_convert_scores_from_phred: .: (0.000559) test_convert_scores_from_phred_to_solexa: .: (0.003387) test_convert_scores_from_solexa: .: (0.001208) test_convert_scores_from_solexa_to_phred: .: (0.001176) test_convert_scores_to_phred: .: (0.000445) test_convert_scores_to_solexa: .: (0.003658) test_p2q: .: (0.001371) test_phred_p2q: .: (0.000935) test_phred_q2p: .: (0.033089) test_q2p: .: (0.034808) test_quality_score_type: .: (0.000515) test_self_convert_scores_to_solexa: .: (0.002822) test_self_p2q: .: (0.001046) test_self_q2p: .: (0.033850) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.001268) test_convert_scores_from_phred: .: (0.002736) test_convert_scores_from_phred_to_solexa: .: (0.003236) test_convert_scores_from_solexa: .: (0.000439) test_convert_scores_from_solexa_to_phred: .: (0.001184) test_convert_scores_to_phred: .: (0.002034) test_convert_scores_to_solexa: .: (0.000540) test_p2q: .: (0.001524) test_q2p: .: (0.046534) test_quality_score_type: .: (0.000554) test_self_convert_scores_to_phred: .: (0.001296) test_self_p2q: .: (0.001562) test_self_q2p: .: (0.037056) test_solexa_p2q: .: (0.001461) test_solexa_q2p: .: (0.037139) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.001332) test_center: .: (0.000732) test_chomp: .: (0.000788) test_chop: .: (0.000765) test_delete: .: (0.000603) test_delete_prefix: .: (0.000626) test_delete_suffix: .: (0.001728) test_downcase: .: (0.000636) test_each_char: .: (0.001513) test_each_char_enum: .: (0.000931) test_each_grapheme_cluster: .: (0.002286) test_each_grapheme_cluster_enum: .: (0.000952) test_each_line: .: (0.000946) test_each_line_enum: .: (0.000819) test_gsub: .: (0.000746) test_gsub_with_block: .: (0.002542) test_ljust: .: (0.000715) test_lstrip: .: (0.000648) test_multiply: .: (0.000616) test_next: .: (0.000590) test_reverse: .: (0.000638) test_rjust: .: (0.000613) test_rstrip: .: (0.000580) test_slice: .: (0.000585) test_slice2: .: (0.000570) test_split: .: (0.000867) test_squeeze: .: (0.000592) test_strip: .: (0.000571) test_sub: .: (0.000640) test_sub_with_block: .: (0.001430) test_succ: .: (0.000631) test_swapcase: .: (0.000586) test_tr: .: (0.000606) test_tr_s: .: (0.001045) test_upcase: .: (0.000689) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.001466) test_partition_nomatch: .: (0.000840) test_partition_sep_TSeq: .: (0.000778) test_partition_sep_regexp: .: (0.000815) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.001548) test_rpartition_nomatch: .: (0.000810) test_rpartition_sep_TSeq: .: (0.000817) test_rpartition_sep_regexp: .: (0.000874) Bio::TestShRNA: test_blocK_it: .: (0.160138) test_blocK_it_: .: (0.158013) test_blocK_it_BLOCK_IT: .: (0.161096) test_blocK_it_BLOCK_iT: .: (0.155262) test_blocK_it_piGene: .: (0.152336) test_bottom_strand: .: (0.156710) test_bottom_strand_class: .: (0.156303) test_bottom_strand_nil: .: (0.152120) test_design: .: (0.154944) test_design_BLOCK_IT: .: (0.158903) test_report: .: (0.154354) test_report_before_design: .: (0.154449) test_top_strand: .: (0.160013) test_top_strand_class: .: (0.161777) test_top_strand_nil: .: (0.158482) Bio::TestShRNANew: test_new: .: (0.002965) Bio::TestSiRNA: test_antisense_size: .: (0.001018) test_design: .: (0.161007) test_design_reynolds: .: (0.195153) test_design_uitei: .: (0.160386) test_max_gc_percent: .: (0.000573) test_min_gc_percent: .: (0.000608) test_reynolds: .: (0.197416) test_reynolds?: .: (0.000763) test_uitei: .: (0.158388) test_uitei?: .: (0.000694) Bio::TestSiRNANew: test_new: .: (0.001953) Bio::TestSiRNAPair: test_antisense: .: (0.156382) test_gc_percent: .: (0.160176) test_report: .: (0.163220) test_rule: .: (0.160663) test_sense: .: (0.160573) test_start: .: (0.160099) test_stop: .: (0.162279) test_target: .: (0.160596) Bio::TestSiRNAPairNew: test_new: .: (0.002252) Bio::TestSim4Report: test_all_hits: .: (0.003019) test_each: .: (0.002166) test_each_hit: .: (0.001598) test_hits: .: (0.001136) test_num_hits: .: (0.000882) test_query_def: .: (0.000962) test_query_id: .: (0.000891) test_query_len: .: (0.000881) test_seq1: .: (0.001683) Bio::TestSim4Report2: test_all_hits: .: (0.003611) test_each: .: (0.001430) test_each_hit: .: (0.002629) test_hits: .: (0.001237) test_num_hits: .: (0.001080) test_query_def: .: (0.001021) test_query_id: .: (0.000991) test_query_len: .: (0.001082) test_seq1: .: (0.001324) Bio::TestSim4Report4: test_all_hits: .: (0.003614) test_each: .: (0.002248) test_each_hit: .: (0.001574) test_hits: .: (0.001375) test_num_hits: .: (0.001099) test_query_def: .: (0.001131) test_query_id: .: (0.001051) test_query_len: .: (0.001051) test_seq1: .: (0.006515) Bio::TestSim4ReportHit: test_align: .: (0.002592) test_complement?: .: (0.001053) test_definition: .: (0.000903) test_each: .: (0.001970) test_exons: .: (0.002076) test_hit_id: .: (0.001106) test_hsps: .: (0.003055) test_introns: .: (0.002120) test_len: .: (0.001139) test_query_def: .: (0.001065) test_query_id: .: (0.001024) test_query_len: .: (0.001125) test_segmentpairs: .: (0.001998) test_seq1: .: (0.001451) test_seq2: .: (0.002405) test_target_def: .: (0.001466) test_target_id: .: (0.001026) test_target_len: .: (0.000997) Bio::TestSim4ReportHit2: test_align: .: (0.002095) test_complement?: .: (0.001013) test_definition: .: (0.001017) test_each: .: (0.001874) test_exons: .: (0.002865) test_hit_id: .: (0.001465) test_hsps: .: (0.001919) test_introns: .: (0.001799) test_len: .: (0.000962) test_query_def: .: (0.000944) test_query_id: .: (0.000954) test_query_len: .: (0.001044) test_segmentpairs: .: (0.002867) test_seq1: .: (0.001513) test_seq2: .: (0.001302) test_target_def: .: (0.001062) test_target_id: .: (0.000970) test_target_len: .: (0.000859) Bio::TestSim4ReportHit4: test_align: .: (0.002291) test_complement?: .: (0.000954) test_definition: .: (0.001850) test_each: .: (0.002632) test_exons: .: (0.002373) test_hit_id: .: (0.001170) test_hsps: .: (0.002168) test_introns: .: (0.003084) test_len: .: (0.001274) test_query_def: .: (0.000970) test_query_id: .: (0.000912) test_query_len: .: (0.000895) test_segmentpairs: .: (0.002393) test_seq1: .: (0.001257) test_seq2: .: (0.001285) test_target_def: .: (0.002156) test_target_id: .: (0.001178) test_target_len: .: (0.001044) Bio::TestSim4ReportSegment: test_from: .: (0.001188) test_self_new: .: (0.000716) test_seq: .: (0.000499) test_to: .: (0.000479) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.002198) test_direction: .: (0.001508) test_hit_from: .: (0.002707) test_hit_to: .: (0.001600) test_hseq: .: (0.001504) test_midline: .: (0.001475) test_percent_identity: .: (0.001527) test_qseq: .: (0.001463) test_query_from: .: (0.002487) test_query_to: .: (0.001920) test_seq1: .: (0.001760) test_seq2: .: (0.001620) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.002147) test_direction: .: (0.001649) test_hit_from: .: (0.001579) test_hit_to: .: (0.001897) test_hseq: .: (0.001551) test_midline: .: (0.001626) test_percent_identity: .: (0.001474) test_qseq: .: (0.001523) test_query_from: .: (0.001454) test_query_to: .: (0.002717) test_seq1: .: (0.002507) test_seq2: .: (0.001863) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.002764) test_direction: .: (0.002085) test_hit_from: .: (0.003063) test_hit_to: .: (0.002646) test_hseq: .: (0.002182) test_midline: .: (0.001890) test_percent_identity: .: (0.001931) test_qseq: .: (0.001803) test_query_from: .: (0.003533) test_query_to: .: (0.002044) test_seq1: .: (0.002121) test_seq2: .: (0.002130) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.004057) test_direction: .: (0.001990) test_hit_from: .: (0.001959) test_hit_to: .: (0.001945) test_hseq: .: (0.001786) test_midline: .: (0.002951) test_percent_identity: .: (0.002433) test_qseq: .: (0.001843) test_query_from: .: (0.001881) test_query_to: .: (0.001775) test_seq1: .: (0.003189) test_seq2: .: (0.002932) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.002593) test_direction: .: (0.001889) test_hit_from: .: (0.003065) test_hit_to: .: (0.002643) test_hseq: .: (0.001865) test_midline: .: (0.001859) test_percent_identity: .: (0.001864) test_qseq: .: (0.003030) test_query_from: .: (0.002578) test_query_to: .: (0.001939) test_seq1: .: (0.002140) test_seq2: .: (0.002193) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.002712) test_direction: .: (0.001456) test_hit_from: .: (0.001439) test_hit_to: .: (0.001366) test_hseq: .: (0.001448) test_midline: .: (0.001406) test_percent_identity: .: (0.001388) test_qseq: .: (0.002510) test_query_from: .: (0.001880) test_query_to: .: (0.001435) test_seq1: .: (0.001737) test_seq2: .: (0.001630) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.002124) test_direction: .: (0.002363) test_hit_from: .: (0.001786) test_hit_to: .: (0.001409) test_hseq: .: (0.001510) test_midline: .: (0.001394) test_percent_identity: .: (0.001343) test_qseq: .: (0.001391) test_query_from: .: (0.002408) test_query_to: .: (0.001746) test_seq1: .: (0.001661) test_seq2: .: (0.001769) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.001106) test_entry_id: .: (0.000529) test_filename: .: (0.000506) test_len: .: (0.000502) test_self_new: .: (0.000567) test_self_parse: .: (0.000728) Bio::TestTMHMMReport: test_entry_id: .: (0.003293) test_exp_aas_in_tmhs: .: (0.001700) test_exp_first_60aa: .: (0.001640) test_helix: .: (0.001892) test_predicted_tmhs: .: (0.002703) test_query_len: .: (0.001644) test_tmhs: .: (0.001785) test_to_s: .: (0.002360) test_total_prob_of_N_in: .: (0.001879) Bio::TestTMHMMReport_reports: test_reports: .: (0.001089) Bio::TestTMHMMTMH: test_entry_id: .: (0.002574) test_pos: .: (0.001746) test_range: .: (0.001667) test_status: .: (0.001729) test_version: .: (0.001655) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.001830) test_cutoff: .: (0.001266) test_entry_id: .: (0.001166) test_length: .: (0.001130) test_loc: .: (0.001172) test_name: .: (0.001119) test_networks: .: (0.001103) test_prediction: .: (0.001281) test_query_len: .: (0.001255) test_query_sequences: .: (0.002074) test_rc: .: (0.001143) test_version: .: (0.001122) Bio::TestTargetPReportConst: test_delimiter: .: (0.001043) test_rs: .: (0.000429) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000910) test_togows_access_wait: .: (2.005558) Bio::TestTogoWSREST: test_debug: .: (0.002211) test_debug_default: .: (0.001949) test_internal_http: .: (0.002037) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.001998) test_entry: .: (0.001129) test_entry_database_list: .: (0.001002) test_new: .: (0.002022) test_new_with_uri_object: .: (0.002354) test_new_with_uri_string: .: (0.002355) test_retrieve: .: (0.001029) test_search: .: (0.001076) test_search_database_list: .: (0.001016) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.005350) test_prepare_return_value: .: (0.002223) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.004373) Bio::TestTree: test_get_edge_distance: .: (0.002480) test_get_edge_distance_string: .: (0.001660) test_get_node_name: .: (0.001195) test_initialize: .: (0.001235) test_options: .: (0.001204) test_root: .: (0.000955) test_root=: .: (0.001212) Bio::TestTree2: test_add_edge: .: (0.005665) test_add_node: .: (0.002476) test_adjacency_matrix: .: (0.002478) test_adjacency_matrix_with_block: .: (0.002638) test_adjacent_nodes: .: (0.002717) test_adjacent_nodes_nonexistent: .: (0.001770) test_ancestors: .: (0.002208) test_children: .: (0.001884) test_clear: .: (0.002124) test_clear_node: .: (0.002589) test_clear_node_nonexistent: .: (0.004249) test_collect_edge!: .: (0.003246) test_collect_node!: .: (0.003393) test_concat: .: (0.003172) test_descendents: .: (0.002300) test_distance_matrix: .: (0.005965) test_each_edge: .: (0.002694) test_each_node: .: (0.002486) test_each_out_edge: .: (0.004109) test_each_out_edge_chimpanzee: .: (0.002217) test_each_out_edge_human: .: (0.002212) test_each_out_edge_mammals: .: (0.002596) test_each_out_edge_nonexistent: .: (0.002344) test_each_out_edge_primates: .: (0.003620) test_each_out_edge_rat: .: (0.002291) test_each_out_edge_rodents: .: (0.002883) test_edges: .: (0.002026) test_get_edge: .: (0.006234) test_get_edge_indirect: .: (0.001866) test_get_edge_merged: .: (0.001846) test_get_edge_nonexistent: .: (0.001711) test_get_node_bootstrap: .: (0.001798) test_get_node_bootstrap_string=: .: (0.001805) test_get_node_by_name: .: (0.003423) test_get_node_by_name_noexistent: .: (0.002115) test_include?: .: (0.002503) test_include_nonexistent: .: (0.001767) test_insert_node: .: (0.005383) test_leaves: .: (0.002333) test_leaves_noargs: .: (0.001951) test_lowest_common_ancestor: .: (0.002104) test_nodes: .: (0.001817) test_number_of_edges: .: (0.001709) test_number_of_nodes: .: (0.001693) test_out_degree: .: (0.002541) test_out_degree_nonexistent: .: (0.001724) test_out_edges: .: (0.002264) test_out_edges_mammals: .: (0.002661) test_out_edges_nonexistent: .: (0.003675) test_out_edges_primates: .: (0.002935) test_out_edges_rodents: .: (0.002899) test_parent: .: (0.002176) test_path: .: (0.002220) test_remove_edge: .: (0.002120) test_remove_edge_if: .: (0.002266) test_remove_edge_if_nothing_removed: .: (0.002443) test_remove_edge_nonexistent: .: (0.002722) test_remove_node: .: (0.002479) test_remove_node_if: .: (0.002009) test_remove_node_if_false: .: (0.002253) test_remove_node_nonexistent: .: (0.002819) test_remove_nonsense_nodes: .: (0.002240) test_subtree: .: (0.002680) test_subtree_with_all_paths: .: (0.004095) test_total_distance: .: (0.001135) Bio::TestTreeEdge: test_distance: .: (0.001100) test_distance=: .: (0.000728) test_distance_string: .: (0.000455) test_distance_string=: .: (0.000671) test_initialize: .: (0.000648) test_inspect: .: (0.000530) test_to_s: .: (0.000449) Bio::TestTreeNode: test_bootstrap: .: (0.001844) test_bootstrap=: .: (0.000737) test_bootstrap_string: .: (0.000421) test_bootstrap_string=: .: (0.000786) test_initialize: .: (0.000579) test_inspect: .: (0.000575) test_name: .: (0.000510) test_to_s: .: (0.000425) Bio::TestUniProt: test_gene_name: .: (0.027630) Bio::TestUniProtKB: test_ac: .: (0.028681) test_accession: .: (0.026468) test_cc: .: (0.037087) test_cc_alternative_products: .: (0.056004) test_cc_database: .: (0.037316) test_cc_mass_spectrometry: .: (0.037008) test_de: .: (0.027407) test_dr: .: (0.039864) test_dr_with_key: .: (0.038826) test_dr_with_key_empty: .: (0.036684) test_dt: .: (0.026587) test_dt_annotation: .: (0.027089) test_dt_created: .: (0.028081) test_dt_sequence: .: (0.075161) test_entry: .: (0.118160) test_ft: .: (0.164386) test_gene_name: .: (0.028191) test_gene_names: .: (0.026210) test_gn: .: (0.027592) test_gn_old_parser: .: (0.026641) test_gn_uniprot_parser: .: (0.027443) test_id_line: .: (0.027495) test_id_line_data_class: .: (0.028181) test_id_line_entry_name: .: (0.026609) test_id_line_molecule_type: .: (0.027459) test_id_line_sequence_length: .: (0.025683) test_kw: .: (0.027006) test_molecule: .: (0.025645) test_oc: .: (0.027238) test_og_1: .: (0.032627) test_og_2: .: (0.026549) test_og_3: .: (0.026889) test_og_4: .: (0.025987) test_og_5: .: (0.026815) test_og_6: .: (0.027472) test_os: .: (0.026505) test_os_access: .: (0.025857) test_os_access2: .: (0.027829) test_ox: .: (0.026419) test_protein_name: .: (0.027447) test_ref: .: (0.064631) test_seq: .: (0.027515) test_sequence_length: .: (0.030865) test_sq: .: (0.027779) test_sq_crc64: .: (0.026554) test_sq_len: .: (0.027550) test_sq_mw: .: (0.026316) test_synonyms: .: (0.027452) Bio::TestUniProtKB_CC: test_allergen: .: (0.001757) test_alternative_products_access_as_hash: .: (0.001234) test_alternative_products_ai: .: (0.001629) test_alternative_products_apu: .: (0.002666) test_alternative_products_as: .: (0.001692) test_alternative_products_rf: .: (0.000491) test_biophysicochemical_properties: .: (0.003929) test_biotechnology: .: (0.001301) test_catalytic_activity: .: (0.001081) test_caution: .: (0.001159) test_cofactor: .: (0.001061) test_developmental_stage: .: (0.001214) test_disease: .: (0.001731) test_domain: .: (0.001976) test_enzyme_regulation: .: (0.002043) test_function: .: (0.001535) test_induction: .: (0.000964) test_interaction: .: (0.001354) test_mass_spectrometry: .: (0.001798) test_miscellaneous: .: (0.001173) test_pathway: .: (0.001405) test_pharmaceutical: .: (0.001243) test_polymorphism: .: (0.002793) test_ptm: .: (0.001278) test_rna_editing: .: (0.001852) test_similarity: .: (0.001156) test_subcellular_location: .: (0.001422) test_subunit: .: (0.001000) test_tissue_specificity: .: (0.001232) test_toxic_dose: .: (0.001079) test_web_resource: .: (0.001726) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.003524) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.003076) test_protein_name: .: (0.002205) test_synonyms: .: (0.002691) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.001337) test_entry: .: (0.000845) test_entry_id: .: (0.000722) test_entry_name: .: (0.000631) test_id_line: .: (0.000617) test_molecule: .: (0.000660) test_sequence_length: .: (0.000631) Bio::TestUniProtKB_P03589: test_ac: .: (0.007105) test_accession: .: (0.007803) test_cc: .: (0.004622) test_cc_alternative_products: .: (0.004459) test_cc_database: .: (0.005644) test_cc_mass_spectrometry: .: (0.004415) test_de: .: (0.003240) test_dr: .: (0.005996) test_dr_with_key: .: (0.005641) test_dr_with_key_empty: .: (0.005062) test_dt: .: (0.003087) test_dt_annotation: .: (0.003917) test_dt_created: .: (0.003253) test_dt_sequence: .: (0.002870) test_entry: .: (0.003151) test_ft: .: (0.004721) test_gene_name: .: (0.003243) test_gene_names: .: (0.003266) test_gn: .: (0.004322) test_gn_old_parser: .: (0.003247) test_gn_uniprot_parser: .: (0.003115) test_id_line: .: (0.004201) test_id_line_data_class: .: (0.002954) test_id_line_entry_name: .: (0.002993) test_id_line_sequence_length: .: (0.003769) test_kw: .: (0.003653) test_oc: .: (0.003162) test_oh: .: (0.006297) test_os: .: (0.003458) test_os_access: .: (0.003067) test_os_access2: .: (0.003075) test_ox: .: (0.003902) test_protein_name: .: (0.003250) test_protein_name_after_calling_de: .: (0.003208) test_ref: .: (0.004526) test_seq: .: (0.005062) test_sequence_length: .: (0.004038) test_sq: .: (0.003450) test_sq_crc64: .: (0.003035) test_sq_len: .: (0.003210) test_sq_mw: .: (0.004172) test_synonyms: .: (0.003318) Bio::TestUniProtKB_P28907: test_ac: .: (0.011882) test_accession: .: (0.009900) test_cc: .: (0.014328) test_cc_alternative_products: .: (0.013866) test_cc_database: .: (0.013041) test_cc_mass_spectrometry: .: (0.014121) test_de: .: (0.010415) test_dr: .: (0.032921) test_dr_with_key: .: (0.025598) test_dr_with_key_empty: .: (0.025280) test_dt: .: (0.010182) test_dt_annotation: .: (0.009967) test_dt_created: .: (0.009629) test_dt_sequence: .: (0.009416) test_entry: .: (0.009910) test_ft: .: (0.019215) test_gene_name: .: (0.010943) test_gene_names: .: (0.010398) test_gn: .: (0.009604) test_gn_old_parser: .: (0.009984) test_gn_uniprot_parser: .: (0.010527) test_id_line: .: (0.010759) test_id_line_data_class: .: (0.010079) test_id_line_entry_name: .: (0.010079) test_id_line_sequence_length: .: (0.010131) test_kw: .: (0.010659) test_oc: .: (0.010424) test_os: .: (0.010706) test_os_access: .: (0.009737) test_os_access2: .: (0.009957) test_ox: .: (0.009997) test_protein_name: .: (0.011185) test_protein_name_after_calling_de: .: (0.010852) test_ref: .: (0.015703) test_seq: .: (0.010441) test_sequence_length: .: (0.009677) test_sq: .: (0.009924) test_sq_crc64: .: (0.011151) test_sq_len: .: (0.010870) test_sq_mw: .: (0.009839) test_synonyms: .: (0.010612) test_synonyms_after_calling_de: .: (0.011232) Bio::TestUniProtKB_P49144: test_ac: .: (0.007617) test_accession: .: (0.004578) test_cc: .: (0.015099) test_cc_alternative_products: .: (0.008897) test_cc_database: .: (0.007047) test_cc_mass_spectrometry: .: (0.008086) test_de: .: (0.006348) test_dr: .: (0.008849) test_dr_with_key: .: (0.009314) test_dr_with_key_empty: .: (0.009456) test_dt: .: (0.004816) test_dt_annotation: .: (0.005183) test_dt_created: .: (0.004613) test_dt_sequence: .: (0.005457) test_entry: .: (0.004662) test_ft: .: (0.011757) test_gene_name: .: (0.005419) test_gene_names: .: (0.004408) test_gn: .: (0.004506) test_gn_old_parser: .: (0.004472) test_gn_uniprot_parser: .: (0.005545) test_id_line: .: (0.004318) test_id_line_data_class: .: (0.005184) test_id_line_entry_name: .: (0.004438) test_id_line_sequence_length: .: (0.005570) test_kw: .: (0.005693) test_oc: .: (0.004843) test_os: .: (0.005609) test_os_access: .: (0.004290) test_os_access2: .: (0.005424) test_ox: .: (0.004458) test_protein_name: .: (0.005473) test_protein_name_after_calling_de: .: (0.004550) test_ref: .: (0.006380) test_seq: .: (0.006074) test_sequence_length: .: (0.004498) test_sq: .: (0.005443) test_sq_crc64: .: (0.004413) test_sq_len: .: (0.005768) test_sq_mw: .: (0.004526) test_synonyms: .: (0.005821) test_synonyms_after_calling_de: .: (0.004730) Bio::TestUniProtKB_Ref: test_RA: .: (0.002524) test_RC: .: (0.001514) test_RG: .: (0.001526) test_RL: .: (0.001435) test_RN: .: (0.002420) test_RP: .: (0.001717) test_RT: .: (0.001479) test_RX: .: (0.001468) test_ref: .: (0.001587) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.002442) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.002588) test_alternative_products_with_ft: .: (0.004256) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.001878) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.001953) test_RL_lines: .: (0.000778) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.003038) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.001299) test_RG_line: .: (0.000802) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.003878) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.001646) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.001176) test_RL_line: .: (0.000716) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.003819) test_RP_line: .: (0.002184) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000835) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.001514) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.001142) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.001224) test_CC_interaction_isoform: .: (0.001033) test_CC_interaction_no_gene_name: .: (0.000962) test_CC_interaction_self_association: .: (0.001133) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.002460) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.001666) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.002295) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.001680) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.001570) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.002398) test_DT_line: .: (0.000889) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.023458) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.004266) test_CC_web_resource: .: (0.000447) test_FT_VER_SEQ: .: (0.001009) test_OH_line_exception: .: (0.001222) test_OH_lines: .: (0.001950) Bio::TestUtils: test_centreOfGravity: .: (0.003770) test_dihedral_angle: .: (0.002290) test_distance: .: (0.002083) test_geometricCentre: .: (0.002641) test_rad2deg: .: (0.001045) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.001475) test_dijkstra_on_weighted_graph: .: (0.000720) Finished in 88.321390416 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 44.62 tests/s, 244.57 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/27617/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/27617/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/27617 and its subdirectories I: Current time: Fri Dec 6 03:25:50 +14 2024 I: pbuilder-time-stamp: 1733405150