Mon May 8 13:14:28 UTC 2023 I: starting to build ruby-bio/bookworm/arm64 on jenkins on '2023-05-08 13:14' Mon May 8 13:14:28 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/27307/console.log Mon May 8 13:14:28 UTC 2023 I: Downloading source for bookworm/ruby-bio=2.0.4-1 --2023-05-08 13:14:29-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/ruby-bio/ruby-bio_2.0.4-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2133 (2.1K) [text/prs.lines.tag] Saving to: ‘ruby-bio_2.0.4-1.dsc’ 0K .. 100% 180M=0s 2023-05-08 13:14:29 (180 MB/s) - ‘ruby-bio_2.0.4-1.dsc’ saved [2133/2133] Mon May 8 13:14:29 UTC 2023 I: ruby-bio_2.0.4-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.4-1 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Nilesh Patra Homepage: https://bioruby.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-bio Vcs-Git: https://salsa.debian.org/ruby-team/ruby-bio.git Testsuite: autopkgtest-pkg-ruby Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Package-List: ruby-bio deb ruby optional arch=all Checksums-Sha1: 2b2f94d3d5cda574424de4b3234ad13c26cd04ef 1392926 ruby-bio_2.0.4.orig.tar.gz 74fd3f5f9f18bd1126ca3aeaf3d7f6015a0f7893 14372 ruby-bio_2.0.4-1.debian.tar.xz Checksums-Sha256: 5077a66de152c646b0a1e7fc53c24fba0c8f71e7cd2eee1aa88437fee936251f 1392926 ruby-bio_2.0.4.orig.tar.gz b33f98c6c6b39d3989fabe2ce30ac2d8b317e800fcffd44f8f24b2a8b7d34ae6 14372 ruby-bio_2.0.4-1.debian.tar.xz Files: a73129f22b820bbe022054c2732660f0 1392926 ruby-bio_2.0.4.orig.tar.gz 827737c24b63aac32929f74731217c2a 14372 ruby-bio_2.0.4-1.debian.tar.xz Ruby-Versions: all -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmNChtsSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxAQoP/RJ7Vq7a1v/SQ7WPjzxj6ni5+EbDtqq4 DW95D9/R5l6V5FkSTu24vhE9Y7kYNdww+KOBSZKeYFHZZULlGCprDYhKFanxVVxh MvN1dKJS5fYOr2NopXHFBGuhyR0HpQRTDLb3OPoPnEto0OQhoh5LaXUbf3T6lKY8 rge/WOmOb94P2JQHRbQrX/lwBjGGaRJ8khDMomSrXOwUJf5eoRqJAm1rWm0vLEFj jJv99aKD/pIYPHu6p8BiRE6VvIqIlS9lVht6d2E9o86rCex4oUxn/Bbt8kx2cYD8 KKPRL99vCXru1puDqohjUFvqnVIxuqmClK33SSNRncJjipZHznqMq2JB35q5tUNu fcbqBDRxx7KOKquIFkb2D/rD6O4fRTd9zizKPKn2RJ6YZjyUl/oKmHkD3dHAcGix lf0uyHC7QFFclt9+9uZwrhhEcJuajcJIqquIKQBj3gwF1jgzp93001R7wpUFAdYL Ung5t4Fg6q2IX8TjXkbA1hGim/kipANJA4aJVMVI3DEEaBMN3xvcgvrBoDbNvuUW gViOQ5ZBQy53F8Qk0Va0K4RWCnGO9XPCbykW05JjQhBdDrany3Tm6em7hjZ3rkTr mS9b8g8++085MhFIgONKl7IjWQeds6WbtuT0DsunzCaR8tABynGYJ/yV0LCQY6T1 xv78VKObPYId =srTx -----END PGP SIGNATURE----- Mon May 8 13:14:29 UTC 2023 I: Checking whether the package is not for us Mon May 8 13:14:29 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Mon May 8 13:14:29 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Mon May 8 13:16:56 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 9 07:37:34 -12 2024 I: pbuilder-time-stamp: 1717961854 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.0.4-1.dsc] I: copying [./ruby-bio_2.0.4.orig.tar.gz] I: copying [./ruby-bio_2.0.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Oct 8 20:31:23 2022 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ruby-bio_2.0.4-1.dsc: no acceptable signature found dpkg-source: info: extracting ruby-bio in ruby-bio-2.0.4 dpkg-source: info: unpacking ruby-bio_2.0.4.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.4-1.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/2006/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2006' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/pbuilderrc_BJ0P --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/b1 --logfile b1/build.log ruby-bio_2.0.4-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 9 04:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2006/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gem2deb; however: Package gem2deb is not installed. pbuilder-satisfydepends-dummy depends on ruby-libxml; however: Package ruby-libxml is not installed. pbuilder-satisfydepends-dummy depends on ruby-test-unit; however: Package ruby-test-unit is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on rdtool; however: Package rdtool is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gem2deb{a} gem2deb-test-runner{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libb-hooks-op-check-perl{a} libbsd0{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libdebhelper-perl{a} libdevel-callchecker-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libksba8{a} libldap-2.5-0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0{a} libosp5{a} libparams-classify-perl{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libregexp-ipv6-perl{a} librole-tiny-perl{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libsub-override-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwww-perl{a} libwww-robotrules-perl{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} rdtool{a} readline-common{a} ruby{a} ruby-all-dev{a} ruby-libxml{a} ruby-net-telnet{a} ruby-rd{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} ruby3.1-dev{a} rubygems-integration{a} sensible-utils{a} sgml-base{a} sgml-data{a} wdiff{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: apt-file curl dctrl-tools debian-keyring dput dput-ng dupload equivs fonts-lato libarchive-cpio-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libjs-jquery libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg ruby3.1-doc strace unzip wget zip 0 packages upgraded, 135 newly installed, 0 to remove and 0 not upgraded. Need to get 47.1 MB of archives. After unpacking 177 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libassuan0 arm64 2.5.5-5 [45.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 gpgconf arm64 2.2.40-1.1 [557 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libksba8 arm64 1.6.3-2 [119 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libnpth0 arm64 1.6-3 [18.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 dirmngr arm64 2.2.40-1.1 [770 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 gnupg-utils arm64 2.2.40-1.1 [880 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 gpg arm64 2.2.40-1.1 [903 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 pinentry-curses arm64 1.2.1-1 [75.2 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 gpg-agent arm64 2.2.40-1.1 [673 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-client arm64 2.2.40-1.1 [532 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-server arm64 2.2.40-1.1 [524 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 gpgsm arm64 2.2.40-1.1 [651 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 gnupg all 2.2.40-1.1 [846 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libdevel-callchecker-perl arm64 0.008-2 [15.9 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 86 http://deb.debian.org/debian bookworm/main arm64 liburi-perl all 5.17-1 [90.4 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libclone-perl arm64 0.46-1 [13.5 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libwww-perl all 6.68-1 [186 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 wdiff arm64 1.2.2-5 [119 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 devscripts arm64 2.23.3 [1073 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libosp5 arm64 1.5.2-13+b2 [884 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 opensp arm64 1.5.2-13+b2 [414 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 docbook-to-man arm64 1:2.0.0-45 [75.6 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian bookworm/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libruby arm64 1:3.1 [4968 B] Get: 117 http://deb.debian.org/debian bookworm/main arm64 ruby-sdbm arm64 1.0.0-5+b1 [14.5 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libruby3.1 arm64 3.1.2-7 [5248 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 ruby3.1 arm64 3.1.2-7 [663 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 ruby arm64 1:3.1 [5868 B] Get: 126 http://deb.debian.org/debian bookworm/main arm64 rake all 13.0.6-3 [83.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 gem2deb-test-runner arm64 2.1 [16.9 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libgmpxx4ldbl arm64 2:6.2.1+dfsg1-1.1 [338 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libgmp-dev arm64 2:6.2.1+dfsg1-1.1 [622 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 ruby3.1-dev arm64 3.1.2-7 [1004 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 ruby-all-dev arm64 1:3.1 [5984 B] Get: 132 http://deb.debian.org/debian bookworm/main arm64 gem2deb arm64 2.1 [53.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 ruby-libxml arm64 3.2.4-2 [75.1 kB] Fetched 47.1 MB in 2s (26.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20366 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... 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 netbase. Preparing to unpack .../002-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../007-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../013-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../017-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../018-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../019-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../020-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../021-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../022-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../023-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../024-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../025-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../027-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../029-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../030-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-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 .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../035-libassuan0_2.5.5-5_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../036-gpgconf_2.2.40-1.1_arm64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../037-libksba8_1.6.3-2_arm64.deb ... Unpacking libksba8:arm64 (1.6.3-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../038-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../039-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../040-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnpth0:arm64. Preparing to unpack .../041-libnpth0_1.6-3_arm64.deb ... Unpacking libnpth0:arm64 (1.6-3) ... Selecting previously unselected package dirmngr. Preparing to unpack .../042-dirmngr_2.2.40-1.1_arm64.deb ... Unpacking dirmngr (2.2.40-1.1) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../043-gnupg-l10n_2.2.40-1.1_all.deb ... Unpacking gnupg-l10n (2.2.40-1.1) ... Selecting previously unselected package gnupg-utils. Preparing to unpack .../044-gnupg-utils_2.2.40-1.1_arm64.deb ... Unpacking gnupg-utils (2.2.40-1.1) ... Selecting previously unselected package gpg. Preparing to unpack .../045-gpg_2.2.40-1.1_arm64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../046-pinentry-curses_1.2.1-1_arm64.deb ... Unpacking pinentry-curses (1.2.1-1) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../047-gpg-agent_2.2.40-1.1_arm64.deb ... Unpacking gpg-agent (2.2.40-1.1) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../048-gpg-wks-client_2.2.40-1.1_arm64.deb ... Unpacking gpg-wks-client (2.2.40-1.1) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../049-gpg-wks-server_2.2.40-1.1_arm64.deb ... Unpacking gpg-wks-server (2.2.40-1.1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../050-gpgsm_2.2.40-1.1_arm64.deb ... Unpacking gpgsm (2.2.40-1.1) ... Selecting previously unselected package gnupg. Preparing to unpack .../051-gnupg_2.2.40-1.1_all.deb ... Unpacking gnupg (2.2.40-1.1) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../052-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 .../053-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 .../054-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 .../055-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 .../056-libio-pty-perl_1%3a1.17-1_arm64.deb ... Unpacking libio-pty-perl (1:1.17-1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../057-libipc-run-perl_20220807.0-1_all.deb ... Unpacking libipc-run-perl (20220807.0-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../058-libclass-method-modifiers-perl_2.14-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.14-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../059-libclass-xsaccessor-perl_1.19-4+b1_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../060-libb-hooks-op-check-perl_0.22-2+b1_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../061-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../062-libdevel-callchecker-perl_0.008-2_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../063-libparams-classify-perl_0.015-2+b1_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../064-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 .../065-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 .../066-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 .../067-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../068-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../069-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../070-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../071-libhttp-date-perl_6.05-2_all.deb ... Unpacking libhttp-date-perl (6.05-2) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../072-libfile-listing-perl_6.15-1_all.deb ... Unpacking libfile-listing-perl (6.15-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../073-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../074-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../075-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../076-libhtml-parser-perl_3.81-1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.81-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../077-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../078-libclone-perl_0.46-1_arm64.deb ... Unpacking libclone-perl:arm64 (0.46-1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../079-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../080-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../081-libhttp-message-perl_6.44-1_all.deb ... Unpacking libhttp-message-perl (6.44-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../082-libhttp-cookies-perl_6.10-1_all.deb ... Unpacking libhttp-cookies-perl (6.10-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../083-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. 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Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../103-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../104-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../105-libruby_1%3a3.1_arm64.deb ... Unpacking libruby:arm64 (1:3.1) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../106-ruby-sdbm_1.0.0-5+b1_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b1) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../107-libbsd0_0.11.7-2_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../108-libedit2_3.1-20221030-2_arm64.deb ... Unpacking libedit2:arm64 (3.1-20221030-2) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../109-libncurses6_6.4-2_arm64.deb ... Unpacking libncurses6:arm64 (6.4-2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../110-libyaml-0-2_0.2.5-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1) ... Selecting previously unselected package libruby3.1:arm64. Preparing to unpack .../111-libruby3.1_3.1.2-7_arm64.deb ... Unpacking libruby3.1:arm64 (3.1.2-7) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../112-ruby3.1_3.1.2-7_arm64.deb ... Unpacking ruby3.1 (3.1.2-7) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../113-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../114-ruby_1%3a3.1_arm64.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package rake. 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Preparing to unpack .../121-gem2deb_2.1_arm64.deb ... Unpacking gem2deb (2.1) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../122-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 .../123-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:arm64. Preparing to unpack .../124-ruby-libxml_3.2.4-2_arm64.deb ... Unpacking ruby-libxml:arm64 (3.2.4-2) ... Setting up libksba8:arm64 (1.6.3-2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up wdiff (1.2.2-5) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libclone-perl:arm64 (0.46-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdebhelper-perl (13.11.4) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up perl-openssl-defaults:arm64 (7+b1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libnpth0:arm64 (1.6-3) ... Setting up file (1:5.44-3) ... Setting up libassuan0:arm64 (2.5.5-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up libosp5 (1.5.2-13+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:arm64 (2:6.2.1+dfsg1-1.1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libncurses6:arm64 (6.4-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-12) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-2+b1) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up ruby-webrick (1.8.1-1) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.09-4) ... 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+b1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up liburi-perl (5.17-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:arm64 (1.92-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up gettext (0.21-12) ... Setting up libgmp-dev:arm64 (2:6.2.1+dfsg1-1.1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libnet-http-perl (6.22-1) ... Setting up opensp (1.5.2-13+b2) ... Setting up libdevel-callchecker-perl:arm64 (0.008-2) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... 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 (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libhtml-parser-perl:arm64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libparams-classify-perl:arm64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-1.1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up gnupg (2.2.40-1.1) ... Setting up libruby:arm64 (1:3.1) ... Setting up libwww-perl (6.68-1) ... Setting up ruby-rubygems (3.3.15-2) ... Setting up devscripts (2.23.3) ... Setting up ruby3.1 (3.1.2-7) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up ruby (1:3.1) ... Setting up rake (13.0.6-3) ... Setting up rdtool (0.6.38-4.1) ... Setting up libruby3.1:arm64 (3.1.2-7) ... Setting up gem2deb-test-runner (2.1) ... Setting up ruby3.1-dev:arm64 (3.1.2-7) ... Setting up ruby-libxml:arm64 (3.2.4-2) ... Setting up ruby-all-dev:arm64 (1:3.1) ... Setting up gem2deb (2.1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-10) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-45) ... Processing triggers for ca-certificates (20230311) ... 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: Running cd /build/ruby-bio-2.0.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.4-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ruby-bio-2.0.4' 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/ruby-bio-2.0.4' 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/ruby-bio-2.0.4' dh_auto_install dh_ruby --install /build/ruby-bio-2.0.4/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/ruby-bio-2.0.4/lib/bio/alignment.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/bl2seq/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/format0.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/format8.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/genomenet.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/ncbioptions.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/remote.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/rexml.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/rpsblast.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast/wublast.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blast.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/blat/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/clustalw/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/clustalw.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/emboss.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/fasta/format10.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/fasta.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/gcg/msf.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/gcg/seq.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/genscan/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/hmmer/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/hmmer.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/iprscan/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/mafft/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/mafft.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/meme/mast/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/meme/mast.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/meme/motif.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/muscle.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/baseml/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/baseml.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/codeml/rates.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/codeml/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/codeml.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/common.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/common_report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/yn00/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/paml/yn00.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/phylip/alignment.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/phylip/distance_matrix.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/probcons.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/psort/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/psort.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/pts1.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/sim4/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/sim4.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/sosui/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/spidey/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/targetp/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/tcoffee.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/appl/tmhmm/report.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/command.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/compat/features.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/compat/references.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/data/aa.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/data/codontable.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/data/na.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/aaindex.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/common.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/embl.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/embl_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/format_embl.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/sptr.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/swissprot.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/trembl.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/uniprot.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/embl/uniprotkb.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fantom.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/defline.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/fasta_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/format_fasta.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/format_qual.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/qual.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta/qual_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fasta.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fastq/fastq_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fastq/format_fastq.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/fastq.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/common.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/ddbj.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/format_genbank.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/genbank.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/genbank_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/genpept.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/genbank/refseq.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/gff.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/go.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/brite.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/common.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/compound.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/drug.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/enzyme.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/expression.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/genes.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/genome.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/glycan.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/keggtab.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/kgml.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/module.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/orthology.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/pathway.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/kegg/reaction.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/lasergene.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/litdb.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/medline.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/nbrf.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/newick.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/nexus.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/atom.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/chain.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/chemicalcomponent.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/model.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/pdb.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/residue.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb/utils.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/pdb.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/prosite.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/rebase.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/sanger_chromatogram/abif.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/sanger_chromatogram/chromatogram.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/sanger_chromatogram/scf.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/soft.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db/transfac.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/db.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/feature.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/das.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/fastacmd.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/fetch.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/autodetection.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/bdb.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/buffer.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/index.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/indexer.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile/splitter.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/flatfile.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/hinv.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/ncbirest.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/pubmed.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/registry.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/io/togows.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/location.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/map.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/pathway.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/reference.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/aa.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/adapter.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/common.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/compat.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/dblink.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/format.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/format_raw.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/generic.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/na.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/quality_score.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence/sequence_masker.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/sequence.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/tree/output.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree/output.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/tree.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/buried.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/helix.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/hydropathy.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/nucleotide.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/strand.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/taylor.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/turn.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme/zappo.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/color_scheme.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/contingency_table.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/analysis.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/ruby-bio-2.0.4/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/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/double_stranded.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/enzymes.yaml /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/single_strand.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme/string_formatting.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/restriction_enzyme.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/util/sirna.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio/version.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/ruby-bio-2.0.4/lib/bio.rb /build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/ruby-bio-2.0.4/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.4.gemspec /usr/bin/ruby3.1 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.1 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/ruby-bio-2.0.4/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/ruby-bio-2.0.4/debian/ruby-bio/usr/share/rubygems-integration/all:/build/ruby-bio-2.0.4/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.1.0:/var/lib/gems/3.1.0:/usr/local/lib/ruby/gems/3.1.0:/usr/lib/ruby/gems/3.1.0:/usr/lib/aarch64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/aarch64-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake -f debian/ruby-tests.rake /usr/bin/ruby3.1 -w -I"test" /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.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 /build/ruby-bio-2.0.4/test/functional/bio/test_command.rb:184: warning: assigned but unused variable - err Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.002048) test_dbs: .: (0.000855) test_go_ids: .: (0.000641) test_go_terms: .: (0.000614) test_parser: .: (0.001286) test_set_date: .: (0.000634) test_set_desc: .: (0.000768) test_to_str: .: (0.000680) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.001978) test_mktmpdir_without_block: .: (0.002278) test_remove_entry_secure: .: (0.001097) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.012702) test_call_command_fork: .: (0.000476) test_call_command_open3: .: (0.014702) test_call_command_popen: .: (0.015926) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.015554) test_call_command_fork: .: (0.000426) test_call_command_open3: .: (0.010984) test_call_command_popen: .: (0.011941) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.011867) test_call_command_fork: .: (0.000440) test_call_command_open3: .: (0.015167) test_call_command_popen: .: (0.011377) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.004186) test_call_command_fork_chdir: .: (0.000732) test_call_command_popen_chdir: .: (0.006307) test_query_command_chdir: .: (0.007792) test_query_command_fork_chdir: .: (0.000844) test_query_command_popen_chdir: .: (0.003488) Bio::FuncTestCommandQuery: test_query_command: .: (0.007096) test_query_command_fork: .: (0.003387) test_query_command_open3: .: (0.012560) test_query_command_popen: .: (0.006431) Bio::FuncTestCommandTmpdir: test_close!: .: (0.001993) test_initialize: .: (0.000908) test_path: .: (0.000742) test_path_after_close: .: (0.001285) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.044886) test_output_fasta: .: (0.040137) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.001168) test_accession: .: (0.000589) test_accessions: .: (0.000559) test_comment: .: (0.000471) test_common_name: .: (0.000803) test_definition: .: (0.001425) test_features: .: (0.001124) test_gi: .: (0.000683) test_keywords: .: (0.000510) test_locus: .: (0.000324) test_nid: .: (0.000612) test_organism: .: (0.000521) test_origin: .: (0.000400) test_references: .: (0.001836) test_segment: .: (0.001124) test_source: .: (0.000879) test_taxonomy: .: (0.000677) test_version: .: (0.000510) test_versions: .: (0.000464) Bio::TestAA: test_13: .: (0.000623) test_1n: .: (0.000257) test_name2one: .: (0.000375) test_name2three: .: (0.000490) test_one2name: .: (0.000292) test_one2three: .: (0.000263) test_three2name: .: (0.000256) test_three2one: .: (0.000333) test_to_1_1: .: (0.000282) test_to_1_3: .: (0.000401) test_to_1_name: .: (0.000319) test_to_3_1: .: (0.000414) test_to_3_3: .: (0.000246) test_to_3_name: .: (0.000321) test_to_re: .: (0.000423) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000613) Bio::TestAAindex: test_api: .: (0.000437) test_auto_aax1: .: (0.000884) test_auto_aax2: .: (0.000622) Bio::TestAAindex1: test_author: .: (0.000982) test_comment: .: (0.002878) test_correlation_coefficient: .: (0.001330) test_dblinks: .: (0.000866) test_definition: .: (0.000744) test_entry_id: .: (0.000691) test_index: .: (0.000927) test_journal: .: (0.000887) test_title: .: (0.000669) Bio::TestAAindex2: test_access_A_R: .: (0.003698) test_access_R_A: .: (0.001787) test_author: .: (0.000694) test_cols: .: (0.000634) test_comment: .: (0.000597) test_dblinks: .: (0.001881) test_definition: .: (0.000799) test_entry_id: .: (0.000607) test_journal: .: (0.000644) test_matrix: .: (0.001799) test_matrix_1_2: .: (0.002951) test_matrix_2_2: .: (0.002141) test_matrix_A_R: .: (0.001796) test_matrix_R_A: .: (0.003044) test_matrix_determinant: .: (0.009549) test_matrix_rank: .: (0.009944) test_matrix_transpose: .: (0.002681) test_rows: .: (0.000699) test_title: .: (0.000674) Bio::TestAAindexConstant: test_delimiter: .: (0.000645) test_tagsize: .: (0.000307) Bio::TestAbif: test_complement: .: (0.122712) test_seq: .: (0.019020) test_to_biosequence: .: (0.020670) Bio::TestActsLikeMap: test_mixin: .: (0.000879) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000912) Bio::TestActsLikeMarker: test_mixin: .: (0.000968) Bio::TestAlignment: test_add_seq_no_key: .: (0.000898) test_add_seq_using_seq_with_aaseq_method: .: (0.000452) test_add_seq_using_seq_with_definition_method: .: (0.000345) test_add_seq_using_seq_with_entry_id_method: .: (0.000381) test_add_seq_using_seq_with_naseq_method: .: (0.000547) test_add_seq_using_seq_with_seq_method: .: (0.000377) test_consensus_iupac_gap_modes: .: (0.001241) test_consensus_iupac_missing_char: .: (0.001468) test_consensus_iupac_missing_char_option: .: (0.000825) test_consensus_iupac_no_gaps: .: (0.000735) test_consensus_iupac_of_ambiguous_bases: .: (0.001044) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.017269) test_consensus_opt_gap_mode: .: (0.003437) test_consensus_opt_missing_char: .: (0.000895) test_consensus_string_no_gaps: .: (0.000689) test_consensus_threshold_four_sequences: .: (0.000985) test_consensus_threshold_two_sequences: .: (0.001096) test_convert_match: .: (0.002016) test_convert_unmatch: .: (0.000491) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000438) test_convert_unmatch_different_match_char: .: (0.000420) test_convert_unmatch_multiple_sequences: .: (0.000624) test_default_gap_char: .: (0.000284) test_default_gap_regexp_matches_default_gap_char: .: (0.000297) test_default_missing_char: .: (0.000258) test_each_site_equal_length: .: (0.000578) test_each_site_unequal_length: .: (0.000539) test_equals: .: (0.000876) test_match_line_protein: .: (0.001576) test_normalizebang_extends_sequences_with_gaps: .: (0.000484) test_seq_length_is_max_seq_length: .: (0.000477) test_seq_length_when_one_sequence: .: (0.000289) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000290) test_seqclass_when_seqclass_set: .: (0.000298) test_seqclass_when_sequence_used: .: (0.000294) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000295) test_set_and_get_gap_char: .: (0.000278) test_store_cannot_override_key: .: (0.000309) test_store_with_default_keys_and_user_defined_keys: .: (0.000332) test_store_with_nil_key_uses_next_number_for_key: .: (0.000435) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000749) test_alignment_concat: .: (0.000483) test_alignment_length: .: (0.000272) test_alignment_lstrip!: .: (0.000643) test_alignment_lstrip_nil: .: (0.000362) test_alignment_normalize!: .: (0.000281) test_alignment_rstrip!: .: (0.000482) test_alignment_rstrip_nil: .: (0.000363) test_alignment_site: .: (0.000614) test_alignment_slice: .: (0.000346) test_alignment_strip!: .: (0.000761) test_alignment_strip_nil: .: (0.000413) test_alignment_subseq: .: (0.001219) test_alignment_window: .: (0.000325) test_collect_each_site: .: (0.000411) test_consensus_each_site_default: .: (0.000474) test_consensus_each_site_gap_mode_1: .: (0.000605) test_consensus_each_site_gap_mode_minus1: .: (0.000480) test_consensus_iupac: .: (0.001024) test_consensus_string_default: .: (0.000470) test_consensus_string_half: .: (0.000409) test_convert_match: .: (0.000385) test_convert_unmatch: .: (0.000471) test_each_seq: .: (0.001323) test_each_site: .: (0.000601) test_each_site_step: .: (0.000429) test_each_window: .: (0.000591) test_match_line: .: (0.002778) test_match_line_amino: .: (0.004392) test_match_line_nuc: .: (0.000726) test_private_alignment_site: .: (0.000403) test_remove_all_gaps!: .: (0.000412) test_seqclass: .: (0.000328) test_seqclass=: .: (0.000477) test_seqclass_default: .: (0.000274) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.010680) test_determine_seq_method: .: (0.005816) test_entries: .: (0.001173) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.001026) test_avoid_same_name_numbering: .: (0.000489) test_clustal_have_same_name_true: .: (0.000518) test_have_same_name_false: .: (0.000442) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000630) test_gap_char_default: .: (0.000322) test_gap_char_never_nil: .: (0.000286) test_gap_regexp: .: (0.000284) test_gap_regexp=: .: (0.000310) test_gap_regexp_never_nil: .: (0.000426) test_get_all_property_default: .: (0.000378) test_get_all_property_nodefault: .: (0.000361) test_is_gap_default_false: .: (0.000326) test_is_gap_default_true: .: (0.000376) test_is_gap_nodefault_false: .: (0.000306) test_is_gap_nodefault_true: .: (0.000309) test_missing_char=: .: (0.000309) test_missing_char_default: .: (0.000285) test_missing_char_never_nil: .: (0.000344) test_seqclass=: .: (0.000327) test_seqclass_default: .: (0.000303) test_seqclass_never_nil: .: (0.000343) test_set_all_property: .: (0.000328) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001886) test_consensus_string_50percent: .: (0.000347) test_consensus_string_50percent_nil: .: (0.000324) test_consensus_string_default: .: (0.000272) test_consensus_string_default_nil: .: (0.000282) test_has_gap_false: .: (0.000344) test_has_gap_true: .: (0.000287) test_match_line_amino_100percent: .: (0.000389) test_match_line_amino_missing: .: (0.000665) test_match_line_amino_strong: .: (0.000375) test_match_line_amino_weak: .: (0.000509) test_match_line_nuc_100percent: .: (0.000382) test_match_line_nuc_missing: .: (0.000442) test_remove_gaps!: .: (0.000329) test_remove_gaps_bang_not_removed: .: (0.000281) Bio::TestAtomFinder: test_atoms: .: (0.055103) test_each_atom: .: (0.000918) test_find_atom: .: (0.000635) Bio::TestBioFastaDefline: test_acc_version: .: (0.001509) test_accession: .: (0.001647) test_accessions: .: (0.001273) test_description: .: (0.001033) test_descriptions: .: (0.001267) test_entry_id: .: (0.000984) test_get: .: (0.001211) test_get_all_by_type: .: (0.001133) test_get_by_type: .: (0.001023) test_gi: .: (0.000935) test_id_strings: .: (0.002284) test_locus: .: (0.000904) test_method_missing: .: (0.001423) test_to_s: .: (0.001154) test_words: .: (0.002526) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.002748) test_goid2term: .: (0.001397) test_parse_goids: .: (0.001284) Bio::TestBioGenBank: test_basecount: .: (0.001329) test_circular: .: (0.000828) test_classification: .: (0.000945) test_date: .: (0.000748) test_date_modified: .: (0.002086) test_division: .: (0.000727) test_each_cds_feature: .: (0.002678) test_each_cds_qualifiers: .: (0.002430) test_each_gene: .: (0.002586) test_entry_id: .: (0.000749) test_length: .: (0.000903) test_locus_circular: .: (0.000844) test_locus_class: .: (0.000919) test_locus_date: .: (0.000908) test_locus_division: .: (0.000958) test_locus_entry_id: .: (0.000841) test_locus_length: .: (0.000785) test_locus_natype: .: (0.000778) test_locus_strand: .: (0.001003) test_natype: .: (0.000723) test_seq: .: (0.000874) test_seq_len: .: (0.000763) test_strand: .: (0.000878) test_strandedness: .: (0.000701) test_to_biosequence: .: (0.006967) Bio::TestBioGenPept: test_circular: .: (0.001127) test_date: .: (0.000745) test_dbsource: .: (0.000685) test_division: .: (0.000895) test_entry_id: .: (0.000579) test_length: .: (0.000626) test_locus: .: (0.000592) test_seq: .: (0.000654) test_seq_len: .: (0.000901) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.001324) test_aaseq: .: (0.000823) test_chromosome: .: (0.000928) test_codon_usage: .: (0.001099) test_cu_list: .: (0.000601) test_dblinks_as_hash: .: (0.000842) test_dblinks_as_strings: .: (0.000797) test_definition: .: (0.000732) test_division: .: (0.000700) test_eclinks: .: (0.000754) test_entry: .: (0.000691) test_entry_id: .: (0.000590) test_gbposition: .: (0.000689) test_gene: .: (0.000616) test_genes: .: (0.000682) test_keggclass: .: (0.000743) test_keggclasses: .: (0.000782) test_locations: .: (0.001078) test_motifs_as_hash: .: (0.000854) test_motifs_as_strings: .: (0.000597) test_name: .: (0.000723) test_names_as_array: .: (0.000794) test_new: .: (0.000648) test_ntlen: .: (0.000946) test_ntseq: .: (0.001106) test_organism: .: (0.000688) test_orthologs_as_hash: .: (0.000719) test_orthologs_as_strings: .: (0.000646) test_pathway: .: (0.016823) test_pathway_after_pathways_as_strings: .: (0.001125) test_pathway_before_pathways_as_strings: .: (0.000866) test_pathways_as_hash: .: (0.000749) test_pathways_as_strings: .: (0.000796) test_position: .: (0.000647) test_structure: .: (0.000708) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.004833) test_comment: .: (0.001179) test_data_source: .: (0.001613) test_definition: .: (0.001049) test_disease: .: (0.001421) test_entry_id: .: (0.001128) test_lineage: .: (0.001189) test_nalen: .: (0.001478) test_name: .: (0.001074) test_new: .: (0.001137) test_num_gene: .: (0.001109) test_num_rna: .: (0.001401) test_original_databases: .: (0.004345) test_original_db: .: (0.001281) test_plasmids: .: (0.001107) test_references: .: (0.013966) test_statistics: .: (0.001407) test_taxid: .: (0.001343) test_taxonomy: .: (0.001747) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001493) test_comment: .: (0.005228) test_data_source: .: (0.000851) test_definition: .: (0.000763) test_disease: .: (0.000765) test_entry_id: .: (0.000942) test_lineage: .: (0.001178) test_nalen: .: (0.000708) test_name: .: (0.000715) test_new: .: (0.000824) test_num_gene: .: (0.000713) test_num_rna: .: (0.000703) test_original_databases: .: (0.000712) test_original_db: .: (0.000875) test_plasmids: .: (0.001139) test_references: .: (0.001101) test_statistics: .: (0.000706) test_taxid: .: (0.000841) test_taxonomy: .: (0.000901) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.001203) test_compounds_as_strings: .: (0.001402) test_dblinks_as_hash: .: (0.000683) test_dblinks_as_strings: .: (0.000537) test_description: .: (0.000623) test_diseases_as_hash: .: (0.000677) test_diseases_as_strings: .: (0.000553) test_entry_id: .: (0.000628) test_enzymes_as_strings: .: (0.000621) test_genes_as_hash: .: (0.000539) test_genes_as_strings: .: (0.000517) test_keggclass: .: (0.000655) test_ko_pathway: .: (0.001051) test_modules_as_hash: .: (0.000667) test_modules_as_strings: .: (0.000557) test_name: .: (0.000773) test_new: .: (0.000614) test_organism: .: (0.000610) test_orthologs_as_hash: .: (0.000567) test_orthologs_as_strings: .: (0.000538) test_pathways_as_hash: .: (0.000621) test_pathways_as_strings: .: (0.000598) test_reactions_as_hash: .: (0.001251) test_reactions_as_strings: .: (0.000577) test_references: .: (0.000561) test_rel_pathways_as_hash: .: (0.000988) test_rel_pathways_as_strings: .: (0.000643) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001640) test_compounds_as_strings: .: (0.001136) test_dblinks_as_hash: .: (0.001573) test_dblinks_as_strings: .: (0.000670) test_description: .: (0.000886) test_diseases_as_hash: .: (0.000712) test_diseases_as_strings: .: (0.000673) test_entry_id: .: (0.000722) test_enzymes_as_strings: .: (0.000641) test_genes_as_hash: .: (0.001106) test_genes_as_strings: .: (0.001692) test_keggclass: .: (0.001126) test_ko_pathway: .: (0.000708) test_modules_as_hash: .: (0.000714) test_modules_as_strings: .: (0.000645) test_name: .: (0.000711) test_new: .: (0.000834) test_organism: .: (0.000746) test_orthologs_as_hash: .: (0.000639) test_orthologs_as_strings: .: (0.001610) test_pathways_as_hash: .: (0.001084) test_pathways_as_strings: .: (0.000668) test_reactions_as_hash: .: (0.000613) test_reactions_as_strings: .: (0.000623) test_references: .: (0.000793) test_rel_pathways_as_hash: .: (0.000749) test_rel_pathways_as_strings: .: (0.000720) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.001028) test_compounds_as_strings: .: (0.000725) test_dblinks_as_hash: .: (0.000966) test_dblinks_as_strings: .: (0.000637) test_description: .: (0.000613) test_diseases_as_hash: .: (0.000523) test_diseases_as_strings: .: (0.000527) test_entry_id: .: (0.000608) test_enzymes_as_strings: .: (0.000531) test_genes_as_hash: .: (0.000511) test_genes_as_strings: .: (0.000522) test_keggclass: .: (0.000791) test_ko_pathway: .: (0.000639) test_modules_as_hash: .: (0.000837) test_modules_as_strings: .: (0.000571) test_name: .: (0.000588) test_new: .: (0.000699) test_organism: .: (0.000606) test_orthologs_as_hash: .: (0.000765) test_orthologs_as_strings: .: (0.000650) test_pathways_as_hash: .: (0.000593) test_pathways_as_strings: .: (0.000704) test_reactions_as_hash: .: (0.000550) test_reactions_as_strings: .: (0.000517) test_references: .: (0.000539) test_rel_pathways_as_hash: .: (0.000638) test_rel_pathways_as_strings: .: (0.000690) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.001027) test_compounds_as_strings: .: (0.000594) test_dblinks_as_hash: .: (0.000688) test_dblinks_as_strings: .: (0.000841) test_description: .: (0.001102) test_diseases_as_hash: .: (0.000712) test_diseases_as_strings: .: (0.000666) test_entry_id: .: (0.001523) test_enzymes_as_strings: .: (0.000727) test_genes_as_hash: .: (0.000602) test_genes_as_strings: .: (0.000599) test_keggclass: .: (0.000826) test_ko_pathway: .: (0.000722) test_modules_as_hash: .: (0.001013) test_modules_as_strings: .: (0.000747) test_name: .: (0.000744) test_new: .: (0.001352) test_organism: .: (0.000730) test_orthologs_as_hash: .: (0.000586) test_orthologs_as_strings: .: (0.000563) test_pathways_as_hash: .: (0.000674) test_pathways_as_strings: .: (0.000602) test_reactions_as_hash: .: (0.000569) test_reactions_as_strings: .: (0.000567) test_references: .: (0.003258) test_rel_pathways_as_hash: .: (0.000986) test_rel_pathways_as_strings: .: (0.000856) Bio::TestBioKeggDRUG: test_activity: .: (0.001276) test_comment: .: (0.000767) test_dblinks_as_hash: .: (0.001140) test_dblinks_as_strings: .: (0.000788) test_entry_id: .: (0.001267) test_formula: .: (0.000687) test_kcf: .: (0.000810) test_mass: .: (0.000756) test_name: .: (0.000778) test_names: .: (0.000766) test_pathways_as_hash: .: (0.000973) test_pathways_as_strings: .: (0.000754) test_products: .: (0.001216) test_remark: .: (0.000818) Bio::TestBioKeggGLYCAN: test_comment: .: (0.001163) test_composition: .: (0.000756) test_compounds: .: (0.000660) test_dblinks_as_hash: .: (0.001377) test_dblinks_as_strings: .: (0.000806) test_entry_id: .: (0.000736) test_enzymes: .: (0.000698) test_kcf: .: (0.000783) test_keggclass: .: (0.000732) test_mass: .: (0.000715) test_name: .: (0.000733) test_orthologs_as_hash: .: (0.001102) test_orthologs_as_strings: .: (0.000781) test_pathways_as_hash: .: (0.001127) test_pathways_as_strings: .: (0.000695) test_reactions: .: (0.000839) test_references: .: (0.000865) test_remark: .: (0.000714) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000997) test_composition: .: (0.000851) test_compounds: .: (0.000635) test_dblinks_as_hash: .: (0.000767) test_dblinks_as_strings: .: (0.001042) test_entry_id: .: (0.000829) test_enzymes: .: (0.000627) test_kcf: .: (0.000505) test_keggclass: .: (0.000585) test_mass: .: (0.000596) test_name: .: (0.000713) test_orthologs_as_hash: .: (0.000597) test_orthologs_as_strings: .: (0.000529) test_pathways_as_hash: .: (0.000548) test_pathways_as_strings: .: (0.000505) test_reactions: .: (0.001260) test_references: .: (0.000635) test_remark: .: (0.000627) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.001600) test_compounds_as_strings: .: (0.000911) test_dblinks_as_hash: .: (0.000678) test_dblinks_as_strings: .: (0.000624) test_description: .: (0.001133) test_diseases_as_hash: .: (0.000784) test_diseases_as_strings: .: (0.000669) test_entry_id: .: (0.000686) test_enzymes_as_strings: .: (0.000586) test_genes_as_hash: .: (0.000753) test_genes_as_strings: .: (0.000625) test_keggclass: .: (0.000708) test_ko_pathway: .: (0.000677) test_modules_as_hash: .: (0.001455) test_modules_as_strings: .: (0.000822) test_name: .: (0.000697) test_new: .: (0.000651) test_organism: .: (0.000652) test_orthologs_as_hash: .: (0.000760) test_orthologs_as_strings: .: (0.000603) test_pathways_as_hash: .: (0.000674) test_pathways_as_strings: .: (0.000611) test_reactions_as_hash: .: (0.002077) test_reactions_as_strings: .: (0.001065) test_references: .: (0.001579) test_rel_pathways_as_hash: .: (0.001104) test_rel_pathways_as_strings: .: (0.001270) Bio::TestBioLITDB: test_author: .: (0.001162) test_entry_id: .: (0.000583) test_field: .: (0.000556) test_journal: .: (0.000540) test_keyword: .: (0.000636) test_reference: .: (0.001303) test_title: .: (0.000680) test_volume: .: (0.001042) Bio::TestBioNBRF: test_aalen: .: (0.001045) test_aaseq: .: (0.000484) test_entry: .: (0.000449) test_length: .: (0.000446) test_nalen: .: (0.000645) test_naseq: .: (0.000542) test_seq: .: (0.000445) test_seq_class: .: (0.000452) test_to_nbrf: .: (0.000519) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000998) test_to_newick_format_leaf: .: (0.001625) test_to_newick_format_leaf_NHX: .: (0.000578) Bio::TestBl2seqReport: test_db_len: .: (0.002040) test_db_num: .: (0.001614) test_new: .: (0.000904) test_undefed_methods: .: (0.003280) test_undefed_methods_for_iteration: .: (0.003418) Bio::TestBl2seqReportConstants: test_rs: .: (0.000665) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.010798) test_hits: .: (0.001157) Bio::TestBlast: test_blast_reports_format0: .: (0.017890) test_blast_reports_format0_with_block: .: (0.003305) test_blast_reports_format7: .: (0.049992) test_blast_reports_format7_with_block: .: (0.050353) test_blast_reports_format7_with_parser: .: (0.048919) test_blast_reports_format7_with_parser_with_block: .: (0.160317) test_blast_reports_format8: .: (0.002326) test_blast_reports_format8_with_block: .: (0.001678) test_blast_reports_format8_with_parser: .: (0.000980) test_blast_reports_format8_with_parser_with_block: .: (0.000870) test_blast_reports_xml: .: (0.048890) test_blast_reports_xml_with_block: .: (0.047576) test_blastll: .: (0.000646) test_db: .: (0.000692) test_exec_genomenet: .: (0.000445) test_exec_local: .: (0.000503) test_exec_ncbi: .: (0.000401) test_filter: .: (0.000491) test_format: .: (0.000645) test_make_command_line: .: (0.001619) test_make_command_line_2: .: (0.001482) test_matrix: .: (0.000660) test_new: .: (0.001317) test_new_opt_string: .: (0.001060) test_option: .: (0.000553) test_option_set: .: (0.000887) test_option_set_m0: .: (0.000780) test_options: .: (0.000507) test_output: .: (0.000499) test_parse_result: .: (0.045729) test_parser: .: (0.000688) test_program: .: (0.000579) test_query: .: (0.000444) test_self_local: .: (0.000949) test_self_remote: .: (0.006030) test_server: .: (0.000696) Bio::TestBlastNCBIOptions: test_add_options: .: (0.001455) test_delete: .: (0.001271) test_equal_equal: .: (0.001661) test_get: .: (0.001230) test_make_command_line_options: .: (0.001037) test_normalize!: .: (0.000792) test_parse: .: (0.000797) test_set: .: (0.002092) Bio::TestBlastReport: test_db: .: (0.047074) test_db_len: .: (0.052284) test_db_num: .: (0.046710) test_each_hit: .: (0.045384) test_each_iteration: .: (0.046320) test_eff_space: .: (0.046603) test_entrez_query: .: (0.049773) test_entropy: .: (0.045576) test_expect: .: (0.045199) test_filter: .: (0.044503) test_gap_extend: .: (0.045847) test_gap_open: .: (0.048432) test_hits: .: (0.046190) test_hsp_len: .: (0.044505) test_inclusion: .: (0.045873) test_iterations: .: (0.044485) test_kappa: .: (0.049247) test_lambda: .: (0.046540) test_matrix: .: (0.046610) test_message: .: (0.045971) test_parameters: .: (0.045999) test_pattern: .: (0.050223) test_program: .: (0.047165) test_query_def: .: (0.047053) test_query_id: .: (0.045035) test_query_len: .: (0.042647) test_reference: .: (0.050565) test_sc_match: .: (0.047444) test_sc_mismatch: .: (0.047457) test_statistics: .: (0.047543) test_version: .: (0.047090) Bio::TestBlastReportDefault: test_db: .: (0.001836) test_db_len: .: (0.001471) test_db_num: .: (0.001722) test_each_hit: .: (0.001478) test_each_iteration: .: (0.001067) test_eff_space: .: (0.001422) test_entropy: .: (0.001351) test_expect: .: (0.001358) test_gap_extend: .: (0.001334) test_gap_open: .: (0.001571) test_gapped_entropy: .: (0.001338) test_gapped_kappa: .: (0.004530) test_gapped_lambda: .: (0.001601) test_hits: .: (0.001211) test_iterations: .: (0.001205) test_kappa: .: (0.001225) test_lambda: .: (0.001191) test_matrix: .: (0.001625) test_message: .: (0.001154) test_pattern: .: (0.001567) test_program: .: (0.001303) test_query_def: .: (0.001189) test_query_len: .: (0.001126) test_reference: .: (0.001277) test_sc_match: .: (0.001364) test_sc_mismatch: .: (0.001506) test_version: .: (0.001139) Bio::TestBlastReportHit: test_Hit_accession: .: (0.048235) test_Hit_bit_score: .: (0.048198) test_Hit_definition: .: (0.047058) test_Hit_evalue: .: (0.046817) test_Hit_hit_id: .: (0.053701) test_Hit_hsps: .: (0.047541) test_Hit_identity: .: (0.048217) test_Hit_lap_at: .: (0.047134) test_Hit_len: .: (0.046792) test_Hit_midline: .: (0.050211) test_Hit_num: .: (0.048091) test_Hit_overlap: .: (0.047448) test_Hit_query_def: .: (0.047607) test_Hit_query_end: .: (0.047650) test_Hit_query_id: .: (0.047374) test_Hit_query_len: .: (0.044158) test_Hit_query_seq: .: (0.044837) test_Hit_query_start: .: (0.047152) test_Hit_taeget_def: .: (0.047282) test_Hit_target_end: .: (0.050851) test_Hit_target_id: .: (0.048063) test_Hit_target_len: .: (0.046946) test_Hit_target_seq: .: (0.047213) test_Hit_target_start: .: (0.050871) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001942) test_Hit_definition: .: (0.001486) test_Hit_evalue: .: (0.001348) test_Hit_hsps: .: (0.001366) test_Hit_identity: .: (0.001352) test_Hit_lap_at: .: (0.002126) test_Hit_len: .: (0.001357) test_Hit_midline: .: (0.002064) test_Hit_overlap: .: (0.001330) test_Hit_query_end: .: (0.001691) test_Hit_query_seq: .: (0.002132) test_Hit_query_start: .: (0.001840) test_Hit_taeget_def: .: (0.001205) test_Hit_target_end: .: (0.001657) test_Hit_target_id: .: (0.001461) test_Hit_target_len: .: (0.001196) test_Hit_target_seq: .: (0.002231) test_Hit_target_start: .: (0.001774) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.135473) test_Hit_bit_score: .: (0.143047) test_Hit_definition: .: (0.139788) test_Hit_evalue: .: (0.129334) test_Hit_hit_id: .: (0.125057) test_Hit_hsps: .: (0.124084) test_Hit_identity: .: (0.118053) test_Hit_lap_at: .: (0.123434) test_Hit_len: .: (0.123718) test_Hit_midline: .: (0.118553) test_Hit_num: .: (0.123585) test_Hit_overlap: .: (0.125854) test_Hit_query_def: .: (0.124381) test_Hit_query_end: .: (0.128075) test_Hit_query_id: .: (0.137406) test_Hit_query_len: .: (0.135031) test_Hit_query_seq: .: (0.138927) test_Hit_query_start: .: (0.143752) test_Hit_taeget_def: .: (0.129123) test_Hit_target_end: .: (0.137253) test_Hit_target_id: .: (0.140792) test_Hit_target_len: .: (0.132917) test_Hit_target_seq: .: (0.137770) test_Hit_target_start: .: (0.146307) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.140973) test_Hit_bit_score: .: (0.143961) test_Hit_definition: .: (0.144058) test_Hit_evalue: .: (0.136974) test_Hit_hit_id: .: (0.141331) test_Hit_hsps: .: (0.140713) test_Hit_identity: .: (0.133184) test_Hit_lap_at: .: (0.137098) test_Hit_len: .: (0.140493) test_Hit_midline: .: (0.139663) test_Hit_num: .: (0.137020) test_Hit_overlap: .: (0.143344) test_Hit_query_def: .: (0.138814) test_Hit_query_end: .: (0.136296) test_Hit_query_id: .: (0.140124) test_Hit_query_len: .: (0.140242) test_Hit_query_seq: .: (0.135459) test_Hit_query_start: .: (0.139084) test_Hit_taeget_def: .: (0.142235) test_Hit_target_end: .: (0.135425) test_Hit_target_id: .: (0.140179) test_Hit_target_len: .: (0.141513) test_Hit_target_seq: .: (0.137232) test_Hit_target_start: .: (0.140297) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.047433) test_Hit_bit_score: .: (0.047181) test_Hit_definition: .: (0.051394) test_Hit_evalue: .: (0.046723) test_Hit_hit_id: .: (0.046414) test_Hit_hsps: .: (0.046593) test_Hit_identity: .: (0.050635) test_Hit_lap_at: .: (0.047446) test_Hit_len: .: (0.047678) test_Hit_midline: .: (0.046378) test_Hit_num: .: (0.046709) test_Hit_overlap: .: (0.049316) test_Hit_query_def: .: (0.047233) test_Hit_query_end: .: (0.046000) test_Hit_query_id: .: (0.046813) test_Hit_query_len: .: (0.047274) test_Hit_query_seq: .: (0.050285) test_Hit_query_start: .: (0.047581) test_Hit_taeget_def: .: (0.046803) test_Hit_target_end: .: (0.046039) test_Hit_target_id: .: (0.050295) test_Hit_target_len: .: (0.047427) test_Hit_target_seq: .: (0.046818) test_Hit_target_start: .: (0.046513) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.001438) test_Hit_bit_score: .: (0.000561) test_Hit_definition: .: (0.000451) test_Hit_evalue: .: (0.000574) test_Hit_hit_id: .: (0.000508) test_Hit_hsps: .: (0.000467) test_Hit_identity: .: (0.000462) test_Hit_lap_at: .: (0.000509) test_Hit_len: .: (0.000469) test_Hit_midline: .: (0.000463) test_Hit_num: .: (0.000674) test_Hit_overlap: .: (0.000493) test_Hit_query_def: .: (0.000525) test_Hit_query_end: .: (0.000502) test_Hit_query_id: .: (0.000510) test_Hit_query_len: .: (0.000932) test_Hit_query_seq: .: (0.000561) test_Hit_query_start: .: (0.000468) test_Hit_taeget_def: .: (0.000479) test_Hit_target_end: .: (0.000466) test_Hit_target_id: .: (0.000464) test_Hit_target_len: .: (0.000561) test_Hit_target_seq: .: (0.000486) test_Hit_target_start: .: (0.000477) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.049746) test_Hsp_bit_score: .: (0.048147) test_Hsp_density: .: (0.047481) test_Hsp_evalue: .: (0.046928) test_Hsp_gaps: .: (0.046971) test_Hsp_hit_frame: .: (0.050218) test_Hsp_hit_from: .: (0.043862) test_Hsp_hit_to: .: (0.046835) test_Hsp_hseq: .: (0.047438) test_Hsp_identity: .: (0.047300) test_Hsp_midline: .: (0.050484) test_Hsp_mismatch_count: .: (0.047025) test_Hsp_num: .: (0.046988) test_Hsp_pattern_from: .: (0.046357) test_Hsp_pattern_to: .: (0.050177) test_Hsp_percent_identity: .: (0.047498) test_Hsp_positive: .: (0.047009) test_Hsp_qseq: .: (0.047083) test_Hsp_query_frame: .: (0.047316) test_Hsp_query_from: .: (0.049849) test_Hsp_query_to: .: (0.046273) test_Hsp_score: .: (0.046262) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.002220) test_Hsp_bit_score: .: (0.001594) test_Hsp_evalue: .: (0.001147) test_Hsp_gaps: .: (0.001316) test_Hsp_hit_frame: .: (0.001211) test_Hsp_hit_from: .: (0.001695) test_Hsp_hit_to: .: (0.001598) test_Hsp_hseq: .: (0.002152) test_Hsp_identity: .: (0.001231) test_Hsp_midline: .: (0.001614) test_Hsp_percent_identity: .: (0.001329) test_Hsp_positive: .: (0.001225) test_Hsp_qseq: .: (0.001778) test_Hsp_query_frame: .: (0.001229) test_Hsp_query_from: .: (0.001814) test_Hsp_query_to: .: (0.001744) test_Hsp_score: .: (0.001171) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.144137) test_Hsp_bit_score: .: (0.254685) test_Hsp_density: .: (0.140049) test_Hsp_evalue: .: (0.144445) test_Hsp_gaps: .: (0.137025) test_Hsp_hit_frame: .: (0.141864) test_Hsp_hit_from: .: (0.143175) test_Hsp_hit_to: .: (0.137416) test_Hsp_hseq: .: (0.141659) test_Hsp_identity: .: (0.140948) test_Hsp_midline: .: (0.133353) test_Hsp_mismatch_count: .: (0.140035) test_Hsp_num: .: (0.140124) test_Hsp_pattern_from: .: (0.134465) test_Hsp_pattern_to: .: (0.140495) test_Hsp_percent_identity: .: (0.138058) test_Hsp_positive: .: (0.130627) test_Hsp_qseq: .: (0.140328) test_Hsp_query_frame: .: (0.137180) test_Hsp_query_from: .: (0.140724) test_Hsp_query_to: .: (0.144117) test_Hsp_score: .: (0.136052) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.141257) test_Hsp_bit_score: .: (0.143767) test_Hsp_density: .: (0.137116) test_Hsp_evalue: .: (0.130180) test_Hsp_gaps: .: (0.131433) test_Hsp_hit_frame: .: (0.137563) test_Hsp_hit_from: .: (0.141793) test_Hsp_hit_to: .: (0.140582) test_Hsp_hseq: .: (0.137989) test_Hsp_identity: .: (0.142787) test_Hsp_midline: .: (0.137532) test_Hsp_mismatch_count: .: (0.140764) test_Hsp_num: .: (0.143393) test_Hsp_pattern_from: .: (0.137139) test_Hsp_pattern_to: .: (0.140869) test_Hsp_percent_identity: .: (0.143689) test_Hsp_positive: .: (0.137028) test_Hsp_qseq: .: (0.142080) test_Hsp_query_frame: .: (0.141657) test_Hsp_query_from: .: (0.140070) test_Hsp_query_to: .: (0.144264) test_Hsp_score: .: (0.141516) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.049502) test_Hsp_bit_score: .: (0.047857) test_Hsp_density: .: (0.047872) test_Hsp_evalue: .: (0.047119) test_Hsp_gaps: .: (0.052079) test_Hsp_hit_frame: .: (0.048291) test_Hsp_hit_from: .: (0.048389) test_Hsp_hit_to: .: (0.048264) test_Hsp_hseq: .: (0.047874) test_Hsp_identity: .: (0.051169) test_Hsp_midline: .: (0.048897) test_Hsp_mismatch_count: .: (0.047448) test_Hsp_num: .: (0.047883) test_Hsp_pattern_from: .: (0.048047) test_Hsp_pattern_to: .: (0.051911) test_Hsp_percent_identity: .: (0.048624) test_Hsp_positive: .: (0.047914) test_Hsp_qseq: .: (0.047754) test_Hsp_query_frame: .: (0.047874) test_Hsp_query_from: .: (0.051432) test_Hsp_query_to: .: (0.048976) test_Hsp_score: .: (0.048150) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.001428) test_Hsp_bit_score: .: (0.000536) test_Hsp_density: .: (0.000520) test_Hsp_evalue: .: (0.000509) test_Hsp_gaps: .: (0.000497) test_Hsp_hit_frame: .: (0.000474) test_Hsp_hit_from: .: (0.000617) test_Hsp_hit_to: .: (0.000522) test_Hsp_hseq: .: (0.000493) test_Hsp_identity: .: (0.000483) test_Hsp_midline: .: (0.000475) test_Hsp_mismatch_count: .: (0.000479) test_Hsp_num: .: (0.001140) test_Hsp_pattern_from: .: (0.000631) test_Hsp_pattern_to: .: (0.000462) test_Hsp_percent_identity: .: (0.000453) test_Hsp_positive: .: (0.000485) test_Hsp_qseq: .: (0.000489) test_Hsp_query_frame: .: (0.000652) test_Hsp_query_from: .: (0.000499) test_Hsp_query_to: .: (0.000492) test_Hsp_score: .: (0.000479) Bio::TestBlastReportIteration: test_hits: .: (0.048219) test_message: .: (0.050757) test_num: .: (0.048390) test_statistics: .: (0.047908) Bio::TestBlastReportIterationDefault: test_hits: .: (0.002092) test_message: .: (0.001051) test_num: .: (0.001032) Bio::TestBlastReportIterationMulti: test_each: .: (0.142109) test_hits: .: (0.138110) test_message: .: (0.143923) test_num: .: (0.139981) test_query_def: .: (0.140265) test_query_id: .: (0.144541) test_query_len: .: (0.141772) test_statistics: .: (0.140297) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.146171) test_hits: .: (0.139102) test_message: .: (0.139788) test_num: .: (0.145119) test_query_def: .: (0.139633) test_query_id: .: (0.141680) test_query_len: .: (0.145051) test_statistics: .: (0.138579) Bio::TestBlastReportIterationREXML: test_hits: .: (0.051434) test_message: .: (0.048092) test_num: .: (0.047363) test_statistics: .: (0.042349) Bio::TestBlastReportIterationTabular: test_hits: .: (0.001118) test_message: .: (0.000491) test_num: .: (0.000459) test_statistics: .: (0.000454) Bio::TestBlastReportMulti: test_db: .: (0.131235) test_db_len: .: (0.124516) test_db_num: .: (0.119067) test_each_hit: .: (0.124801) test_each_iteration: .: (0.122119) test_eff_space: .: (0.120079) test_entropy: .: (0.124038) test_expect: .: (0.121808) test_filter: .: (0.119530) test_gap_extend: .: (0.124809) test_gap_open: .: (0.121342) test_hits: .: (0.119264) test_hsp_len: .: (0.123260) test_iterations: .: (0.121426) test_kappa: .: (0.117893) test_lambda: .: (0.122363) test_matrix: .: (0.126254) test_message: .: (0.122447) test_parameters: .: (0.128566) test_pattern: .: (0.128110) test_program: .: (0.123327) test_query_def: .: (0.130627) test_query_id: .: (0.141124) test_query_len: .: (0.129577) test_reference: .: (0.137795) test_reports: .: (0.137967) test_statistics: .: (0.134298) test_version: .: (0.136016) Bio::TestBlastReportMultiREXML: test_db: .: (0.135524) test_db_len: .: (0.134383) test_db_num: .: (0.131515) test_each_hit: .: (0.137438) test_each_iteration: .: (0.138100) test_eff_space: .: (0.133519) test_entropy: .: (0.138487) test_expect: .: (0.138931) test_filter: .: (0.132057) test_gap_extend: .: (0.137195) test_gap_open: .: (0.136428) test_hits: .: (0.136344) test_hsp_len: .: (0.131341) test_iterations: .: (0.135028) test_kappa: .: (0.131298) test_lambda: .: (0.129703) test_matrix: .: (0.134495) test_message: .: (0.136030) test_parameters: .: (0.132915) test_pattern: .: (0.129793) test_program: .: (0.135092) test_query_def: .: (0.133276) test_query_id: .: (0.127101) test_query_len: .: (0.130443) test_reference: .: (0.132804) test_reports: .: (0.131164) test_statistics: .: (0.128763) test_version: .: (0.128409) Bio::TestBlastReportREXML: test_db: .: (0.042585) test_db_len: .: (0.043686) test_db_num: .: (0.049560) test_each_hit: .: (0.045084) test_each_iteration: .: (0.045579) test_eff_space: .: (0.043732) test_entrez_query: .: (0.048491) test_entropy: .: (0.045255) test_expect: .: (0.045310) test_filter: .: (0.043132) test_gap_extend: .: (0.049702) test_gap_open: .: (0.048052) test_hits: .: (0.046682) test_hsp_len: .: (0.044807) test_inclusion: .: (0.045631) test_iterations: .: (0.050866) test_kappa: .: (0.047530) test_lambda: .: (0.047552) test_matrix: .: (0.049510) test_message: .: (0.052302) test_parameters: .: (0.049920) test_pattern: .: (0.048175) test_program: .: (0.048940) test_query_def: .: (0.051357) test_query_id: .: (0.051076) test_query_len: .: (0.049816) test_reference: .: (0.048725) test_sc_match: .: (0.049639) test_sc_mismatch: .: (0.049869) test_statistics: .: (0.045301) test_version: .: (0.049024) Bio::TestBlastReportTabular: test_db: .: (0.001121) test_db_len: .: (0.000808) test_db_num: .: (0.000722) test_each_hit: .: (0.000559) test_each_iteration: .: (0.000511) test_eff_space: .: (0.000507) test_entrez_query: .: (0.000529) test_entropy: .: (0.000491) test_expect: .: (0.000609) test_filter: .: (0.000463) test_gap_extend: .: (0.000440) test_gap_open: .: (0.000449) test_hits: .: (0.000471) test_hsp_len: .: (0.000461) test_inclusion: .: (0.000452) test_iterations: .: (0.000862) test_kappa: .: (0.000588) test_lambda: .: (0.000465) test_matrix: .: (0.000463) test_message: .: (0.000475) test_parameters: .: (0.000624) test_pattern: .: (0.000559) test_program: .: (0.000524) test_query_def: .: (0.000548) test_query_id: .: (0.000532) test_query_len: .: (0.000507) test_reference: .: (0.000494) test_sc_match: .: (0.000497) test_sc_mismatch: .: (0.000461) test_statistics: .: (0.000466) test_version: .: (0.000669) Bio::TestChain: test_aaseq: .: (0.001019) test_addLigand: .: (0.000365) test_addResidue: .: (0.000343) test_atom_seq: .: (0.000377) test_comp: .: (0.000428) test_each: .: (0.000354) test_each_heterogen: .: (0.000423) test_each_residue: .: (0.000417) test_get_heterogen_by_id: .: (0.000400) test_get_residue_by_id: .: (0.000395) test_inspect: .: (0.000506) test_rehash: .: (0.000381) test_rehash_heterogens: .: (0.000939) test_rehash_residues: .: (0.000341) test_square_brace: .: (0.000359) test_to_s: .: (0.000407) Bio::TestChainFinder: test_chains: .: (0.000823) test_each_chain: .: (0.000416) test_find_chain: .: (0.000379) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.032003) test_header: .: (0.002024) test_match_line: .: (0.006631) test_sequence0: .: (0.002425) test_sequence1: .: (0.001858) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.032047) test_header: .: (0.003144) test_match_line: .: (0.002562) test_sequence0: .: (0.002496) test_sequence1: .: (0.003197) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.037577) test_header: .: (0.002072) test_match_line: .: (0.002214) test_sequence0: .: (0.001927) test_sequence1: .: (0.002018) Bio::TestCodonTable: test_Tables: .: (0.000721) test_accessor: .: (0.000574) test_definition: .: (0.000298) test_each: .: (0.000639) test_revtrans: .: (0.000506) test_self_accessor: .: (0.000310) test_self_copy: .: (0.001982) test_set_accessor: .: (0.349007) test_start: .: (0.000360) test_start_codon?: .: (0.000336) test_stop: .: (0.000289) test_stop_codon?: .: (0.000324) test_table: .: (0.000434) Bio::TestCodonTableConstants: test_Definitions: .: (0.000664) test_Starts: .: (0.000582) test_Tables: .: (0.000265) test_stops: .: (0.000318) Bio::TestColorScheme: test_buried: .: (0.002980) Bio::TestCommand: test_command_constants: .: (0.000643) test_escape_shell: .: (0.000586) test_escape_shell_unix: .: (0.000377) test_escape_shell_windows: .: (0.000381) test_make_cgi_params_by_array_of_array: .: (0.001183) test_make_cgi_params_by_array_of_hash: .: (0.000862) test_make_cgi_params_by_array_of_string: .: (0.000666) test_make_cgi_params_by_hash_in_string: .: (0.001415) test_make_cgi_params_by_hash_in_symbol: .: (0.001718) test_make_cgi_params_by_string: .: (0.000652) test_make_command_line: .: (0.000401) test_make_command_line_unix: .: (0.000342) test_make_command_line_windows: .: (0.000388) test_safe_command_line_array: .: (0.000431) test_safe_command_line_array_passthrough: .: (0.000365) Bio::TestContingencyTable: test_lite_example: .: (0.369858) Bio::TestDB: test_entry_id: .: (0.000864) test_exists: .: (0.000288) test_fetch: .: (0.000669) test_get: .: (0.000279) test_open: .: (0.000279) test_tags: .: (0.000289) Bio::TestDataType: test_const_like_method: .: (0.001559) test_pdb_achar: .: (0.000846) test_pdb_atom: .: (0.001016) test_pdb_character: .: (0.000754) test_pdb_date: .: (0.000623) test_pdb_idcode: .: (0.000805) test_pdb_integer: .: (0.000289) test_pdb_list: .: (0.000322) test_pdb_lstring: .: (0.000572) test_pdb_real: .: (0.000447) test_pdb_resudue_name: .: (0.000650) test_pdb_slist: .: (0.000308) test_pdb_string: .: (0.000681) test_pdb_stringrj: .: (0.000320) test_pdb_symop: .: (0.000626) test_specification_list: .: (0.000368) Bio::TestEMBL: test_ac: .: (0.002292) test_accession: .: (0.001093) test_cc: .: (0.000962) test_de: .: (0.001255) test_division: .: (0.001594) test_dr: .: (0.000979) test_dt: .: (0.001153) test_dt_created: .: (0.001076) test_dt_iterator: .: (0.001036) test_dt_updated: .: (0.001732) test_each_cds: .: (0.001624) test_each_gene: .: (0.001890) test_entry: .: (0.001329) test_fh: .: (0.001746) test_ft: .: (0.001574) test_ft_accessor: .: (0.001745) test_ft_iterator: .: (0.001962) test_id_line: .: (0.001214) test_id_line_data_class: .: (0.001353) test_id_line_division: .: (0.001117) test_id_line_entry_name: .: (0.001550) test_id_line_iterator: .: (0.001151) test_id_line_molecule_type: .: (0.001110) test_id_line_sequence_length: .: (0.001291) test_kw: .: (0.001164) test_molecule: .: (0.001466) test_oc: .: (0.001478) test_og: .: (0.001012) test_os: .: (0.001146) test_ref: .: (0.006648) test_references: .: (0.002253) test_seq: .: (0.001984) test_sequence_length: .: (0.001809) test_sq: .: (0.001238) test_sq_get: .: (0.001125) test_sv: .: (0.001310) test_version: .: (0.001500) Bio::TestEMBL89: test_ac: .: (0.001787) test_accession: .: (0.001122) test_cc: .: (0.000964) test_de: .: (0.001876) test_division: .: (0.001176) test_dr: .: (0.000957) test_dt: .: (0.001170) test_dt_created: .: (0.001045) test_dt_iterator: .: (0.001237) test_dt_updated: .: (0.001251) test_each_cds: .: (0.001557) test_each_gene: .: (0.001538) test_entry: .: (0.001430) test_fh: .: (0.000996) test_ft: .: (0.001727) test_ft_accessor: .: (0.001745) test_ft_iterator: .: (0.001799) test_id_line: .: (0.001151) test_id_line_data_class: .: (0.001115) test_id_line_division: .: (0.001484) test_id_line_entry_name: .: (0.001119) test_id_line_iterator: .: (0.001085) test_id_line_molecule_type: .: (0.001351) test_id_line_sequence_length: .: (0.001319) test_id_line_sequence_version: .: (0.001110) test_kw: .: (0.001319) test_molecule: .: (0.001153) test_oc: .: (0.001211) test_og: .: (0.001175) test_os: .: (0.001121) test_ref: .: (0.001295) test_references: .: (0.002227) test_seq: .: (0.001899) test_sequence_length: .: (0.001164) test_sq: .: (0.001062) test_sq_get: .: (0.001278) test_sv: .: (0.001198) test_version: .: (0.001143) Bio::TestEMBLAPI: test_ac: .: (0.001192) test_accessions: .: (0.000546) Bio::TestEMBLCommon: test_ac: .: (0.000763) test_accession: .: (0.000279) test_accessions: .: (0.000275) test_de: .: (0.000276) test_definition: .: (0.000495) test_description: .: (0.000296) test_dr: .: (0.000285) test_keywords: .: (0.000279) test_kw: .: (0.000279) test_oc: .: (0.000277) test_og: .: (0.000280) test_os: .: (0.000279) test_ref: .: (0.000280) test_references: .: (0.000415) Bio::TestEMBLDB: test_fetch: .: (0.000944) test_p_entry2hash: .: (0.000281) Bio::TestEMBLToBioSequence: test_classification: .: (0.011850) test_date_created: .: (0.001964) test_date_modified: .: (0.001438) test_definition: .: (0.001258) test_division: .: (0.001560) test_entry_id: .: (0.001391) test_entry_version: .: (0.001391) test_features: .: (0.001742) test_keywords: .: (0.001338) test_molecule_type: .: (0.001311) test_primary_accession: .: (0.001236) test_references: .: (0.002197) test_release_created: .: (0.001385) test_release_modified: .: (0.001332) test_secondary_accessions: .: (0.001289) test_sequence_version: .: (0.001377) test_species: .: (0.001550) test_topology: .: (0.001322) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.010335) test_date_created: .: (0.009532) test_date_modified: .: (0.010042) test_definition: .: (0.010038) test_division: .: (0.010421) test_entry_id: .: (0.009930) test_entry_version: .: (0.010568) test_features: .: (0.010997) test_keywords: .: (0.010403) test_molecule_type: .: (0.017709) test_primary_accession: .: (0.011051) test_references: .: (0.011255) test_release_created: .: (0.010391) test_release_modified: .: (0.009927) test_secondary_accessions: .: (0.010497) test_sequence_version: .: (0.010270) test_species: .: (0.010638) test_topology: .: (0.009833) Bio::TestFasta: test_db: .: (0.000726) test_format: .: (0.000296) test_format_arg_integer: .: (0.000331) test_format_arg_str: .: (0.000311) test_ktup: .: (0.000303) test_matrix: .: (0.000534) test_option: .: (0.000486) test_options: .: (0.000348) test_output: .: (0.000261) test_program: .: (0.000304) test_server: .: (0.000304) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000899) test_accession: .: (0.000390) test_accessions: .: (0.000404) test_description: .: (0.000358) test_descriptions: .: (0.000846) test_entry_id: .: (0.000349) test_get_all_by_type: .: (0.000347) test_gi: .: (0.000514) test_id_strings: .: (0.000542) test_list_ids: .: (0.000376) test_locus: .: (0.000361) test_words: .: (0.000473) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000758) test_accession: .: (0.000541) test_accessions: .: (0.000448) test_description: .: (0.000370) test_descriptions: .: (0.000382) test_emb: .: (0.000416) test_entry_id: .: (0.000845) test_get_all_by_type: .: (0.000551) test_get_emb: .: (0.000424) test_gi: .: (0.000386) test_id_strings: .: (0.000549) test_list_ids: .: (0.000377) test_locus: .: (0.000383) test_words: .: (0.000518) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000710) test_accession: .: (0.000399) test_accessions: .: (0.000387) test_description: .: (0.000355) test_descriptions: .: (0.000353) test_entry_id: .: (0.000337) test_get_all_by_type: .: (0.000528) test_gi: .: (0.000830) test_id_strings: .: (0.000516) test_list_ids: .: (0.000359) test_locus: .: (0.000352) test_sp: .: (0.000392) test_words: .: (0.000670) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000883) test_accession: .: (0.000520) test_accessions: .: (0.000530) test_description: .: (0.000463) test_descriptions: .: (0.000705) test_entry_id: .: (0.000951) test_get_all_by_type: .: (0.000456) test_gi: .: (0.000473) test_id_strings: .: (0.000793) test_list_ids: .: (0.000726) test_locus: .: (0.000514) test_words: .: (0.000826) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000770) test_accession: .: (0.000562) test_accessions: .: (0.000483) test_description: .: (0.000404) test_descriptions: .: (0.000400) test_entry_id: .: (0.000404) test_get_all_by_type: .: (0.000437) test_gi: .: (0.000649) test_id_strings: .: (0.000722) test_list_ids: .: (0.000433) test_locus: .: (0.000399) test_words: .: (0.000658) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.001500) test_accession: .: (0.000343) test_accessions: .: (0.000316) test_description: .: (0.000304) test_descriptions: .: (0.000306) test_entry_id: .: (0.000290) test_get_all_by_type: .: (0.000304) test_gi: .: (0.000533) test_id_strings: .: (0.000440) test_list_ids: .: (0.000325) test_locus: .: (0.000319) test_words: .: (0.000391) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000705) test_accession: .: (0.000586) test_accessions: .: (0.001019) test_description: .: (0.000375) test_descriptions: .: (0.000363) test_entry_id: .: (0.000339) test_get: .: (0.000370) test_get_all_by_type: .: (0.000356) test_id_strings: .: (0.000605) test_list_ids: .: (0.000356) test_locus: .: (0.000341) test_sp: .: (0.000381) test_words: .: (0.000560) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000936) test_accession: .: (0.000406) test_accessions: .: (0.000374) test_description: .: (0.000352) test_descriptions: .: (0.001037) test_entry_id: .: (0.000360) test_get: .: (0.000593) test_get_all_by_type: .: (0.000349) test_id_strings: .: (0.000652) test_list_ids: .: (0.000355) test_locus: .: (0.000354) test_tr: .: (0.000415) test_words: .: (0.000858) Bio::TestFastaFirstName: test_first_name1: .: (0.000713) test_first_name_multi_identifier: .: (0.000346) test_first_name_single_worded_defintion: .: (0.000312) test_no_definition: .: (0.000302) test_space_before_first_name: .: (0.000332) test_tabbed_defintion: .: (0.001188) Bio::TestFastaFormat: test_aalen: .: (0.000757) test_aaseq: .: (0.000374) test_acc_version: .: (0.000505) test_accession: .: (0.000474) test_accessions: .: (0.000586) test_data: .: (0.000352) test_definition: .: (0.000341) test_entry: .: (0.000351) test_entry_id: .: (0.000465) test_entry_overrun: .: (0.000335) test_first_name: .: (0.000358) test_gi: .: (0.000705) test_identifiers: .: (0.000505) test_length: .: (0.000368) test_query: .: (0.000643) test_seq: .: (0.000356) Bio::TestFastaFormatConst: test_delimiter: .: (0.000666) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000842) test_data: .: (0.000337) test_definition: .: (0.000336) test_entry: .: (0.000333) test_entry_id: .: (0.000711) test_first_name: .: (0.000395) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000679) test_naseq: .: (0.000353) test_naseq_class: .: (0.000765) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000940) Bio::TestFastaInitialize: test_new_1: .: (0.001565) test_option: .: (0.000315) test_option_backward_compatibility: .: (0.000402) Bio::TestFastaNumericFormat: test_arg: .: (0.000916) test_data: .: (0.000457) test_definition: .: (0.000328) test_each: .: (0.000409) test_entry: .: (0.001378) test_entry_id: .: (0.000388) test_length: .: (0.000392) test_to_biosequence: .: (0.002870) Bio::TestFastaQuery: test_query: .: (0.000546) test_self_local: .: (0.000209) test_self_parser: .: (0.000193) test_self_remote: .: (0.000203) Bio::TestFastacmd: test_database: .: (0.000597) test_fastacmd: .: (0.000262) test_methods: .: (0.000451) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.002430) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.001959) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001481) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.001621) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.002570) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.001761) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.001753) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.001455) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001808) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001479) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.001544) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.002330) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.001643) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.014235) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.004420) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.002693) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001713) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.001540) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.019895) test_error_probabilities_as_sanger: .: (0.019286) test_error_probabilities_as_solexa: .: (0.018867) test_quality_scores_as_illumina: .: (0.001519) test_quality_scores_as_sanger: .: (0.000919) test_quality_scores_as_solexa: .: (0.001192) test_validate_format: .: (0.002218) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.003263) test_entry_id: .: (0.003601) test_error_probabilities: .: (0.597551) test_nalen: .: (0.003678) test_naseq: .: (0.003970) test_quality_scores: .: (0.006225) test_quality_string: .: (0.003210) test_roundtrip: .: (0.501739) test_seq: .: (0.003848) test_sequence_string: .: (0.003545) test_to_biosequence: .: (0.481598) test_to_biosequence_and_output: .: (0.014712) test_to_s: .: (0.003890) test_validate_format: .: (0.003317) test_validate_format_with_array: .: (0.004079) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.001737) test_mask_20_with_empty_string: .: (0.001338) test_mask_20_with_longer_string: .: (0.001187) test_mask_20_with_x: .: (0.001186) test_mask_60: .: (0.001906) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.026478) test_error_probabilities_as_sanger: .: (0.024847) test_error_probabilities_as_solexa: .: (0.025467) test_quality_scores_as_illumina: .: (0.001546) test_quality_scores_as_sanger: .: (0.001481) test_quality_scores_as_solexa: .: (0.001245) test_validate_format: .: (0.002141) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.019310) test_error_probabilities_as_sanger: .: (0.022211) test_error_probabilities_as_solexa: .: (0.020389) test_quality_scores_as_illumina: .: (0.001955) test_quality_scores_as_sanger: .: (0.001294) test_quality_scores_as_solexa: .: (0.001571) test_validate_format: .: (0.002294) Bio::TestFeature: test_append: .: (0.000705) test_append_nil: .: (0.000304) test_assoc: .: (0.000338) test_each: .: (0.000277) test_feature: .: (0.000252) test_locations: .: (0.000621) test_new: .: (0.000289) test_position: .: (0.000288) test_qualifiers: .: (0.000278) Bio::TestFeatures: test_append: .: (0.000875) test_arg: .: (0.000396) test_each: .: (0.000486) test_features: .: (0.000357) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.003100) test_aaindex2: .: (0.000696) test_blast: .: (0.000552) test_blastxml: .: (0.001337) test_embl: .: (0.000848) test_embl_oldrelease: .: (0.000718) test_fastaformat: .: (0.001654) test_fastanumericformat: .: (0.000439) test_fastq: .: (0.000785) test_genbank: .: (0.000602) test_genpept: .: (0.000610) test_hmmer: .: (0.000701) test_maxml_cluster: .: (0.010021) test_maxml_sequence: .: (0.000419) test_medline: .: (0.000488) test_prosite: .: (0.006876) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.006111) test_transfac: .: (0.005528) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000887) test_auto_1arg_filename: .: (0.001388) test_auto_1arg_io: .: (0.001012) test_auto_1arg_io_with_block: .: (0.002143) test_auto_1arg_with_block: .: (0.002630) test_auto_2arg_filename_mode: .: (0.001350) test_auto_2arg_filename_mode_with_block: .: (0.001985) test_auto_3arg: .: (0.001021) test_auto_3arg_with_block: .: (0.002244) test_foreach: .: (0.002120) test_new_2arg_class: .: (0.000587) test_new_2arg_nil: .: (0.000956) test_open_0arg: .: (0.000428) test_open_1arg_class: .: (0.000375) test_open_1arg_filename: .: (0.001171) test_open_1arg_io: .: (0.000972) test_open_1arg_io_with_block: .: (0.002659) test_open_1arg_nil: .: (0.000517) test_open_1arg_with_block: .: (0.002003) test_open_2arg_autodetect: .: (0.001228) test_open_2arg_autodetect_io: .: (0.000984) test_open_2arg_autodetect_io_with_block: .: (0.002669) test_open_2arg_autodetect_with_block: .: (0.002160) test_open_2arg_class: .: (0.000737) test_open_2arg_class_io: .: (0.000593) test_open_2arg_class_io_with_block: .: (0.001632) test_open_2arg_class_with_block: .: (0.002248) test_open_2arg_filename_mode: .: (0.001259) test_open_2arg_filename_mode_with_block: .: (0.002334) test_open_3arg: .: (0.002202) test_open_3arg_with_block: .: (0.006060) test_open_4arg: .: (0.005246) test_to_a: .: (0.002001) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.001384) test_close: .: (0.000476) test_dbclass: .: (0.000573) test_dbclass_eq: .: (0.000575) test_dbclass_nil: .: (0.000689) test_each: .: (0.001414) test_each_entry: .: (0.001663) test_ended_pos: .: (0.000916) test_entry_pos_flag: .: (0.000555) test_entry_raw: .: (0.001301) test_eof?: .: (0.000914) test_next_entry: .: (0.001200) test_path: .: (0.000463) test_pos: .: (0.000830) test_raw: .: (0.001217) test_rewind: .: (0.000731) test_start_pos: .: (0.000913) test_start_pos_ended_pos_not_recorded: .: (0.000908) test_to_io: .: (0.000547) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.001019) test_simpleformat2: .: (0.000860) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000678) test_eof_false_after_prefetch: .: (0.001091) test_eof_false_first: .: (0.000406) test_eof_true: .: (0.000513) test_getc: .: (0.000382) test_getc_after_prefetch: .: (0.000354) test_gets: .: (0.000362) test_gets_equal_prefetch_gets: .: (0.000390) test_gets_paragraph_mode: .: (0.000481) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000728) test_gets_paragraph_mode_within_buffer: .: (0.001208) test_gets_rs: .: (0.000471) test_gets_rs_equal_prefetch_gets: .: (0.000496) test_gets_rs_within_buffer: .: (0.000940) test_pos: .: (0.000727) test_pos=: .: (0.000420) test_prefetch_buffer: .: (0.000361) test_prefetch_gets: .: (0.000403) test_prefetch_gets_with_arg: .: (0.000452) test_rewind: .: (0.000341) test_skip_spaces: .: (0.000419) test_to_io: .: (0.000622) test_ungetc: .: (0.000420) test_ungetc_after_prefetch: .: (0.000426) test_ungets: .: (0.000487) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000770) test_self_open_file: .: (0.000649) test_self_open_file_with_block: .: (0.000581) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000751) test_parse_file_open_arg_int_perm: .: (0.000690) test_parse_file_open_arg_int_perm_opt: .: (0.000324) test_parse_file_open_arg_integer: .: (0.000421) test_parse_file_open_arg_nil: .: (0.000287) test_parse_file_open_arg_opt: .: (0.000515) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000359) test_parse_file_open_arg_str: .: (0.000343) test_parse_file_open_arg_str_opt: .: (0.000388) test_parse_file_open_arg_str_perm: .: (0.000350) test_parse_file_open_arg_str_perm_opt: .: (0.000369) test_parse_file_open_arg_str_with_enc: .: (0.000578) test_parse_file_open_arg_str_with_ext_enc: .: (0.000344) test_parse_file_open_mode_integer: .: (0.000290) test_parse_file_open_mode_nil: .: (0.000326) test_parse_file_open_mode_str: .: (0.000335) test_parse_file_open_mode_str_with_enc: .: (0.000345) test_parse_file_open_mode_str_with_ext_enc: .: (0.000343) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.001341) test_entry: .: (0.000368) test_entry_ended_pos: .: (0.000323) test_entry_pos_flag: .: (0.000349) test_entry_start_pos: .: (0.000327) test_get_entry: .: (0.000481) test_rewind: .: (0.000587) test_skip_leader: .: (0.000422) test_stream: .: (0.000300) test_stream_pos: .: (0.000391) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000707) test_delimiter_overrun: .: (0.000306) test_entry: .: (0.000600) test_entry_ended_pos: .: (0.000418) test_entry_ended_pos_default_nil: .: (0.000370) test_entry_start_pos: .: (0.000794) test_entry_start_pos_default_nil: .: (0.000372) test_get_entry: .: (0.000741) test_get_parsed_entry: .: (0.001062) test_header: .: (0.000336) test_skip_leader: .: (0.000469) test_skip_leader_without_header: .: (0.000455) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.001055) test_entry_ended_pos: .: (0.000839) test_entry_start_pos: .: (0.001075) test_flag_to_fetch_header: .: (0.000628) test_get_entry: .: (0.001236) test_get_parsed_entry: .: (0.001037) test_rewind: .: (0.000744) test_skip_leader: .: (0.000443) Bio::TestGCGMsf: test_alignment: .: (0.002985) test_checksum: .: (0.000942) test_compcheck: .: (0.000712) test_date: .: (0.000667) test_description: .: (0.001002) test_entry_id: .: (0.000888) test_gap_length_weight: .: (0.000729) test_gap_weight: .: (0.000702) test_heading: .: (0.000686) test_length: .: (0.000645) test_seq_type: .: (0.000954) test_symbol_comparison_table: .: (0.001144) test_validate_checksum: .: (0.004313) Bio::TestGFF: test_record_class: .: (0.001814) test_records: .: (0.001453) Bio::TestGFF2: test_const_version: .: (0.001964) test_gff_version: .: (0.001170) test_metadata: .: (0.001237) test_metadata_size: .: (0.001820) test_records_size: .: (0.001194) test_to_s: .: (0.002947) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000798) test_attributes_case2: .: (0.000719) test_attributes_incompatible_backslash_semicolon: .: (0.000624) Bio::TestGFF2MetaData: test_data: .: (0.000566) test_directive: .: (0.000253) test_parse: .: (0.000318) Bio::TestGFF2Record: test_attribute: .: (0.001504) test_attribute_nonexistent: .: (0.010088) test_attributes: .: (0.001085) test_attributes_to_hash: .: (0.000801) test_comment_only?: .: (0.000677) test_delete_attribute: .: (0.000824) test_delete_attribute_multiple: .: (0.001120) test_delete_attribute_multiple2: .: (0.001546) test_delete_attribute_multiple_nil: .: (0.000824) test_delete_attribute_nil: .: (0.000980) test_delete_attribute_nonexistent: .: (0.000781) test_delete_attributes: .: (0.000797) test_delete_attributes_multiple: .: (0.001419) test_delete_attributes_nonexistent: .: (0.000994) test_end: .: (0.000869) test_eqeq: .: (0.001752) test_eqeq_false: .: (0.002374) test_feature: .: (0.000659) test_frame: .: (0.000662) test_get_attribute: .: (0.001017) test_get_attribute_nonexistent: .: (0.000678) test_get_attributes: .: (0.001482) test_get_attributes_nonexistent: .: (0.000921) test_replace_attributes: .: (0.000847) test_replace_attributes_multiple_multiple_over: .: (0.000846) test_replace_attributes_multiple_multiple_same: .: (0.000849) test_replace_attributes_multiple_multiple_two: .: (0.001539) test_replace_attributes_multiple_single: .: (0.000829) test_replace_attributes_nonexistent: .: (0.000796) test_replace_attributes_nonexistent_multiple: .: (0.000959) test_replace_attributes_single_multiple: .: (0.000837) test_score: .: (0.000662) test_self_parse: .: (0.002470) test_seqname: .: (0.000661) test_set_attribute: .: (0.000757) test_set_attribute_multiple: .: (0.000776) test_set_attribute_nonexistent: .: (0.001417) test_sort_attributes_by_tag!: .: (0.001000) test_sort_attributes_by_tag_bang_test2: .: (0.000970) test_sort_attributes_by_tag_bang_with_block: .: (0.001167) test_source: .: (0.000696) test_start: .: (0.000684) test_strand: .: (0.001110) test_to_s: .: (0.001320) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000698) test_comment_eq: .: (0.000302) test_comment_only?: .: (0.000320) test_comment_only_false: .: (0.000387) test_to_s: .: (0.000332) test_to_s_not_empty: .: (0.000561) Bio::TestGFF3: test_const_version: .: (0.003213) test_gff_version: .: (0.001634) test_records: .: (0.003603) test_sequence_regions: .: (0.002071) test_sequences: .: (0.002658) test_to_s: .: (0.003929) Bio::TestGFF3MetaData: test_data: .: (0.000695) test_directive: .: (0.000285) test_parse: .: (0.000343) Bio::TestGFF3Record: test_attributes: .: (0.001446) test_end: .: (0.000743) test_feature: .: (0.000710) test_frame: .: (0.001198) test_id: .: (0.000992) test_score: .: (0.000738) test_seqname: .: (0.000746) test_source: .: (0.000777) test_start: .: (0.001572) test_strand: .: (0.000706) test_to_s: .: (0.001174) test_to_s_attr_order_changed: .: (0.001642) Bio::TestGFF3RecordEscape: test_escape: .: (0.000828) test_escape_attribute: .: (0.000962) test_escape_seqid: .: (0.000764) test_unescape: .: (0.000540) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.001129) test_eqeq: .: (0.000761) test_new_from_sequences_na: .: (0.000829) test_new_from_sequences_na_aa: .: (0.000985) test_new_from_sequences_na_aa_boundary_gap: .: (0.002242) test_new_from_sequences_na_aa_example: .: (0.001117) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.001003) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000991) test_process_sequences_na: .: (0.000878) test_process_sequences_na_aa: .: (0.000718) test_process_sequences_na_aa_reverse_frameshift: .: (0.001351) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000946) test_process_sequences_na_aa_tooshort: .: (0.001090) test_process_sequences_na_tooshort: .: (0.000872) test_to_s: .: (0.000615) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000939) test_attributes_one: .: (0.001034) test_attributes_with_escaping: .: (0.000481) test_id_multiple: .: (0.000791) test_id_multiple2: .: (0.000853) test_id_replace: .: (0.000490) test_id_set: .: (0.000560) test_initialize_9: .: (0.000298) test_phase: .: (0.000488) test_score: .: (0.000564) test_to_s_void: .: (0.000479) Bio::TestGFF3RecordTarget: test_end: .: (0.001602) test_parse: .: (0.000590) test_start: .: (0.000550) test_strand: .: (0.000360) test_target_id: .: (0.000337) test_to_s: .: (0.000597) Bio::TestGFF3SequenceRegion: test_end: .: (0.000671) test_parse: .: (0.000740) test_seqid: .: (0.000368) test_start: .: (0.000346) test_to_s: .: (0.001195) Bio::TestGFFRecord: test_attributes: .: (0.000780) test_comment: .: (0.000458) test_end: .: (0.000368) test_feature: .: (0.000368) test_frame: .: (0.000371) test_score: .: (0.000360) test_seqname: .: (0.000359) test_source: .: (0.000357) test_start: .: (0.000460) test_strand: .: (0.000417) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000599) Bio::TestGeneAssociation: test_aspect: .: (0.001156) test_assigned_by: .: (0.000332) test_date: .: (0.000445) test_db: .: (0.000356) test_db_object_id: .: (0.000351) test_db_object_name: .: (0.000352) test_db_object_symbol: .: (0.000339) test_db_object_synonym: .: (0.000371) test_db_object_type: .: (0.000338) test_db_reference: .: (0.000336) test_evidence: .: (0.000490) test_goid: .: (0.000433) test_parser: .: (0.001999) test_qualifier: .: (0.000350) test_taxon: .: (0.000335) test_to_str: .: (0.000451) test_with: .: (0.000363) Bio::TestGenscanReport: test_date_run: .: (0.003203) test_gccontent: .: (0.002534) test_genscan_version: .: (0.002390) test_isochore: .: (0.003387) test_length: .: (0.001824) test_matrix: .: (0.002243) test_predictions_size: .: (0.003043) test_query_name: .: (0.002082) test_time: .: (0.003002) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.002918) test_donor_score: .: (0.002265) test_exon_type: .: (0.002586) test_exon_type_long: .: (0.002430) test_first: .: (0.002719) test_initiation_score: .: (0.002142) test_last: .: (0.019218) test_number: .: (0.020281) test_p_value: .: (0.023019) test_phase: .: (0.023064) test_range: .: (0.010687) test_score: .: (0.019224) test_strand: .: (0.007438) test_t_score: .: (0.031611) test_termination_score: .: (0.002350) Bio::TestGenscanReportGene: test_aaseq: .: (0.003417) test_naseq: .: (0.002276) test_number: .: (0.002723) test_polyA: .: (0.002342) test_promoter: .: (0.002274) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.004084) test_reports_ary_contents: .: (0.002222) Bio::TestHMMERReportConstants: test_rs: .: (0.000820) Bio::TestHMMERReportHit: test_accession: .: (0.002791) test_append_hsp: .: (0.002143) test_bit_score: .: (0.001932) test_definition: .: (0.002018) test_description: .: (0.002417) test_each: .: (0.001936) test_each_hsp: .: (0.002010) test_entry_id: .: (0.002316) test_evalue: .: (0.002050) test_hit: .: (0.001856) test_hit_id: .: (0.001954) test_hsps: .: (0.002203) test_num: .: (0.001856) test_score: .: (0.001747) test_target_def: .: (0.001818) test_target_id: .: (0.002442) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.002111) test_each: .: (0.001912) test_each_hit: .: (0.002217) test_histogram: .: (0.001983) test_hits: .: (0.001721) test_hsps: .: (0.001923) test_parameter: .: (0.002635) test_program: .: (0.001952) test_query_info: .: (0.002046) test_statistical_detail: .: (0.002177) test_total_seq_searched: .: (0.001923) test_whole_seq_top_hits: .: (0.001696) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.003205) test_histogram: .: (0.002287) test_statistical_detail: .: (0.002150) test_total_seq_searched: .: (0.002178) test_whole_seq_top_hit: .: (0.002736) Bio::TestHMMERReportHsp: test_accession: .: (0.002168) test_bit_score: .: (0.001976) test_csline: .: (0.002325) test_domain: .: (0.002038) test_evalue: .: (0.001769) test_flatseq: .: (0.001978) test_hmm_f: .: (0.002316) test_hmm_t: .: (0.001889) test_hmmseq: .: (0.001947) test_hsp: .: (0.001777) test_midline: .: (0.002437) test_query_frame: .: (0.001847) test_query_from: .: (0.001946) test_query_seq: .: (0.001724) test_query_to: .: (0.002750) test_rfline: .: (0.001803) test_score: .: (0.001986) test_seq_f: .: (0.001763) test_seq_ft: .: (0.002500) test_seq_t: .: (0.001934) test_set_alignment: .: (0.001611) test_targat_to: .: (0.002609) test_target_frame: .: (0.001812) test_target_from: .: (0.002014) test_target_seq: .: (0.001720) Bio::TestHetatmFinder: test_each_hetatm: .: (0.001969) test_find_hetatm: .: (0.000652) test_hetatms: .: (0.000811) Bio::TestHeterogen: test_addAtom: .: (0.001145) test_each: .: (0.000572) test_each_hetatm: .: (0.001128) test_get_residue_id_from_atom: .: (0.000477) test_het_atom: .: (0.000515) test_iCode: .: (0.000480) test_inspect: .: (0.000629) test_resSeq: .: (0.000443) test_sort: .: (0.000554) test_square_bracket: .: (0.000508) test_to_s: .: (0.001789) test_update_resudue_id: .: (0.000446) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000749) test_find_heterogen: .: (0.000375) test_heterogens: .: (0.000536) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000818) test_match_description: .: (0.000455) test_match_evalue: .: (0.000434) test_match_ipr_description: .: (0.000453) test_match_ipr_id: .: (0.000440) test_match_match_end: .: (0.001310) test_match_match_start: .: (0.000416) test_match_method: .: (0.000404) test_matches_size: .: (0.000401) test_query_id: .: (0.000415) test_query_length: .: (0.000412) Bio::TestIprscanRawReport: test_entry_id: .: (0.007193) test_match_accession: .: (0.007273) test_match_crc64: .: (0.006842) test_match_date: .: (0.006739) test_match_description: .: (0.014198) test_match_evalue: .: (0.007082) test_match_go_terms: .: (0.006791) test_match_ipr_description: .: (0.007804) test_match_ipr_id: .: (0.007100) test_match_match_end: .: (0.006891) test_match_match_start: .: (0.007323) test_match_method: .: (0.006756) test_match_query_id: .: (0.006218) test_match_query_length: .: (0.006618) test_match_status: .: (0.006014) test_obj: .: (0.006201) test_query_id: .: (0.010259) test_query_length: .: (0.006640) test_self_reports_in_raw: .: (0.013037) Bio::TestIprscanReport: test_output_raw: .: (0.002165) test_to_raw: .: (0.001463) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.002404) test_match_accession: .: (0.001392) test_match_date: .: (0.001536) test_match_description: .: (0.001371) test_match_evalue: .: (0.002180) test_match_go_terms: .: (0.001440) test_match_ipr_description: .: (0.001524) test_match_ipr_id: .: (0.001393) test_match_match_end: .: (0.001793) test_match_match_start: .: (0.001556) test_match_method: .: (0.001332) test_match_status: .: (0.001448) test_matches_size: .: (0.001836) test_query_id: .: (0.001366) test_query_length: .: (0.001335) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.002700) test_to_hash_match?: .: (0.001964) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.004370) Bio::TestKeggCompound: test_comment: .: (0.001293) test_dblinks_as_hash: .: (0.000962) test_dblinks_as_strings: .: (0.000788) test_entry_id: .: (0.000960) test_enzymes: .: (0.002009) test_formula: .: (0.000918) test_kcf: .: (0.000771) test_mass: .: (0.000770) test_name: .: (0.000827) test_names: .: (0.000812) test_pathways_as_hash: .: (0.001615) test_pathways_as_strings: .: (0.001260) test_reactions: .: (0.001786) test_remark: .: (0.000824) test_rpairs: .: (0.000751) Bio::TestKeggEnzyme: test_all_reac: .: (0.001828) test_classes: .: (0.001645) test_cofactors: .: (0.001099) test_comment: .: (0.001269) test_dblinks_as_hash: .: (0.001302) test_dblinks_as_strings: .: (0.001284) test_diseases: .: (0.001061) test_entry: .: (0.001941) test_entry_id: .: (0.001332) test_genes: .: (0.044646) test_genes_as_hash: .: (0.041789) test_genes_as_strings: .: (0.013078) test_inhibitors: .: (0.001272) test_iubmb_reactions: .: (0.001385) test_kegg_reactions: .: (0.001338) test_motifs: .: (0.001087) test_name: .: (0.001536) test_names: .: (0.002364) test_obsolete?: .: (0.001355) test_orthologs_as_hash: .: (0.001232) test_orthologs_as_strings: .: (0.001079) test_pathways_as_hash: .: (0.001655) test_pathways_as_strings: .: (0.001952) test_products: .: (0.001622) test_reaction: .: (0.001159) test_structures: .: (0.001642) test_substrates: .: (0.001137) test_sysname: .: (0.001085) Bio::TestKeggGenesDblinks: test_data: .: (0.001257) test_dblinks_0: .: (0.000440) test_dblinks_1: .: (0.000395) test_dblinks_2: .: (0.000393) Bio::TestKeggGenesStructure: test_data: .: (0.000745) test_ids: .: (0.000747) test_ids_in_array: .: (0.000503) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.028791) test_graphics__size: .: (0.037481) test_id: .: (0.028824) test_link: .: (0.031066) test_name: .: (0.028189) test_reaction: .: (0.144774) test_type: .: (0.026883) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.027376) test_graphics__size: .: (0.027048) test_id: .: (0.026951) test_link: .: (0.027948) test_name: .: (0.026894) test_reaction: .: (0.026777) test_type: .: (0.029210) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.026497) test_category: .: (0.026269) test_entry_id: .: (0.026059) test_fgcolor=: .: (0.026295) test_height=: .: (0.026658) test_label=: .: (0.025784) test_shape=: .: (0.028748) test_width=: .: (0.026728) test_x=: .: (0.027076) test_y=: .: (0.026133) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.025803) test_graphics__size: .: (0.026681) test_id: .: (0.025860) test_link: .: (0.026088) test_name: .: (0.029515) test_reaction: .: (0.026515) test_type: .: (0.026371) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000708) test_graphics=: .: (0.000329) test_id=: .: (0.000362) test_link=: .: (0.000703) test_name=: .: (0.000406) test_reaction=: .: (0.000331) test_type=: .: (0.000323) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000766) test_category=: .: (0.000430) test_entry_id=: .: (0.000406) test_fgcolor=: .: (0.000459) test_height=: .: (0.000397) test_label=: .: (0.000455) test_pathway=: .: (0.000822) test_shape=: .: (0.000429) test_width=: .: (0.000393) test_x=: .: (0.000596) test_y=: .: (0.000409) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.025995) test_coords: .: (0.026791) test_fgcolor: .: (0.025764) test_height: .: (0.025885) test_name: .: (0.029014) test_type: .: (0.026886) test_width: .: (0.026098) test_x: .: (0.025907) test_y: .: (0.025965) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.026983) test_coords: .: (0.025987) test_fgcolor: .: (0.028257) test_height: .: (0.026841) test_name: .: (0.026221) test_type: .: (0.026175) test_width: .: (0.026224) test_x: .: (0.026366) test_y: .: (0.026065) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000722) test_coords=: .: (0.000390) test_fgcolor=: .: (0.000343) test_height=: .: (0.000311) test_name=: .: (0.000330) test_type=: .: (0.000342) test_width=: .: (0.000330) test_x=: .: (0.000323) test_y=: .: (0.000322) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.028813) test_entries__size: .: (0.027136) test_image: .: (0.026213) test_link: .: (0.026281) test_name: .: (0.026288) test_number: .: (0.026404) test_org: .: (0.025833) test_reactions=: .: (0.026254) test_reactions__size: .: (0.029136) test_relations=: .: (0.026904) test_relations__size: .: (0.026407) test_title: .: (0.025969) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.051642) test_name: .: (0.054450) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000801) test_initialize_0: .: (0.000267) test_initialize_1: .: (0.000303) test_initialize_2: .: (0.000300) test_name=: .: (0.000368) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.027530) test_name: .: (0.026584) test_products: .: (0.026594) test_substrates: .: (0.026360) test_type: .: (0.026355) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000827) test_name=: .: (0.000367) test_products=: .: (0.000347) test_substraces=: .: (0.000371) test_type=: .: (0.000365) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000738) test_entry_id=: .: (0.000428) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.025847) test_entry2: .: (0.029160) test_name: .: (0.025715) test_type: .: (0.026548) test_value: .: (0.025665) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000655) test_node1=: .: (0.000414) test_node2=: .: (0.000397) test_rel=: .: (0.000406) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000674) test_entry2=: .: (0.000888) test_name=: .: (0.000349) test_type=: .: (0.000340) test_value=: .: (0.000340) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.051255) test_name: .: (0.053607) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000740) test_initialize_0: .: (0.000260) test_initialize_1: .: (0.000272) test_initialize_2: .: (0.000279) test_name=: .: (0.000373) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000712) test_initialize_0: .: (0.000814) test_initialize_1: .: (0.000287) test_initialize_2: .: (0.000274) test_name=: .: (0.000356) Bio::TestKeggModule: test_compounds: .: (0.001484) test_compounds_as_hash: .: (0.000873) test_compounds_as_strings: .: (0.000720) test_definition: .: (0.000882) test_entry_id: .: (0.000630) test_keggclass: .: (0.001008) test_name: .: (0.000677) test_new: .: (0.000563) test_orthologs: .: (0.000968) test_orthologs_as_array: .: (0.000921) test_orthologs_as_hash: .: (0.000818) test_orthologs_as_strings: .: (0.000676) test_pathways: .: (0.000725) test_pathways_as_hash: .: (0.000608) test_pathways_as_strings: .: (0.000953) test_reactions: .: (0.000808) test_reactions_as_hash: .: (0.000955) test_reactions_as_strings: .: (0.000718) Bio::TestKeggOrthology: test_dblinks: .: (0.001515) test_dblinks_as_hash: .: (0.001154) test_dblinks_as_strings: .: (0.000929) test_definition: .: (0.001476) test_entry_id: .: (0.001075) test_genes_as_hash: .: (0.034870) test_genes_as_strings: .: (0.011239) test_keggclass: .: (0.001452) test_keggclasses: .: (0.001885) test_modules: .: (0.001109) test_modules_as_hash: .: (0.001089) test_modules_as_strings: .: (0.000940) test_name: .: (0.001000) test_names: .: (0.001161) test_pathways_as_strings: .: (0.000987) test_pathways_in_keggclass: .: (0.001262) test_references: .: (0.002086) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.001034) test_compounds_as_strings: .: (0.000574) test_dblinks_as_hash: .: (0.000694) test_dblinks_as_strings: .: (0.000606) test_description: .: (0.000681) test_diseases_as_hash: .: (0.000586) test_diseases_as_strings: .: (0.000581) test_entry_id: .: (0.000672) test_enzymes_as_strings: .: (0.000681) test_genes_as_hash: .: (0.000575) test_genes_as_strings: .: (0.000584) test_keggclass: .: (0.000666) test_ko_pathway: .: (0.000789) test_modules_as_hash: .: (0.000857) test_modules_as_strings: .: (0.000637) test_name: .: (0.000663) test_organism: .: (0.000626) test_orthologs_as_hash: .: (0.000748) test_orthologs_as_strings: .: (0.001079) test_pathways_as_hash: .: (0.000647) test_pathways_as_strings: .: (0.000590) test_reactions_as_hash: .: (0.000570) test_reactions_as_strings: .: (0.000592) test_references: .: (0.000599) test_rel_pathways_as_hash: .: (0.000749) test_rel_pathways_as_strings: .: (0.000654) Bio::TestKeggReaction: test_definition: .: (0.001371) test_entry_id: .: (0.001201) test_enzymes: .: (0.000791) test_equation: .: (0.000663) test_name: .: (0.000764) test_orthologs_as_hash: .: (0.000848) test_orthologs_as_strings: .: (0.000692) test_pathways_as_hash: .: (0.000725) test_pathways_as_strings: .: (0.000818) test_rpairs_as_hash: .: (0.000831) test_rpairs_as_strings: .: (0.001295) test_rpairs_as_tokens: .: (0.000786) Bio::TestLasergene: test_methods: .: (0.018790) Bio::TestLocations: test_complement: .: (0.001100) test_hat: .: (0.000456) test_normal: .: (0.000396) test_replace_single_base: .: (0.000358) test_should_not_modify_argument: .: (0.000329) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.017223) test_locations_to_s: .: (0.005363) Bio::TestMEDLINE: test_authors: .: (0.002308) test_authors_with_last_name_all_caps: .: (0.000368) test_authors_with_suffix: .: (0.000362) Bio::TestMEDLINE_20146148: test_ab: .: (0.002459) test_ad: .: (0.001162) test_au: .: (0.001085) test_authors: .: (0.002075) test_doi: .: (0.001247) test_dp: .: (0.001264) test_ip: .: (0.001134) test_mh: .: (0.001870) test_pages: .: (0.001465) test_pg: .: (0.001115) test_pii: .: (0.001121) test_pmid: .: (0.001271) test_pt: .: (0.002586) test_reference: .: (0.001942) test_self_new: .: (0.001125) test_so: .: (0.002069) test_ta: .: (0.001366) test_ti: .: (0.001283) test_ui: .: (0.001122) test_vi: .: (0.001920) test_year: .: (0.001492) Bio::TestMapSimple: test_attributes: .: (0.000912) Bio::TestMapping: test_add_mapping_as_map: .: (0.000942) test_add_mapping_as_marker: .: (0.000682) test_contains_marker?: .: (0.000416) test_mapped_to?: .: (0.000394) test_mapping_location_comparison: .: (0.001824) test_mappings_as_map_each: .: (0.000572) test_mappings_as_marker_each: .: (0.000550) test_mappings_on: .: (0.000539) test_multiple_mappings_between_same_marker_and_map: .: (0.001056) test_positions_on: .: (0.000593) test_raise_error_kind_of: .: (0.001379) Bio::TestMast: test_check_options_with_empty_opts: .: (0.001764) test_check_options_with_invalid_opts: .: (0.000946) test_check_options_with_valid_opts: .: (0.000523) test_command_to_be_run: .: (0.000528) test_config_defaults: .: (0.000416) test_minimal_config: .: (0.000446) test_more_config: .: (0.000418) test_run: .: (0.000291) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.001382) test_report_has_motifs: .: (0.000750) Bio::TestModel: test_addChain: .: (0.001436) test_comp: .: (0.000432) test_each: .: (0.000351) test_each_chain: .: (0.000328) test_inspect: .: (0.000314) test_rehash: .: (0.000274) test_square_brace: .: (0.000307) test_to_s: .: (0.000317) Bio::TestModelFinder: test_find_model: .: (0.000717) Bio::TestMotif: test_creation_and_attributes: .: (0.000734) test_length: .: (0.000279) Bio::TestMyGraph: test_cliquishness: .: (0.002270) Bio::TestNA: test_accessor: .: (0.000583) test_na: .: (0.000264) test_name: .: (0.000266) test_names: .: (0.000256) test_to_re: .: (0.000857) test_weight: .: (0.000336) test_weight_rna: .: (0.000313) Bio::TestNAConstants: test_NAMES: .: (0.000565) test_NAMES_1_to_name: .: (0.000277) test_WEIGHT: .: (0.000297) Bio::TestNATranslate: test_translate: .: (0.001995) test_translate_1: .: (0.000514) test_translate_2: .: (0.000330) test_translate_3: .: (0.000320) test_translate_4: .: (0.000542) test_translate_5: .: (0.000523) test_translate_6: .: (0.000332) Bio::TestNCBIDB: test_fetch: .: (0.000765) test_p_entry2hash: .: (0.000243) test_p_subtag2array: .: (0.000236) test_p_toptag2array: .: (0.000231) Bio::TestNewick: test_reparse: .: (0.004718) test_reparse_before_lazy_parsing: .: (0.001196) test_string_tree: .: (0.002139) Bio::TestNewick2: test_string_tree: .: (0.001919) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.001658) test_parse_newick_leaf: .: (0.000605) test_parse_newick_tokenize: .: (0.000989) Bio::TestNexus: test_nexus: .: (0.035026) Bio::TestOSLine: test_period_trancation_O63147: .: (0.001432) test_uncapitalized_letter_Q32725_9POAL: .: (0.000476) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000671) test_load_parameters: .: (0.000373) test_parameters: .: (0.000273) test_set_default_parameters: .: (0.000530) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.001824) test_expected_parameters_set_in_control_file: .: (0.001784) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000793) test_new_with_parameters: .: (0.000356) test_new_with_two_argument: .: (0.000347) test_new_without_argument: .: (0.000313) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.005212) test_rates_hundred_and_fiftieth_position: .: (0.004752) test_rates_last_position: .: (0.004780) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.016307) test_tree: .: (0.015880) test_tree_length: .: (0.015891) test_tree_log_likelihood: .: (0.015837) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.001340) test_parameters_should_be_loaded_from_control: .: (0.001326) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.003430) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000894) test_dN_dS: .: (0.000487) test_kappa: .: (0.000479) test_lnL: .: (0.000443) test_m3_classes: .: (0.000714) test_m3_lnL: .: (0.000645) test_m3_to_s: .: (0.000446) test_m3_tree: .: (0.001766) test_omega: .: (0.000576) test_to_s: .: (0.000571) test_tree: .: (0.001195) test_tree_length: .: (0.000454) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.001547) test_p: .: (0.001005) test_position: .: (0.001387) test_probability: .: (0.000945) test_w: .: (0.000975) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.012222) test_graph_omega: .: (0.001361) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.001044) test_footer: .: (0.000475) test_header: .: (0.001275) test_initialize: .: (0.000492) test_models: .: (0.000671) test_nb_sites: .: (0.001724) test_num_codons: .: (0.000506) test_num_sequences: .: (0.000487) test_significant: .: (0.000643) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.001933) test_nb_sites: .: (0.000723) test_significant: .: (0.000607) test_sites: .: (0.004066) Bio::TestPDB: test_accession: .: (0.003550) test_addModel: .: (0.003088) test_authors: .: (0.002376) test_bracket: .: (0.003380) test_classification: .: (0.002428) test_dbref: .: (0.003308) test_definition: .: (0.002599) test_each: .: (0.003190) test_each_model: .: (0.002444) test_entry_id: .: (0.002905) test_helix: .: (0.003099) test_inspect: .: (0.003118) test_jrnl: .: (0.002405) test_keywords: .: (0.002364) test_record: .: (0.002836) test_remark: .: (0.003135) test_seqres: .: (0.003673) test_sheet: .: (0.004689) test_ssbond: .: (0.002557) test_to_s: .: (0.004365) test_turn: .: (0.002286) test_version: .: (0.003256) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.001005) test_U12: .: (0.000456) test_U13: .: (0.000424) test_U22: .: (0.000416) test_U23: .: (0.000414) test_U33: .: (0.000425) test_altLoc: .: (0.000422) test_chainID: .: (0.000432) test_charge: .: (0.000420) test_element: .: (0.000406) test_iCode: .: (0.000417) test_name: .: (0.000415) test_resName: .: (0.001135) test_resSeq: .: (0.000437) test_segID: .: (0.000410) test_serial: .: (0.000401) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000830) test_anisou: .: (0.000295) test_chainID: .: (0.000292) test_charge: .: (0.000474) test_comparable: .: (0.000398) test_do_parse: .: (0.000319) test_element: .: (0.000298) test_iCode: .: (0.000306) test_name: .: (0.000301) test_occupancy: .: (0.001074) test_original_data: .: (0.000495) test_record_name: .: (0.000307) test_resName: .: (0.000298) test_resSeq: .: (0.000299) test_residue: .: (0.000302) test_segID: .: (0.000304) test_serial: .: (0.000295) test_sigatm: .: (0.000295) test_tempFactor: .: (0.000417) test_ter: .: (0.000368) test_to_a: .: (0.000334) test_to_s: .: (0.000422) test_x: .: (0.000411) test_xyz: .: (0.000441) test_y: .: (0.000591) test_z: .: (0.000960) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000759) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000651) test_idcode: .: (0.000317) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000834) test_chainID2: .: (0.000416) test_icode1: .: (0.000408) test_icode2: .: (0.000420) test_measure: .: (0.000417) test_modNum: .: (0.000409) test_pep1: .: (0.000411) test_pep2: .: (0.001127) test_seqNum1: .: (0.000427) test_seqNum2: .: (0.000406) test_serNum: .: (0.000421) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.008982) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000859) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000713) test_alpha: .: (0.000360) test_b: .: (0.000350) test_beta: .: (0.000386) test_c: .: (0.000370) test_gamma: .: (0.000359) test_sGroup: .: (0.001040) test_z: .: (0.000358) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000898) test_database: .: (0.000506) test_dbAccession: .: (0.000496) test_dbIdCode: .: (0.000519) test_dbseqBegin: .: (0.000504) test_dbseqEnd: .: (0.000502) test_idCode: .: (0.000534) test_idbnsBeg: .: (0.000518) test_insertBegin: .: (0.000535) test_insertEnd: .: (0.001052) test_seqBegin: .: (0.000476) test_seqEnd: .: (0.000494) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000725) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000608) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000654) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000729) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000689) test_depDate: .: (0.000373) test_idCode: .: (0.000354) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.001780) test_hetID: .: (0.000407) test_iCode: .: (0.000410) test_numHetAtoms: .: (0.000403) test_seqNum: .: (0.000512) test_text: .: (0.000433) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000715) test_anisou: .: (0.000338) test_chainID: .: (0.000321) test_charge: .: (0.000294) test_comparable: .: (0.000408) test_do_parse: .: (0.000350) test_element: .: (0.000367) test_iCode: .: (0.000480) test_name: .: (0.000394) test_occupancy: .: (0.001074) test_original_data: .: (0.000418) test_record_name: .: (0.000310) test_resName: .: (0.008516) test_resSeq: .: (0.000456) test_residue: .: (0.000324) test_segID: .: (0.000319) test_serial: .: (0.000312) test_sigatm: .: (0.000322) test_tempFactor: .: (0.000472) test_ter: .: (0.000323) test_to_a: .: (0.000586) test_to_s: .: (0.000473) test_x: .: (0.000504) test_xyz: .: (0.000420) test_y: .: (0.010731) test_z: .: (0.000559) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.022594) test_ChainH: .: (0.000733) test_ICode1: .: (0.019923) test_altLoc1: .: (0.000737) test_altLoc2: .: (0.000562) test_altLocH: .: (0.013290) test_chainID2: .: (0.000685) test_iCode2: .: (0.000546) test_iCodeH: .: (0.017838) test_name1: .: (0.000569) test_name2: .: (0.000528) test_nameH: .: (0.017945) test_resName1: .: (0.000617) test_resName2: .: (0.013732) test_resSeq1: .: (0.004880) test_resSeq2: .: (0.010264) test_resSeqH: .: (0.000736) test_sym1: .: (0.010896) test_sym2: .: (0.018095) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000835) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000805) test_altLoc2: .: (0.004785) test_chainID1: .: (0.000476) test_chainID2: .: (0.000467) test_iCode1: .: (0.000482) test_iCode2: .: (0.000498) test_name1: .: (0.000493) test_name2: .: (0.000531) test_resName1: .: (0.000498) test_resName2: .: (0.001151) test_resSeq1: .: (0.000456) test_resSeq2: .: (0.000432) test_sym1: .: (0.000689) test_sym2: .: (0.000479) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000765) test_numCoord: .: (0.000345) test_numHelix: .: (0.000333) test_numHet: .: (0.000335) test_numRemark: .: (0.000536) test_numSeq: .: (0.000346) test_numSheet: .: (0.000340) test_numSite: .: (0.000335) test_numTer: .: (0.000333) test_numTurn: .: (0.001126) test_numXform: .: (0.000545) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000703) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000732) test_comment: .: (0.000395) test_iCode: .: (0.000385) test_idCode: .: (0.000669) test_resName: .: (0.000438) test_seqNum: .: (0.000417) test_stdRes: .: (0.000405) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000776) test_Mn2: .: (0.000339) test_Mn3: .: (0.001080) test_Vn: .: (0.000350) test_iGiven: .: (0.000331) test_serial: .: (0.000315) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000684) test_Mn2: .: (0.000388) test_Mn3: .: (0.000335) test_Vn: .: (0.000329) test_iGiven: .: (0.000342) test_serial: .: (0.000341) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000771) test_Mn2: .: (0.004731) test_Mn3: .: (0.000427) test_Vn: .: (0.000339) test_iGiven: .: (0.000352) test_serial: .: (0.000337) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.001182) test_rIdCode: .: (0.000360) test_repDate: .: (0.000324) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000650) test_On2: .: (0.000298) test_On3: .: (0.000288) test_Tn: .: (0.000470) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000700) test_modId: .: (0.000383) test_modNum: .: (0.000350) test_modType: .: (0.000377) test_record: .: (0.000393) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.001733) test_text: .: (0.000331) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000670) test_Sn2: .: (0.000315) test_Sn3: .: (0.000304) test_Un: .: (0.000322) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000643) test_Sn2: .: (0.000312) test_Sn3: .: (0.000318) test_Un: .: (0.000304) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000626) test_Sn2: .: (0.000355) test_Sn3: .: (0.000314) test_Un: .: (0.000316) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.001206) test_conflict: .: (0.000417) test_database: .: (0.000625) test_dbIdCode: .: (0.000454) test_dbRes: .: (0.000417) test_dbSeq: .: (0.000414) test_iCode: .: (0.000416) test_idCode: .: (0.000413) test_resName: .: (0.000406) test_seqNum: .: (0.004908) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000843) test_numRes: .: (0.000432) test_resName: .: (0.000470) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000931) test_curChainId: .: (0.000545) test_curICode: .: (0.000532) test_curResName: .: (0.000534) test_curResSeq: .: (0.000781) test_endChainID: .: (0.000590) test_endICode: .: (0.000565) test_endResName: .: (0.000544) test_endSeqNum: .: (0.001141) test_initChainID: .: (0.000606) test_initICode: .: (0.000533) test_initResName: .: (0.000514) test_initSeqNum: .: (0.000580) test_numStrands: .: (0.000553) test_prevAtom: .: (0.000681) test_prevChainId: .: (0.000572) test_prevICode: .: (0.000620) test_prevResName: .: (0.000540) test_prevResSeq: .: (0.000558) test_sense: .: (0.001293) test_sheetID: .: (0.000533) test_strand: .: (0.000557) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000921) test_chainID: .: (0.000584) test_charge: .: (0.000484) test_element: .: (0.000466) test_iCode: .: (0.000483) test_name: .: (0.000450) test_resName: .: (0.000451) test_resSeq: .: (0.000430) test_segID: .: (0.004824) test_serial: .: (0.001078) test_sigOcc: .: (0.000455) test_sigTemp: .: (0.000450) test_sigX: .: (0.000451) test_sigY: .: (0.000553) test_sigZ: .: (0.000446) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000879) test_SigmaU12: .: (0.000438) test_SigmaU13: .: (0.000435) test_SigmaU22: .: (0.000459) test_SigmaU23: .: (0.000451) test_SigmaU33: .: (0.000433) test_altLoc: .: (0.000454) test_chainID: .: (0.000426) test_charge: .: (0.001071) test_element: .: (0.008896) test_iCode: .: (0.000537) test_name: .: (0.000469) test_resName: .: (0.000460) test_resSeq: .: (0.000585) test_segID: .: (0.000492) test_serial: .: (0.000432) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000912) test_chainID2: .: (0.000460) test_chainID3: .: (0.000457) test_chainID4: .: (0.000454) test_iCode1: .: (0.001095) test_iCode2: .: (0.000474) test_iCode3: .: (0.000451) test_iCode4: .: (0.000442) test_numRes: .: (0.000436) test_resName1: .: (0.000442) test_resName2: .: (0.000805) test_resName3: .: (0.000534) test_resName4: .: (0.000499) test_seq1: .: (0.000511) test_seq2: .: (0.000500) test_seq3: .: (0.000566) test_seq4: .: (0.000510) test_seqNum: .: (0.001128) test_siteID: .: (0.000500) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000882) test_altLoc2: .: (0.000424) test_atom1: .: (0.000405) test_atom2: .: (0.000406) test_chainID1: .: (0.000411) test_chainID2: .: (0.000404) test_iCode1: .: (0.000409) test_iCode2: .: (0.000445) test_resName1: .: (0.000388) test_resName2: .: (0.000391) test_resSeq1: .: (0.000386) test_resSeq2: .: (0.000388) test_sym1: .: (0.000990) test_sym2: .: (0.008638) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000916) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000677) test_sIdCode: .: (0.000355) test_sprsdeDate: .: (0.000375) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000755) test_iCode: .: (0.000395) test_resName: .: (0.000370) test_resSeq: .: (0.000364) test_serial: .: (0.000370) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000706) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.001214) test_t1: .: (0.000378) test_t2: .: (0.000363) test_t3: .: (0.000353) test_text: .: (0.008656) Bio::TestPROSITE: test_ac: .: (0.004571) test_cc: .: (0.004068) test_de: .: (0.003752) test_division: .: (0.012563) test_dr: .: (0.056125) test_dt: .: (0.008617) test_false_neg: .: (0.004175) test_false_pos: .: (0.012167) test_false_positive_sequences: .: (0.009011) test_list_falsenegative: .: (0.044150) test_list_falsepositive: .: (0.048214) test_list_potentialhit: .: (0.048173) test_list_truepositive: .: (0.049309) test_list_unknown: .: (0.045657) test_list_xref: .: (0.039318) test_ma: .: (0.004011) test_max_repeat: .: (0.004024) test_name: .: (0.003883) test_nr: .: (0.004343) test_pa: .: (0.004209) test_pa2re: .: (0.004337) test_partial: .: (0.004247) test_pdb_xref: .: (0.004142) test_pdoc_xref: .: (0.004045) test_positive: .: (0.004385) test_positive_hits: .: (0.004237) test_positive_sequences: .: (0.004387) test_release: .: (0.004477) test_ru: .: (0.004160) test_self_pa2re: .: (0.004196) test_site: .: (0.004169) test_skip_flag: .: (0.004256) test_swissprot_release_number: .: (0.004278) test_swissprot_release_sequences: .: (0.004408) test_taxon_range: .: (0.004330) test_total: .: (0.004305) test_total_hits: .: (0.004175) test_total_sequences: .: (0.004407) test_unknown: .: (0.004422) test_unknown_hits: .: (0.004334) test_unknown_sequences: .: (0.004527) Bio::TestPROSITEConst: test_delimiter: .: (0.000766) test_tagsize: .: (0.000252) Bio::TestPTS1: test_function_set: .: (0.000747) test_function_set_number_1: .: (0.000494) test_function_set_number_2: .: (0.000320) test_function_set_number_3: .: (0.000391) test_function_show: .: (0.000295) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000598) Bio::TestPTS1New: test_fungi: .: (0.000656) test_general: .: (0.000340) test_metazoa: .: (0.000362) Bio::TestQualifier: test_qualifier: .: (0.000571) test_value: .: (0.000322) Bio::TestREBASE: test_methods: .: (0.002957) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.002689) test_bit_score: .: (0.001763) test_evalue: .: (0.001876) test_gaps: .: (0.001818) test_hit_from: .: (0.002066) test_hit_to: .: (0.001850) test_hseq: .: (0.001985) test_identity: .: (0.001781) test_midline: .: (0.010811) test_percent_identity: .: (0.002033) test_positive: .: (0.001724) test_qseq: .: (0.001968) test_query_from: .: (0.001870) test_query_to: .: (0.002617) test_score: .: (0.001779) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.002107) test_hits_size: .: (0.005885) test_iterations_size: .: (0.003665) test_program: .: (0.001627) test_query_def: .: (0.003672) test_query_len: .: (0.005362) test_version: .: (0.001664) test_version_date: .: (0.001451) test_version_number: .: (0.001465) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.004178) test_definition: .: (0.001949) test_evalue: .: (0.001968) test_hsps_size: .: (0.001627) test_identity: .: (0.003351) test_lap_at: .: (0.002396) test_len: .: (0.001640) test_midline: .: (0.001912) test_overlap: .: (0.001888) test_query_end: .: (0.004052) test_query_seq: .: (0.002199) test_query_start: .: (0.002058) test_target_def: .: (0.001923) test_target_end: .: (0.003252) test_target_len: .: (0.002207) test_target_seq: .: (0.002237) test_target_start: .: (0.002087) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.002288) test_get_entry: .: (0.001619) test_rewind: .: (0.000385) test_skip_leader: .: (0.000636) Bio::TestReference: test_abstract: .: (0.000640) test_affiliations: .: (0.000304) test_authors: .: (0.000292) test_format_bibitem: .: (0.000612) test_format_bibtex: .: (0.000758) test_format_bibtex_with_arguments: .: (0.000651) test_format_cell: .: (0.002135) test_format_current: .: (0.000420) test_format_endnote: .: (0.000411) test_format_general: .: (0.000416) test_format_genome_biol: .: (0.000423) test_format_genome_res: .: (0.000372) test_format_nar: .: (0.000361) test_format_nature: .: (0.000584) test_format_rd: .: (0.000432) test_format_science: .: (0.000578) test_format_trends: .: (0.000323) test_issue: .: (0.001605) test_journal: .: (0.000464) test_mesh: .: (0.000320) test_pages: .: (0.000285) test_pubmed: .: (0.000292) test_pubmed_url: .: (0.000305) test_url: .: (0.000283) test_volume: .: (0.000286) test_year: .: (0.000261) Bio::TestReference_noURL: test_format_endnote: .: (0.000846) test_url: .: (0.000310) Bio::TestReferences: test_append: .: (0.000808) test_each: .: (0.002394) Bio::TestRelation: test_comparison_operator: .: (0.000861) test_uniq: .: (0.000450) Bio::TestResidue: test_addAtom: .: (0.001072) test_each: .: (0.000628) test_each_atom: .: (0.000567) test_get_residue_id_from_atom: .: (0.000532) test_het_atom: .: (0.000602) test_iCode: .: (0.000534) test_inspect: .: (0.000868) test_resSeq: .: (0.000664) test_sort: .: (0.000601) test_square_bracket: .: (0.000529) test_to_s: .: (0.000740) test_update_resudue_id: .: (0.000488) Bio::TestResidueFinder: test_each_residue: .: (0.001991) test_find_residue: .: (0.000427) test_residues: .: (0.000417) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.339504) test_cut_from_bio_sequence_na: .: (0.119789) test_cut_without_permutations: .: (0.072067) test_view_ranges: .: (0.071562) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.004468) test_cuts_after_remove_incomplete_cuts: .: (0.002006) test_strands_for_display: .: (0.012830) test_strands_for_display_current: .: (0.002279) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.002477) test_fragments_for_display_1: .: (0.002860) test_fragments_for_display_10: .: (0.002756) test_fragments_for_display_2: .: (0.003156) test_fragments_for_display_3: .: (0.004689) test_fragments_for_display_4: .: (0.003437) test_fragments_for_display_5: .: (0.002170) test_fragments_for_display_6: .: (0.002498) test_fragments_for_display_7: .: (0.002219) test_fragments_for_display_8: .: (0.002020) test_fragments_for_display_9: .: (0.002357) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.001355) test_obj_3: .: (0.000811) test_obj_7: .: (0.000674) test_obj_z: .: (0.000714) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.001714) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000934) test_bracket_eq: .: (0.000502) test_concat: .: (0.000570) test_delete: .: (0.000430) test_dup: .: (0.000541) test_each: .: (0.000537) test_eqeq: .: (0.000373) test_eqeq_false: .: (0.000342) test_eqeq_other: .: (0.000308) test_eqeq_self: .: (0.000452) test_include?: .: (0.000735) test_internal_data: .: (0.000331) test_internal_data_eq: .: (0.000353) test_length: .: (0.000313) test_ltlt: .: (0.000333) test_ltlt_larger: .: (0.000330) test_ltlt_middle: .: (0.000325) test_plus: .: (0.000568) test_plus_error: .: (0.000550) test_push: .: (0.000405) test_reverse_each: .: (0.000542) test_self_bracket: .: (0.000348) test_self_new: .: (0.000434) test_size: .: (0.000340) test_sort!: .: (0.000328) test_to_a: .: (0.000368) test_uniq!: .: (0.000295) test_unshift: .: (0.000518) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.015154) test_complement: .: (0.014189) test_complement_with_cut_symbols: .: (0.014143) test_cut_locations: .: (0.013386) test_cut_locations_in_enzyme_notation: .: (0.013740) test_primary: .: (0.014217) test_primary_with_cut_symbols: .: (0.014229) test_to_re: .: (0.013819) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.003379) test_align_with_cuts: .: (0.002481) test_argument_error: .: (0.003676) test_ds: .: (0.002818) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.001618) test_complement: .: (0.000594) test_contents: .: (0.000587) test_primary: .: (0.000554) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.001264) test_complement: .: (0.001005) test_contents: .: (0.000609) test_primary: .: (0.000574) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000996) test_contents: .: (0.000549) test_primary: .: (0.000571) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.001123) test_complement_to_array_index: .: (0.000963) test_complement_to_array_index_class: .: (0.000752) test_contents: .: (0.000887) test_primary: .: (0.000538) test_primary_to_array_index: .: (0.000742) test_primary_to_array_index_class: .: (0.000761) test_to_array_index: .: (0.001487) test_to_array_index_class: .: (0.001426) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.001298) test_rebase: .: (0.000426) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.003736) test_creation_with_no_cuts: .: (0.002052) test_cut_locations: .: (0.001844) test_cut_locations_in_enzyme_notation: .: (0.002077) test_orientation: .: (0.001377) test_pattern: .: (0.001739) test_pattern_palindromic?: .: (0.002433) test_stripped: .: (0.001860) test_to_re: .: (0.001434) test_with_cut_symbols: .: (0.001909) test_with_spaces: .: (0.001961) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.003376) test_creation_with_no_cuts: .: (0.002285) test_cut_locations: .: (0.001788) test_cut_locations_in_enzyme_notation: .: (0.001852) test_orientation: .: (0.001428) test_pattern: .: (0.002006) test_pattern_palindromic?: .: (0.002175) test_stripped: .: (0.001857) test_to_re: .: (0.001818) test_with_cut_symbols: .: (0.001814) test_with_spaces: .: (0.001756) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.002185) test_initialize_with_pattern: .: (0.001230) test_max: .: (0.000467) test_min: .: (0.000499) test_to_array_index: .: (0.000550) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000798) test_bracket_eq: .: (0.000432) test_concat: .: (0.000346) test_delete: .: (0.000309) test_dup: .: (0.000660) test_each: .: (0.000463) test_eqeq: .: (0.000292) test_eqeq_false: .: (0.000281) test_eqeq_other: .: (0.000252) test_eqeq_self: .: (0.000550) test_include?: .: (0.000445) test_internal_data_hash: .: (0.000301) test_internal_data_hash_eq: .: (0.000364) test_length: .: (0.000277) test_ltlt: .: (0.000322) test_ltlt_noeffect: .: (0.000311) test_plus: .: (0.000307) test_plus_error: .: (0.000464) test_private_push_element: .: (0.000322) test_private_push_element_intermediate: .: (0.000490) test_private_push_element_last: .: (0.000344) test_private_push_element_noeffect: .: (0.000306) test_private_sorted_keys: .: (0.000312) test_private_unshift_element: .: (0.000330) test_private_unshift_element_first: .: (0.000773) test_private_unshift_element_intermediate: .: (0.000325) test_private_unshift_element_noeffect: .: (0.000295) test_push: .: (0.000357) test_reverse_each: .: (0.000510) test_self_bracket: .: (0.000294) test_self_new: .: (0.000375) test_size: .: (0.000306) test_sort!: .: (0.000296) test_to_a: .: (0.000309) test_uniq!: .: (0.000286) test_unshift: .: (0.000525) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000747) test_left_padding: .: (0.000756) test_right_padding: .: (0.000373) test_strip_padding: .: (0.000384) Bio::TestSOFT: test_dataset: .: (0.023315) test_series: .: (0.023497) Bio::TestSOSUIReport: test_entry_id: .: (0.001036) test_prediction: .: (0.000481) test_tmh: .: (0.000474) test_tmhs: .: (0.000542) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000557) test_rs: .: (0.000271) Bio::TestSOSUITMH: test_grade: .: (0.001127) test_range: .: (0.000481) test_sequence: .: (0.000441) Bio::TestSampleGraph: test_bellman_ford: .: (0.001539) test_bfs_shortest_path: .: (0.000563) test_breadth_first_search: .: (0.000524) test_depth_first_search: .: (0.000907) test_dijkstra: .: (0.000701) test_dump_list: .: (0.001227) test_dump_matrix: .: (0.000885) test_extract_subgraph_by_label: .: (0.000569) test_extract_subgraph_by_list: .: (0.000591) test_extract_subgraph_retains_disconnected_nodes: .: (0.000620) test_small_world_aka_node_degree_histogram: .: (0.000505) test_to_matrix: .: (0.001064) test_to_matrix_fixed_index: .: (0.000759) test_undirected_cliquishness: .: (0.001185) Bio::TestScf_version_2: test_complement: .: (0.026097) test_seq: .: (0.025138) test_to_biosequence: .: (0.024690) Bio::TestScf_version_3: test_complement: .: (0.072964) test_seq: .: (0.071736) test_to_biosequence: .: (0.071825) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000891) test_AA_new_sequence_all_legal_symbols: .: (0.000311) test_AA_new_sequence_removes_whitespace: .: (0.000293) test_AA_new_sequence_upcases_symbols: .: (0.000284) test_DNA_new_blank_sequence: .: (0.000271) test_DNA_new_sequence_downcases_symbols: .: (0.000286) test_DNA_new_sequence_removes_whitespace: .: (0.000289) test_NA_randomize_with_counts: .: (0.002824) test_NA_randomize_with_counts_and_block: .: (0.003374) test_RNA_new_sequence: .: (0.000351) test_ambiguous_dna_sequence_complement: .: (0.000342) test_ambiguous_rna_sequence_complement: .: (0.000314) test_amino_acid_codes: .: (0.000421) test_amino_acid_molecular_weight: .: (0.000769) test_amino_acid_names: .: (0.000819) test_amino_acid_randomize_can_be_chained: .: (0.003831) test_amino_acid_randomize_has_same_composition: .: (0.001862) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.002372) test_dna_composition: .: (0.000424) test_dna_gc_percent: .: (0.000464) test_dna_molecular_weight: .: (0.000571) test_dna_pikachu: .: (0.000459) test_dna_sequence_complement: .: (0.000299) test_dna_sequence_translate: .: (0.001382) test_dna_to_re: .: (0.000534) test_element_reference_operator_with_one_argument: .: (0.000303) test_element_reference_operator_with_two_arguments: .: (0.000771) test_invalid_nucleic_acid_illegal_bases: .: (0.000421) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000411) test_nucleic_acid_names: .: (0.000326) test_randomize_dna_can_be_chained: .: (0.001145) test_randomize_dna_retains_composition: .: (0.001079) test_randomize_dna_with_block: .: (0.001388) test_rna_composition: .: (0.000386) test_rna_gc_percent: .: (0.000446) test_rna_molecular_weight: .: (0.000532) test_rna_pikachu: .: (0.000312) test_rna_sequence_complement: .: (0.000311) test_rna_sequence_translate: .: (0.001300) test_rna_to_re: .: (0.000539) test_total: .: (0.000365) test_two_consecutive_dna_randomizations_not_equal: .: (0.000996) test_valid_dna_sequence_illegal_bases: .: (0.000723) Bio::TestSequenceAA: test_codes: .: (0.000767) test_molecular_weight: .: (0.000516) test_names: .: (0.000331) test_to_re: .: (0.000652) test_to_s: .: (0.000267) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000836) Bio::TestSequenceAANew: test_new: .: (0.000563) test_new_n: .: (0.000292) test_new_r: .: (0.000263) test_new_t: .: (0.000413) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.001146) test_concat: .: (0.000319) test_push: .: (0.000291) test_seq: .: (0.000277) test_splicing: .: (0.000564) test_sum: .: (0.000296) test_to_s: .: (0.000291) test_to_str: .: (0.000276) test_total: .: (0.000312) test_window_search: .: (0.000946) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000608) test_normalize_A: .: (0.000311) test_normalize_a: .: (0.000284) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.003517) test_randomize_with_block: .: (0.013364) test_randomize_with_hash: .: (0.015197) test_randomize_with_hash_block: .: (0.017454) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/ruby-bio-2.0.4/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== : (0.003277) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/ruby-bio-2.0.4/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.003070) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000876) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000372) test_subseq_returns_subsequence: .: (0.000310) test_to_s_returns_self_as_string: .: (0.000372) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000690) test_window_search_with_width_3_step_two_with_residual: .: (0.000489) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000692) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.001246) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000946) test_na_self_randomize: .: (0.000518) Bio::TestSequenceDBLink: test_database: .: (0.000566) test_id: .: (0.000250) test_secondary_ids: .: (0.000260) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000713) test_parse_uniprot_DR_line: .: (0.000448) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.003564) test_output_width_35: .: (0.000929) test_output_width_nil: .: (0.001286) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.001630) test_output_after_adding_sequence: .: (0.001005) test_output_after_truncating_sequence: .: (0.000691) test_output_from_error_probabilities: .: (0.009389) test_output_width45: .: (0.000721) test_output_with_converting_score_phred2solexa: .: (0.002383) test_output_with_converting_score_solexa2phred: .: (0.000981) test_output_with_default_score: .: (0.000731) Bio::TestSequenceMasker: test_mask: .: (0.000857) test_mask_with_enumerator: .: (0.000657) test_mask_with_enumerator_empty_mask_char: .: (0.000476) test_mask_with_enumerator_excess: .: (0.001794) test_mask_with_enumerator_longer_mask_char: .: (0.000485) test_mask_with_enumerator_shorter: .: (0.000773) test_mask_with_error_probability: .: (0.000482) test_mask_with_quality_score: .: (0.000457) Bio::TestSequenceNA: test_at_content: .: (0.001416) test_at_skew: .: (0.001120) test_codon_usage: .: (0.000421) test_complement: .: (0.000330) test_dna: .: (0.000745) test_dna!: .: (0.000315) test_forward_complement: .: (0.000519) test_gc_content: .: (0.001075) test_gc_percent: .: (0.000596) test_gc_skew: .: (0.001250) test_iliegal_bases: .: (0.000337) test_molecular_weight: .: (0.000606) test_names: .: (0.000510) test_reverse_complement: .: (0.000567) test_rna: .: (0.000337) test_rna!: .: (0.000310) test_splicing: .: (0.000578) test_to_re: .: (0.000690) test_to_s: .: (0.000263) Bio::TestSequenceNACommon: test_composition: .: (0.000783) test_concat: .: (0.000281) test_push: .: (0.000265) test_seq: .: (0.000271) test_splicing: .: (0.000598) test_sum: .: (0.000292) test_to_s: .: (0.000262) test_to_str: .: (0.000283) test_total: .: (0.000313) test_window_search: .: (0.000841) Bio::TestSequenceNANew: test_new: .: (0.000750) test_new_n: .: (0.000324) test_new_r: .: (0.000290) test_new_t: .: (0.000289) Bio::TestSequenceNATranslation: test_translate: .: (0.001442) test_translate_0: .: (0.003347) test_translate_1: .: (0.001416) test_translate_2: .: (0.000832) test_translate_3: .: (0.000737) test_translate_4: .: (0.000853) test_translate_5: .: (0.000889) test_translate_6: .: (0.000849) test_translate_7: .: (0.002235) test_translate_given_codon_table: .: (0.124002) test_translate_n1: .: (0.002140) test_translate_n2: .: (0.002067) test_translate_n3: .: (0.001981) test_translate_unknown_o: .: (0.001466) test_translate_unknown_x: .: (0.000987) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000634) test_convert_scores_from_phred_to_solexa: .: (0.001493) test_convert_scores_from_solexa_to_phred: .: (0.000566) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000599) test_convert_scores_from_phred: .: (0.000264) test_convert_scores_from_phred_to_solexa: .: (0.001296) test_convert_scores_from_solexa: .: (0.000705) test_convert_scores_from_solexa_to_phred: .: (0.000903) test_convert_scores_to_phred: .: (0.000277) test_convert_scores_to_solexa: .: (0.001249) test_p2q: .: (0.000615) test_phred_p2q: .: (0.000456) test_phred_q2p: .: (0.017422) test_q2p: .: (0.017877) test_quality_score_type: .: (0.000323) test_self_convert_scores_to_solexa: .: (0.001543) test_self_p2q: .: (0.000521) test_self_q2p: .: (0.016313) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.001325) test_convert_scores_from_phred: .: (0.001556) test_convert_scores_from_phred_to_solexa: .: (0.001397) test_convert_scores_from_solexa: .: (0.000250) test_convert_scores_from_solexa_to_phred: .: (0.000524) test_convert_scores_to_phred: .: (0.000516) test_convert_scores_to_solexa: .: (0.000265) test_p2q: .: (0.000652) test_q2p: .: (0.018231) test_quality_score_type: .: (0.000352) test_self_convert_scores_to_phred: .: (0.000586) test_self_p2q: .: (0.000792) test_self_q2p: .: (0.022675) test_solexa_p2q: .: (0.000861) test_solexa_q2p: .: (0.020027) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000831) test_center: .: (0.000376) test_chomp: .: (0.000442) test_chop: .: (0.000416) test_delete: .: (0.000499) test_delete_prefix: .: (0.000414) test_delete_suffix: .: (0.000672) test_downcase: .: (0.000369) test_each_char: .: (0.000636) test_each_char_enum: .: (0.000714) test_each_grapheme_cluster: .: (0.001060) test_each_grapheme_cluster_enum: .: (0.000544) test_each_line: .: (0.000548) test_each_line_enum: .: (0.000485) test_gsub: .: (0.000642) test_gsub_with_block: .: (0.002089) test_ljust: .: (0.000365) test_lstrip: .: (0.000345) test_multiply: .: (0.000482) test_next: .: (0.000383) test_reverse: .: (0.000351) test_rjust: .: (0.000345) test_rstrip: .: (0.000340) test_slice: .: (0.000359) test_slice2: .: (0.000348) test_split: .: (0.000467) test_squeeze: .: (0.000520) test_strip: .: (0.000359) test_sub: .: (0.000405) test_sub_with_block: .: (0.001349) test_succ: .: (0.000351) test_swapcase: .: (0.000349) test_tr: .: (0.000488) test_tr_s: .: (0.000340) test_upcase: .: (0.000349) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000842) test_partition_nomatch: .: (0.000439) test_partition_sep_TSeq: .: (0.000431) test_partition_sep_regexp: .: (0.000622) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.001272) test_rpartition_nomatch: .: (0.000448) test_rpartition_sep_TSeq: .: (0.000431) test_rpartition_sep_regexp: .: (0.000592) Bio::TestShRNA: test_blocK_it: .: (0.227891) test_blocK_it_: .: (0.092482) test_blocK_it_BLOCK_IT: .: (0.091082) test_blocK_it_BLOCK_iT: .: (0.091323) test_blocK_it_piGene: .: (0.086522) test_bottom_strand: .: (0.086864) test_bottom_strand_class: .: (0.087824) test_bottom_strand_nil: .: (0.085227) test_design: .: (0.085465) test_design_BLOCK_IT: .: (0.088187) test_report: .: (0.084718) test_report_before_design: .: (0.086639) test_top_strand: .: (0.085411) test_top_strand_class: .: (0.085275) test_top_strand_nil: .: (0.086487) Bio::TestShRNANew: test_new: .: (0.001491) Bio::TestSiRNA: test_antisense_size: .: (0.000625) test_design: .: (0.084490) test_design_reynolds: .: (0.107995) test_design_uitei: .: (0.085428) test_max_gc_percent: .: (0.000921) test_min_gc_percent: .: (0.000254) test_reynolds: .: (0.106610) test_reynolds?: .: (0.000478) test_uitei: .: (0.088463) test_uitei?: .: (0.000425) Bio::TestSiRNANew: test_new: .: (0.001255) Bio::TestSiRNAPair: test_antisense: .: (0.086974) test_gc_percent: .: (0.086371) test_report: .: (0.085970) test_rule: .: (0.085652) test_sense: .: (0.086773) test_start: .: (0.086213) test_stop: .: (0.083182) test_target: .: (0.086837) Bio::TestSiRNAPairNew: test_new: .: (0.001284) Bio::TestSim4Report: test_all_hits: .: (0.001438) test_each: .: (0.000672) test_each_hit: .: (0.001122) test_hits: .: (0.000887) test_num_hits: .: (0.000560) test_query_def: .: (0.000578) test_query_id: .: (0.000556) test_query_len: .: (0.000558) test_seq1: .: (0.000882) Bio::TestSim4Report2: test_all_hits: .: (0.001090) test_each: .: (0.000686) test_each_hit: .: (0.001211) test_hits: .: (0.000734) test_num_hits: .: (0.000506) test_query_def: .: (0.000505) test_query_id: .: (0.000504) test_query_len: .: (0.000506) test_seq1: .: (0.000805) Bio::TestSim4Report4: test_all_hits: .: (0.001018) test_each: .: (0.000648) test_each_hit: .: (0.001142) test_hits: .: (0.000925) test_num_hits: .: (0.000604) test_query_def: .: (0.000573) test_query_id: .: (0.000583) test_query_len: .: (0.000590) test_seq1: .: (0.000919) Bio::TestSim4ReportHit: test_align: .: (0.001258) test_complement?: .: (0.000575) test_definition: .: (0.000560) test_each: .: (0.001687) test_exons: .: (0.001191) test_hit_id: .: (0.000597) test_hsps: .: (0.001107) test_introns: .: (0.001058) test_len: .: (0.000635) test_query_def: .: (0.000758) test_query_id: .: (0.000602) test_query_len: .: (0.001140) test_segmentpairs: .: (0.001251) test_seq1: .: (0.000956) test_seq2: .: (0.000746) test_target_def: .: (0.000560) test_target_id: .: (0.000528) test_target_len: .: (0.000534) Bio::TestSim4ReportHit2: test_align: .: (0.001149) test_complement?: .: (0.000532) test_definition: .: (0.000609) test_each: .: (0.001100) test_exons: .: (0.000927) test_hit_id: .: (0.000485) test_hsps: .: (0.001008) test_introns: .: (0.001231) test_len: .: (0.000572) test_query_def: .: (0.000632) test_query_id: .: (0.000539) test_query_len: .: (0.000529) test_segmentpairs: .: (0.001199) test_seq1: .: (0.000741) test_seq2: .: (0.000685) test_target_def: .: (0.000545) test_target_id: .: (0.000676) test_target_len: .: (0.000532) Bio::TestSim4ReportHit4: test_align: .: (0.002031) test_complement?: .: (0.000785) test_definition: .: (0.000610) test_each: .: (0.001470) test_exons: .: (0.001591) test_hit_id: .: (0.000660) test_hsps: .: (0.001780) test_introns: .: (0.001528) test_len: .: (0.000618) test_query_def: .: (0.000573) test_query_id: .: (0.000559) test_query_len: .: (0.000545) test_segmentpairs: .: (0.001940) test_seq1: .: (0.000805) test_seq2: .: (0.000638) test_target_def: .: (0.000644) test_target_id: .: (0.000529) test_target_len: .: (0.000524) Bio::TestSim4ReportSegment: test_from: .: (0.000605) test_self_new: .: (0.000368) test_seq: .: (0.000259) test_to: .: (0.000247) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.001960) test_direction: .: (0.000901) test_hit_from: .: (0.000998) test_hit_to: .: (0.000825) test_hseq: .: (0.000810) test_midline: .: (0.000828) test_percent_identity: .: (0.001022) test_qseq: .: (0.001410) test_query_from: .: (0.000971) test_query_to: .: (0.001105) test_seq1: .: (0.001039) test_seq2: .: (0.000968) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.001310) test_direction: .: (0.001322) test_hit_from: .: (0.000925) test_hit_to: .: (0.000929) test_hseq: .: (0.000839) test_midline: .: (0.000841) test_percent_identity: .: (0.000778) test_qseq: .: (0.000906) test_query_from: .: (0.000769) test_query_to: .: (0.001205) test_seq1: .: (0.000868) test_seq2: .: (0.001013) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.001329) test_direction: .: (0.001372) test_hit_from: .: (0.001256) test_hit_to: .: (0.001082) test_hseq: .: (0.001082) test_midline: .: (0.001202) test_percent_identity: .: (0.001597) test_qseq: .: (0.001250) test_query_from: .: (0.001043) test_query_to: .: (0.001057) test_seq1: .: (0.001252) test_seq2: .: (0.001950) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.001653) test_direction: .: (0.001116) test_hit_from: .: (0.001064) test_hit_to: .: (0.001221) test_hseq: .: (0.001652) test_midline: .: (0.001202) test_percent_identity: .: (0.001113) test_qseq: .: (0.000959) test_query_from: .: (0.000940) test_query_to: .: (0.001742) test_seq1: .: (0.001288) test_seq2: .: (0.001117) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.001602) test_direction: .: (0.001807) test_hit_from: .: (0.001506) test_hit_to: .: (0.001038) test_hseq: .: (0.000993) test_midline: .: (0.001180) test_percent_identity: .: (0.001750) test_qseq: .: (0.001046) test_query_from: .: (0.001202) test_query_to: .: (0.001006) test_seq1: .: (0.001180) test_seq2: .: (0.001359) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.001100) test_direction: .: (0.000840) test_hit_from: .: (0.000809) test_hit_to: .: (0.000811) test_hseq: .: (0.001274) test_midline: .: (0.000921) test_percent_identity: .: (0.000699) test_qseq: .: (0.000724) test_query_from: .: (0.000801) test_query_to: .: (0.000729) test_seq1: .: (0.001552) test_seq2: .: (0.000965) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.001269) test_direction: .: (0.000884) test_hit_from: .: (0.000828) test_hit_to: .: (0.000822) test_hseq: .: (0.001369) test_midline: .: (0.000854) test_percent_identity: .: (0.000748) test_qseq: .: (0.000749) test_query_from: .: (0.000938) test_query_to: .: (0.000829) test_seq1: .: (0.000970) test_seq2: .: (0.001559) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000772) test_entry_id: .: (0.000312) test_filename: .: (0.000310) test_len: .: (0.000310) test_self_new: .: (0.000362) test_self_parse: .: (0.000569) Bio::TestTMHMMReport: test_entry_id: .: (0.001400) test_exp_aas_in_tmhs: .: (0.000953) test_exp_first_60aa: .: (0.001031) test_helix: .: (0.000977) test_predicted_tmhs: .: (0.000832) test_query_len: .: (0.000937) test_tmhs: .: (0.001369) test_to_s: .: (0.001083) test_total_prob_of_N_in: .: (0.000820) Bio::TestTMHMMReport_reports: test_reports: .: (0.000663) Bio::TestTMHMMTMH: test_entry_id: .: (0.001136) test_pos: .: (0.001285) test_range: .: (0.001048) test_status: .: (0.000924) test_version: .: (0.000905) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.001180) test_cutoff: .: (0.000605) test_entry_id: .: (0.001047) test_length: .: (0.000570) test_loc: .: (0.000712) test_name: .: (0.000609) test_networks: .: (0.000612) test_prediction: .: (0.000649) test_query_len: .: (0.000623) test_query_sequences: .: (0.000584) test_rc: .: (0.000616) test_version: .: (0.000620) Bio::TestTargetPReportConst: test_delimiter: .: (0.001143) test_rs: .: (0.000277) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000592) test_togows_access_wait: .: (2.003684) Bio::TestTogoWSREST: test_debug: .: (0.001399) test_debug_default: .: (0.000535) test_internal_http: .: (0.000572) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000591) test_entry: .: (0.000269) test_entry_database_list: .: (0.000259) test_new: .: (0.000608) test_new_with_uri_object: .: (0.000705) test_new_with_uri_string: .: (0.000713) test_retrieve: .: (0.000298) test_search: .: (0.000278) test_search_database_list: .: (0.000272) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.001482) test_prepare_return_value: .: (0.000703) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.001087) Bio::TestTree: test_get_edge_distance: .: (0.000750) test_get_edge_distance_string: .: (0.005424) test_get_node_name: .: (0.000345) test_initialize: .: (0.000347) test_options: .: (0.000303) test_root: .: (0.000232) test_root=: .: (0.000282) Bio::TestTree2: test_add_edge: .: (0.001107) test_add_node: .: (0.000682) test_adjacency_matrix: .: (0.000697) test_adjacency_matrix_with_block: .: (0.000691) test_adjacent_nodes: .: (0.000798) test_adjacent_nodes_nonexistent: .: (0.000481) test_ancestors: .: (0.000594) test_children: .: (0.000502) test_clear: .: (0.000836) test_clear_node: .: (0.000649) test_clear_node_nonexistent: .: (0.000750) test_collect_edge!: .: (0.000833) test_collect_node!: .: (0.001050) test_concat: .: (0.000814) test_descendents: .: (0.000563) test_distance_matrix: .: (0.006104) test_each_edge: .: (0.000897) test_each_node: .: (0.000728) test_each_out_edge: .: (0.000605) test_each_out_edge_chimpanzee: .: (0.000573) test_each_out_edge_human: .: (0.000937) test_each_out_edge_mammals: .: (0.000674) test_each_out_edge_nonexistent: .: (0.000522) test_each_out_edge_primates: .: (0.001012) test_each_out_edge_rat: .: (0.004920) test_each_out_edge_rodents: .: (0.000957) test_edges: .: (0.000561) test_get_edge: .: (0.001189) test_get_edge_indirect: .: (0.011693) test_get_edge_merged: .: (0.001002) test_get_edge_nonexistent: .: (0.000471) test_get_node_bootstrap: .: (0.000478) test_get_node_bootstrap_string=: .: (0.000493) test_get_node_by_name: .: (0.000736) test_get_node_by_name_noexistent: .: (0.000744) test_include?: .: (0.000665) test_include_nonexistent: .: (0.000485) test_insert_node: .: (0.000799) test_leaves: .: (0.005832) test_leaves_noargs: .: (0.000674) test_lowest_common_ancestor: .: (0.000608) test_nodes: .: (0.000516) test_number_of_edges: .: (0.000473) test_number_of_nodes: .: (0.000780) test_out_degree: .: (0.000635) test_out_degree_nonexistent: .: (0.000459) test_out_edges: .: (0.000573) test_out_edges_mammals: .: (0.000647) test_out_edges_nonexistent: .: (0.000476) test_out_edges_primates: .: (0.001047) test_out_edges_rodents: .: (0.000822) test_parent: .: (0.000856) test_path: .: (0.000561) test_remove_edge: .: (0.000531) test_remove_edge_if: .: (0.000576) test_remove_edge_if_nothing_removed: .: (0.000627) test_remove_edge_nonexistent: .: (0.001404) test_remove_node: .: (0.001413) test_remove_node_if: .: (0.000519) test_remove_node_if_false: .: (0.000546) test_remove_node_nonexistent: .: (0.001113) test_remove_nonsense_nodes: .: (0.000648) test_subtree: .: (0.000747) test_subtree_with_all_paths: .: (0.001064) test_total_distance: .: (0.000871) Bio::TestTreeEdge: test_distance: .: (0.000662) test_distance=: .: (0.000424) test_distance_string: .: (0.000863) test_distance_string=: .: (0.000409) test_initialize: .: (0.000430) test_inspect: .: (0.000284) test_to_s: .: (0.000273) Bio::TestTreeNode: test_bootstrap: .: (0.000596) test_bootstrap=: .: (0.000381) test_bootstrap_string: .: (0.000259) test_bootstrap_string=: .: (0.000804) test_initialize: .: (0.000376) test_inspect: .: (0.000381) test_name: .: (0.000300) test_to_s: .: (0.000270) Bio::TestUniProt: test_gene_name: .: (0.014767) Bio::TestUniProtKB: test_ac: .: (0.018804) test_accession: .: (0.014481) test_cc: .: (0.024278) test_cc_alternative_products: .: (0.019389) test_cc_database: .: (0.019089) test_cc_mass_spectrometry: .: (0.018845) test_de: .: (0.013389) test_dr: .: (0.019560) test_dr_with_key: .: (0.057380) test_dr_with_key_empty: .: (0.119162) test_dt: .: (0.013460) test_dt_annotation: .: (0.013731) test_dt_created: .: (0.014289) test_dt_sequence: .: (0.013403) test_entry: .: (0.014625) test_ft: .: (0.040651) test_gene_name: .: (0.014258) test_gene_names: .: (0.015336) test_gn: .: (0.014003) test_gn_old_parser: .: (0.013620) test_gn_uniprot_parser: .: (0.014952) test_id_line: .: (0.013349) test_id_line_data_class: .: (0.018578) test_id_line_entry_name: .: (0.014269) test_id_line_molecule_type: .: (0.013490) test_id_line_sequence_length: .: (0.013676) test_kw: .: (0.013897) test_molecule: .: (0.015181) test_oc: .: (0.015853) test_og_1: .: (0.014186) test_og_2: .: (0.014713) test_og_3: .: (0.014987) test_og_4: .: (0.014030) test_og_5: .: (0.013918) test_og_6: .: (0.014332) test_os: .: (0.013297) test_os_access: .: (0.016745) test_os_access2: .: (0.013880) test_ox: .: (0.014345) test_protein_name: .: (0.014432) test_ref: .: (0.034888) test_seq: .: (0.016151) test_sequence_length: .: (0.014668) test_sq: .: (0.013875) test_sq_crc64: .: (0.014531) test_sq_len: .: (0.013950) test_sq_mw: .: (0.013394) test_synonyms: .: (0.013995) Bio::TestUniProtKB_CC: test_allergen: .: (0.000921) test_alternative_products_access_as_hash: .: (0.000691) test_alternative_products_ai: .: (0.000868) test_alternative_products_apu: .: (0.002260) test_alternative_products_as: .: (0.001039) test_alternative_products_rf: .: (0.000282) test_biophysicochemical_properties: .: (0.001710) test_biotechnology: .: (0.000747) test_catalytic_activity: .: (0.000619) test_caution: .: (0.000684) test_cofactor: .: (0.000977) test_developmental_stage: .: (0.000719) test_disease: .: (0.004912) test_domain: .: (0.001059) test_enzyme_regulation: .: (0.001077) test_function: .: (0.000777) test_induction: .: (0.000609) test_interaction: .: (0.000831) test_mass_spectrometry: .: (0.001226) test_miscellaneous: .: (0.001306) test_pathway: .: (0.000732) test_pharmaceutical: .: (0.001070) test_polymorphism: .: (0.000922) test_ptm: .: (0.000593) test_rna_editing: .: (0.000757) test_similarity: .: (0.000574) test_subcellular_location: .: (0.000779) test_subunit: .: (0.000548) test_tissue_specificity: .: (0.001316) test_toxic_dose: .: (0.000872) test_web_resource: .: (0.001017) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.001304) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.001935) test_protein_name: .: (0.001722) test_synonyms: .: (0.001639) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000744) test_entry: .: (0.000364) test_entry_id: .: (0.000349) test_entry_name: .: (0.000364) test_id_line: .: (0.000409) test_molecule: .: (0.000380) test_sequence_length: .: (0.000980) Bio::TestUniProtKB_P28907: test_ac: .: (0.005813) test_accession: .: (0.005295) test_cc: .: (0.007568) test_cc_alternative_products: .: (0.007085) test_cc_database: .: (0.007588) test_cc_mass_spectrometry: .: (0.006948) test_de: .: (0.005683) test_dr: .: (0.013943) test_dr_with_key: .: (0.014625) test_dr_with_key_empty: .: (0.014430) test_dt: .: (0.006894) test_dt_annotation: .: (0.005957) test_dt_created: .: (0.005934) test_dt_sequence: .: (0.005730) test_entry: .: (0.006504) test_ft: .: (0.010403) test_gene_name: .: (0.005783) test_gene_names: .: (0.005539) test_gn: .: (0.005642) test_gn_old_parser: .: (0.006388) test_gn_uniprot_parser: .: (0.005381) test_id_line: .: (0.005241) test_id_line_data_class: .: (0.005338) test_id_line_entry_name: .: (0.005756) test_id_line_sequence_length: .: (0.005235) test_kw: .: (0.005290) test_oc: .: (0.005168) test_os: .: (0.005416) test_os_access: .: (0.005565) test_os_access2: .: (0.005685) test_ox: .: (0.010470) test_protein_name: .: (0.006219) test_protein_name_after_calling_de: .: (0.006722) test_ref: .: (0.008349) test_seq: .: (0.005732) test_sequence_length: .: (0.005345) test_sq: .: (0.006390) test_sq_crc64: .: (0.005319) test_sq_len: .: (0.005301) test_sq_mw: .: (0.009733) test_synonyms: .: (0.006216) test_synonyms_after_calling_de: .: (0.010617) Bio::TestUniProtKB_Ref: test_RA: .: (0.001351) test_RC: .: (0.001648) test_RG: .: (0.000772) test_RL: .: (0.000806) test_RN: .: (0.000789) test_RP: .: (0.000996) test_RT: .: (0.001755) test_RX: .: (0.000856) test_ref: .: (0.001057) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000860) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.002360) test_alternative_products_with_ft: .: (0.002576) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.001276) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.001982) test_RL_lines: .: (0.000512) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.001853) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000988) test_RG_line: .: (0.000530) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.002623) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000996) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000715) test_RL_line: .: (0.000464) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.002188) test_RP_line: .: (0.002205) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000494) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000935) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000825) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000604) test_CC_interaction_isoform: .: (0.000561) test_CC_interaction_no_gene_name: .: (0.000637) test_CC_interaction_self_association: .: (0.000742) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.001095) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.001750) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.001564) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.001077) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.001094) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.001546) test_DT_line: .: (0.000616) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.010125) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.002847) test_CC_web_resource: .: (0.000278) test_FT_VER_SEQ: .: (0.000633) test_OH_line_exception: .: (0.001042) test_OH_lines: .: (0.001109) Bio::TestUtils: test_centreOfGravity: .: (0.002282) test_dihedral_angle: .: (0.001084) test_distance: .: (0.001131) test_geometricCentre: .: (0.000945) test_rad2deg: .: (0.003881) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.001453) test_dijkstra_on_weighted_graph: .: (0.000451) Finished in 48.55546646 seconds. ------------------------------------------------------------------------------- 3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 79.43 tests/s, 442.50 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/ruby-bio-2.0.4' 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_2.0.4-1_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.4-1_arm64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.4-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/2006 and its subdirectories I: Current time: Sun Jun 9 07:39:54 -12 2024 I: pbuilder-time-stamp: 1717961994 Mon May 8 13:16:57 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Mon May 8 13:16:57 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Mon May 8 13:18:42 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Mon May 8 13:18:43 UTC 2023 I: ruby-bio_2.0.4-1_arm64.changes: Format: 1.8 Date: Sun, 09 Oct 2022 13:54:56 +0530 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Ruby Team Changed-By: Nilesh Patra Description: ruby-bio - Ruby tools for computational molecular biology Changes: ruby-bio (2.0.4-1) unstable; urgency=medium . * New upstream version 2.0.4 * Update copyright * Bump Standards-Version to 4.6.1 (no changes needed) Checksums-Sha1: e3cb105a411931cce42849200c67f43c1702b15e 654676 ruby-bio_2.0.4-1_all.deb 0cd64c10f11046d94db12a2cdaed6b0e5b393227 8395 ruby-bio_2.0.4-1_arm64.buildinfo Checksums-Sha256: 3e8f9547e50199c92950c8a83142c34d210c7b675d54697c53707646cb0ac50e 654676 ruby-bio_2.0.4-1_all.deb 05be47061e4dd0cc57d2a172c557844f1b6799badcc62a176adf5ffb7a918e6f 8395 ruby-bio_2.0.4-1_arm64.buildinfo Files: 2e4e47c285c3625b3a158fdc12e29110 654676 ruby optional ruby-bio_2.0.4-1_all.deb 02509378ad2c0ec9f1487be1e0056e91 8395 ruby optional ruby-bio_2.0.4-1_arm64.buildinfo Mon May 8 13:18:44 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/ruby-bio_2.0.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/ruby-bio_2.0.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/ruby-bio_2.0.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/b1/ruby-bio_2.0.4-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.11Ga1a0I/b2/ruby-bio_2.0.4-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.315s) 0.315s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.020s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon May 8 13:18:45 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Mon May 8 13:18:45 UTC 2023 I: ruby-bio from bookworm built successfully and reproducibly on arm64. Mon May 8 13:18:46 UTC 2023 I: Submitting .buildinfo files to external archives: Mon May 8 13:18:46 UTC 2023 I: Submitting 12K b1/ruby-bio_2.0.4-1_arm64.buildinfo.asc Mon May 8 13:18:47 UTC 2023 I: Submitting 12K b2/ruby-bio_2.0.4-1_arm64.buildinfo.asc Mon May 8 13:18:48 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 8 13:18:48 UTC 2023 I: Done submitting .buildinfo files. Mon May 8 13:18:48 UTC 2023 I: Removing signed ruby-bio_2.0.4-1_arm64.buildinfo.asc files: removed './b1/ruby-bio_2.0.4-1_arm64.buildinfo.asc' removed './b2/ruby-bio_2.0.4-1_arm64.buildinfo.asc'