Sun Apr 23 07:16:25 UTC 2023 I: starting to build ruby-bio/bookworm/amd64 on jenkins on '2023-04-23 07:16' Sun Apr 23 07:16:25 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/13886/console.log Sun Apr 23 07:16:25 UTC 2023 I: Downloading source for bookworm/ruby-bio=2.0.4-1 --2023-04-23 07:16:26-- 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% 133M=0s 2023-04-23 07:16:26 (133 MB/s) - ‘ruby-bio_2.0.4-1.dsc’ saved [2133/2133] Sun Apr 23 07:16:26 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----- Sun Apr 23 07:16:26 UTC 2023 I: Checking whether the package is not for us Sun Apr 23 07:16:26 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Apr 23 07:16:26 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Apr 23 07:18:52 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 22 19:16:28 -12 2023 I: pbuilder-time-stamp: 1682234188 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/828210/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d1bb992942e34b05a113c387c040dea1' 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='828210' 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.0lFmHjuG/pbuilderrc_MGMz --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.0lFmHjuG/b1 --logfile b1/build.log ruby-bio_2.0.4-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/828210/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: amd64 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 ... 19596 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 48.3 MB of archives. After unpacking 168 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 86 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.3 [1072 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libosp5 amd64 1.5.2-13+b2 [934 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 opensp amd64 1.5.2-13+b2 [421 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 docbook-to-man amd64 1:2.0.0-45 [77.4 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 117 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7 [5401 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7 [663 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get: 126 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 gem2deb-test-runner amd64 2.1 [16.9 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libgmpxx4ldbl amd64 2:6.2.1+dfsg1-1.1 [338 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libgmp-dev amd64 2:6.2.1+dfsg1-1.1 [641 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 ruby3.1-dev amd64 3.1.2-7 [1001 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 ruby-all-dev amd64 1:3.1 [5976 B] Get: 132 http://deb.debian.org/debian bookworm/main amd64 gem2deb amd64 2.1 [53.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 ruby-libxml amd64 3.2.4-2 [83.3 kB] Fetched 48.3 MB in 2s (27.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.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:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 20346 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.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_amd64.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_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../007-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../013-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-3_amd64.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:amd64. Preparing to unpack .../027-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../029-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.21-12_amd64.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:amd64. Preparing to unpack .../035-libassuan0_2.5.5-5_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../036-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../037-libksba8_1.6.3-2_amd64.deb ... Unpacking libksba8:amd64 (1.6.3-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../038-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../039-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../040-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnpth0:amd64. Preparing to unpack .../041-libnpth0_1.6-3_amd64.deb ... Unpacking libnpth0:amd64 (1.6-3) ... Selecting previously unselected package dirmngr. Preparing to unpack .../042-dirmngr_2.2.40-1.1_amd64.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_amd64.deb ... Unpacking gnupg-utils (2.2.40-1.1) ... Selecting previously unselected package gpg. 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Setting up libclone-perl:amd64 (0.46-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (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:amd64 (1:5.44-3) ... Setting up perl-openssl-defaults:amd64 (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:amd64 (1.6-3) ... Setting up file (1:5.44-3) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libosp5 (1.5.2-13+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:amd64 (2:6.2.1+dfsg1-1.1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libncurses6:amd64 (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:amd64 (0.22-2+b1) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up libsasl2-2:amd64 (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:amd64 (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:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... 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:amd64 (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:amd64 (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:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (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:amd64 (0.008-2) ... Setting up libldap-2.5-0:amd64 (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:amd64 (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:amd64 (3.11.2-6) ... Setting up libparams-classify-perl:amd64 (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:amd64 (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:amd64 (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:amd64 (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:amd64 (3.1.2-7) ... Setting up gem2deb-test-runner (2.1) ... Setting up ruby3.1-dev:amd64 (3.1.2-7) ... Setting up ruby-libxml:amd64 (3.2.4-2) ... Setting up ruby-all-dev:amd64 (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 amd64 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/x86_64-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-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: .: (0.000759) test_dbs: .: (0.000263) test_go_ids: .: (0.000265) test_go_terms: .: (0.000522) test_parser: .: (0.005127) test_set_date: .: (0.000288) test_set_desc: .: (0.000271) test_to_str: .: (0.000300) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000842) test_mktmpdir_without_block: .: (0.000593) test_remove_entry_secure: .: (0.000566) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.036354) test_call_command_fork: .: (0.000202) test_call_command_open3: .: (0.035132) test_call_command_popen: .: (0.035882) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.031887) test_call_command_fork: .: (0.000222) test_call_command_open3: .: (0.043429) test_call_command_popen: .: (0.027937) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.031822) test_call_command_fork: .: (0.000215) test_call_command_open3: .: (0.035437) test_call_command_popen: .: (0.027963) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.015422) test_call_command_fork_chdir: .: (0.000399) test_call_command_popen_chdir: .: (0.015320) test_query_command_chdir: .: (0.015931) test_query_command_fork_chdir: .: (0.000430) test_query_command_popen_chdir: .: (0.011369) Bio::FuncTestCommandQuery: test_query_command: .: (0.059774) test_query_command_fork: .: (0.011793) test_query_command_open3: .: (0.075777) test_query_command_popen: .: (0.067937) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000994) test_initialize: .: (0.000457) test_path: .: (0.000278) test_path_after_close: .: (0.000514) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.045797) test_output_fasta: .: (0.124954) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000519) test_accession: .: (0.000275) test_accessions: .: (0.000259) test_comment: .: (0.000217) test_common_name: .: (0.000331) test_definition: .: (0.000323) test_features: .: (0.001037) test_gi: .: (0.000231) test_keywords: .: (0.000214) test_locus: .: (0.000153) test_nid: .: (0.000244) test_organism: .: (0.000248) test_origin: .: (0.000195) test_references: .: (0.001104) test_segment: .: (0.000249) test_source: .: (0.001962) test_taxonomy: .: (0.000259) test_version: .: (0.000254) test_versions: .: (0.000489) Bio::TestAA: test_13: .: (0.000344) test_1n: .: (0.000140) test_name2one: .: (0.000205) test_name2three: .: (0.000167) test_one2name: .: (0.000141) test_one2three: .: (0.000141) test_three2name: .: (0.000139) test_three2one: .: (0.000171) test_to_1_1: .: (0.000162) test_to_1_3: .: (0.000262) test_to_1_name: .: (0.000170) test_to_3_1: .: (0.000140) test_to_3_3: .: (0.000157) test_to_3_name: .: (0.000187) test_to_re: .: (0.000209) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000321) Bio::TestAAindex: test_api: .: (0.000225) test_auto_aax1: .: (0.000385) test_auto_aax2: .: (0.000302) Bio::TestAAindex1: test_author: .: (0.000440) test_comment: .: (0.001101) test_correlation_coefficient: .: (0.000822) test_dblinks: .: (0.000336) test_definition: .: (0.000309) test_entry_id: .: (0.000302) test_index: .: (0.000446) test_journal: .: (0.000360) test_title: .: (0.000302) Bio::TestAAindex2: test_access_A_R: .: (0.001878) test_access_R_A: .: (0.001007) test_author: .: (0.000357) test_cols: .: (0.000601) test_comment: .: (0.000316) test_dblinks: .: (0.000304) test_definition: .: (0.000847) test_entry_id: .: (0.000363) test_journal: .: (0.000322) test_matrix: .: (0.000920) test_matrix_1_2: .: (0.001193) test_matrix_2_2: .: (0.001412) test_matrix_A_R: .: (0.001058) test_matrix_R_A: .: (0.001231) test_matrix_determinant: .: (0.006417) test_matrix_rank: .: (0.006481) test_matrix_transpose: .: (0.001290) test_rows: .: (0.000285) test_title: .: (0.000606) Bio::TestAAindexConstant: test_delimiter: .: (0.000367) test_tagsize: .: (0.000132) Bio::TestAbif: test_complement: .: (0.016782) test_seq: .: (0.015549) test_to_biosequence: .: (0.016641) Bio::TestActsLikeMap: test_mixin: .: (0.000480) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000758) Bio::TestActsLikeMarker: test_mixin: .: (0.000331) Bio::TestAlignment: test_add_seq_no_key: .: (0.000464) test_add_seq_using_seq_with_aaseq_method: .: (0.000206) test_add_seq_using_seq_with_definition_method: .: (0.000158) test_add_seq_using_seq_with_entry_id_method: .: (0.000172) test_add_seq_using_seq_with_naseq_method: .: (0.000230) test_add_seq_using_seq_with_seq_method: .: (0.000169) test_consensus_iupac_gap_modes: .: (0.000690) test_consensus_iupac_missing_char: .: (0.000648) test_consensus_iupac_missing_char_option: .: (0.000365) test_consensus_iupac_no_gaps: .: (0.000531) test_consensus_iupac_of_ambiguous_bases: .: (0.000778) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.009278) test_consensus_opt_gap_mode: .: (0.001465) test_consensus_opt_missing_char: .: (0.000460) test_consensus_string_no_gaps: .: (0.000441) test_consensus_threshold_four_sequences: .: (0.000631) test_consensus_threshold_two_sequences: .: (0.000673) test_convert_match: .: (0.000630) test_convert_unmatch: .: (0.000296) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000281) test_convert_unmatch_different_match_char: .: (0.000217) test_convert_unmatch_multiple_sequences: .: (0.000367) test_default_gap_char: .: (0.000138) test_default_gap_regexp_matches_default_gap_char: .: (0.000187) test_default_missing_char: .: (0.000142) test_each_site_equal_length: .: (0.000277) test_each_site_unequal_length: .: (0.000267) test_equals: .: (0.000367) test_match_line_protein: .: (0.001217) test_normalizebang_extends_sequences_with_gaps: .: (0.000267) test_seq_length_is_max_seq_length: .: (0.000202) test_seq_length_when_one_sequence: .: (0.000129) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000165) test_seqclass_when_seqclass_set: .: (0.000276) test_seqclass_when_sequence_used: .: (0.000127) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000109) test_set_and_get_gap_char: .: (0.000140) test_store_cannot_override_key: .: (0.000116) test_store_with_default_keys_and_user_defined_keys: .: (0.000136) test_store_with_nil_key_uses_next_number_for_key: .: (0.000163) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000356) test_alignment_concat: .: (0.000524) test_alignment_length: .: (0.000131) test_alignment_lstrip!: .: (0.000268) test_alignment_lstrip_nil: .: (0.000196) test_alignment_normalize!: .: (0.000148) test_alignment_rstrip!: .: (0.000294) test_alignment_rstrip_nil: .: (0.000197) test_alignment_site: .: (0.000169) test_alignment_slice: .: (0.000226) test_alignment_strip!: .: (0.000340) test_alignment_strip_nil: .: (0.000251) test_alignment_subseq: .: (0.000245) test_alignment_window: .: (0.000170) test_collect_each_site: .: (0.000575) test_consensus_each_site_default: .: (0.000258) test_consensus_each_site_gap_mode_1: .: (0.000279) test_consensus_each_site_gap_mode_minus1: .: (0.000272) test_consensus_iupac: .: (0.000621) test_consensus_string_default: .: (0.000273) test_consensus_string_half: .: (0.000218) test_convert_match: .: (0.000243) test_convert_unmatch: .: (0.000163) test_each_seq: .: (0.000193) test_each_site: .: (0.000392) test_each_site_step: .: (0.000302) test_each_window: .: (0.000325) test_match_line: .: (0.001699) test_match_line_amino: .: (0.002667) test_match_line_nuc: .: (0.000324) test_private_alignment_site: .: (0.000182) test_remove_all_gaps!: .: (0.000216) test_seqclass: .: (0.000204) test_seqclass=: .: (0.000205) test_seqclass_default: .: (0.000131) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.006828) test_determine_seq_method: .: (0.003837) test_entries: .: (0.000659) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000829) test_avoid_same_name_numbering: .: (0.000235) test_clustal_have_same_name_true: .: (0.000213) test_have_same_name_false: .: (0.000172) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000396) test_gap_char_default: .: (0.000175) test_gap_char_never_nil: .: (0.000152) test_gap_regexp: .: (0.000173) test_gap_regexp=: .: (0.000186) test_gap_regexp_never_nil: .: (0.000173) test_get_all_property_default: .: (0.000183) test_get_all_property_nodefault: .: (0.000225) test_is_gap_default_false: .: (0.000229) test_is_gap_default_true: .: (0.000204) test_is_gap_nodefault_false: .: (0.000166) test_is_gap_nodefault_true: .: (0.000205) test_missing_char=: .: (0.000156) test_missing_char_default: .: (0.000149) test_missing_char_never_nil: .: (0.000157) test_seqclass=: .: (0.000182) test_seqclass_default: .: (0.000204) test_seqclass_never_nil: .: (0.000149) test_set_all_property: .: (0.000181) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001434) test_consensus_string_50percent: .: (0.000187) test_consensus_string_50percent_nil: .: (0.000162) test_consensus_string_default: .: (0.000151) test_consensus_string_default_nil: .: (0.000196) test_has_gap_false: .: (0.000166) test_has_gap_true: .: (0.000166) test_match_line_amino_100percent: .: (0.000298) test_match_line_amino_missing: .: (0.000304) test_match_line_amino_strong: .: (0.000266) test_match_line_amino_weak: .: (0.000270) test_match_line_nuc_100percent: .: (0.000194) test_match_line_nuc_missing: .: (0.000185) test_remove_gaps!: .: (0.000397) test_remove_gaps_bang_not_removed: .: (0.000174) Bio::TestAtomFinder: test_atoms: .: (0.033805) test_each_atom: .: (0.000430) test_find_atom: .: (0.000298) Bio::TestBioFastaDefline: test_acc_version: .: (0.001170) test_accession: .: (0.000768) test_accessions: .: (0.000750) test_description: .: (0.000540) test_descriptions: .: (0.000641) test_entry_id: .: (0.000648) test_get: .: (0.000762) test_get_all_by_type: .: (0.000508) test_get_by_type: .: (0.000534) test_gi: .: (0.000496) test_id_strings: .: (0.013091) test_locus: .: (0.000522) test_method_missing: .: (0.000797) test_to_s: .: (0.000675) test_words: .: (0.002317) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.001415) test_goid2term: .: (0.000603) test_parse_goids: .: (0.001296) Bio::TestBioGenBank: test_basecount: .: (0.000693) test_circular: .: (0.000445) test_classification: .: (0.000584) test_date: .: (0.000460) test_date_modified: .: (0.001657) test_division: .: (0.000471) test_each_cds_feature: .: (0.001833) test_each_cds_qualifiers: .: (0.001610) test_each_gene: .: (0.001799) test_entry_id: .: (0.000588) test_length: .: (0.000350) test_locus_circular: .: (0.000368) test_locus_class: .: (0.000404) test_locus_date: .: (0.000480) test_locus_division: .: (0.000747) test_locus_entry_id: .: (0.000506) test_locus_length: .: (0.000761) test_locus_natype: .: (0.000494) test_locus_strand: .: (0.000489) test_natype: .: (0.000430) test_seq: .: (0.000477) test_seq_len: .: (0.000449) test_strand: .: (0.000372) test_strandedness: .: (0.001072) test_to_biosequence: .: (0.004175) Bio::TestBioGenPept: test_circular: .: (0.000623) test_date: .: (0.000294) test_dbsource: .: (0.000289) test_division: .: (0.000306) test_entry_id: .: (0.000290) test_length: .: (0.000289) test_locus: .: (0.000296) test_seq: .: (0.000905) test_seq_len: .: (0.000386) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000648) test_aaseq: .: (0.000433) test_chromosome: .: (0.000360) test_codon_usage: .: (0.000530) test_cu_list: .: (0.000540) test_dblinks_as_hash: .: (0.000424) test_dblinks_as_strings: .: (0.000557) test_definition: .: (0.000350) test_division: .: (0.000315) test_eclinks: .: (0.000369) test_entry: .: (0.000298) test_entry_id: .: (0.000287) test_gbposition: .: (0.000377) test_gene: .: (0.000776) test_genes: .: (0.000499) test_keggclass: .: (0.000886) test_keggclasses: .: (0.000317) test_locations: .: (0.000430) test_motifs_as_hash: .: (0.000346) test_motifs_as_strings: .: (0.000240) test_name: .: (0.000519) test_names_as_array: .: (0.000296) test_new: .: (0.000266) test_ntlen: .: (0.000340) test_ntseq: .: (0.000418) test_organism: .: (0.000261) test_orthologs_as_hash: .: (0.000321) test_orthologs_as_strings: .: (0.000278) test_pathway: .: (0.000313) test_pathway_after_pathways_as_strings: .: (0.000488) test_pathway_before_pathways_as_strings: .: (0.000400) test_pathways_as_hash: .: (0.000287) test_pathways_as_strings: .: (0.000242) test_position: .: (0.000407) test_structure: .: (0.000255) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.001692) test_comment: .: (0.000512) test_data_source: .: (0.000497) test_definition: .: (0.000491) test_disease: .: (0.000488) test_entry_id: .: (0.000508) test_lineage: .: (0.000604) test_nalen: .: (0.000730) test_name: .: (0.000465) test_new: .: (0.000452) test_num_gene: .: (0.000514) test_num_rna: .: (0.000558) test_original_databases: .: (0.000544) test_original_db: .: (0.000551) test_plasmids: .: (0.000846) test_references: .: (0.004354) test_statistics: .: (0.000630) test_taxid: .: (0.000586) test_taxonomy: .: (0.000634) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001240) test_comment: .: (0.000334) test_data_source: .: (0.000270) test_definition: .: (0.000280) test_disease: .: (0.000274) test_entry_id: .: (0.000291) test_lineage: .: (0.000331) test_nalen: .: (0.000291) test_name: .: (0.000294) test_new: .: (0.000450) test_num_gene: .: (0.000574) test_num_rna: .: (0.000265) test_original_databases: .: (0.000282) test_original_db: .: (0.000349) test_plasmids: .: (0.000490) test_references: .: (0.000551) test_statistics: .: (0.000480) test_taxid: .: (0.000353) test_taxonomy: .: (0.000581) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000533) test_compounds_as_strings: .: (0.000247) test_dblinks_as_hash: .: (0.000225) test_dblinks_as_strings: .: (0.000281) test_description: .: (0.000251) test_diseases_as_hash: .: (0.000221) test_diseases_as_strings: .: (0.000214) test_entry_id: .: (0.000519) test_enzymes_as_strings: .: (0.000265) test_genes_as_hash: .: (0.000206) test_genes_as_strings: .: (0.000518) test_keggclass: .: (0.000279) test_ko_pathway: .: (0.000251) test_modules_as_hash: .: (0.000273) test_modules_as_strings: .: (0.000248) test_name: .: (0.000267) test_new: .: (0.000288) test_organism: .: (0.000242) test_orthologs_as_hash: .: (0.000219) test_orthologs_as_strings: .: (0.000236) test_pathways_as_hash: .: (0.000227) test_pathways_as_strings: .: (0.000210) test_reactions_as_hash: .: (0.000226) test_reactions_as_strings: .: (0.000215) test_references: .: (0.000206) test_rel_pathways_as_hash: .: (0.000254) test_rel_pathways_as_strings: .: (0.000222) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001107) test_compounds_as_strings: .: (0.000486) test_dblinks_as_hash: .: (0.000288) test_dblinks_as_strings: .: (0.000711) test_description: .: (0.000326) test_diseases_as_hash: .: (0.000290) test_diseases_as_strings: .: (0.000245) test_entry_id: .: (0.000282) test_enzymes_as_strings: .: (0.000275) test_genes_as_hash: .: (0.000657) test_genes_as_strings: .: (0.000293) test_keggclass: .: (0.000265) test_ko_pathway: .: (0.000246) test_modules_as_hash: .: (0.000519) test_modules_as_strings: .: (0.000282) test_name: .: (0.000291) test_new: .: (0.000287) test_organism: .: (0.000318) test_orthologs_as_hash: .: (0.000297) test_orthologs_as_strings: .: (0.000274) test_pathways_as_hash: .: (0.000322) test_pathways_as_strings: .: (0.000295) test_reactions_as_hash: .: (0.000284) test_reactions_as_strings: .: (0.000518) test_references: .: (0.000277) test_rel_pathways_as_hash: .: (0.000306) test_rel_pathways_as_strings: .: (0.000304) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000677) test_compounds_as_strings: .: (0.000230) test_dblinks_as_hash: .: (0.000205) test_dblinks_as_strings: .: (0.000193) test_description: .: (0.000239) test_diseases_as_hash: .: (0.000200) test_diseases_as_strings: .: (0.000202) test_entry_id: .: (0.000502) test_enzymes_as_strings: .: (0.000285) test_genes_as_hash: .: (0.000281) test_genes_as_strings: .: (0.000271) test_keggclass: .: (0.000307) test_ko_pathway: .: (0.000596) test_modules_as_hash: .: (0.000245) test_modules_as_strings: .: (0.000233) test_name: .: (0.000260) test_new: .: (0.000245) test_organism: .: (0.000216) test_orthologs_as_hash: .: (0.000539) test_orthologs_as_strings: .: (0.000247) test_pathways_as_hash: .: (0.000217) test_pathways_as_strings: .: (0.000209) test_reactions_as_hash: .: (0.000219) test_reactions_as_strings: .: (0.000514) test_references: .: (0.000199) test_rel_pathways_as_hash: .: (0.000218) test_rel_pathways_as_strings: .: (0.000250) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000483) test_compounds_as_strings: .: (0.000361) test_dblinks_as_hash: .: (0.000336) test_dblinks_as_strings: .: (0.000268) test_description: .: (0.000806) test_diseases_as_hash: .: (0.000283) test_diseases_as_strings: .: (0.000234) test_entry_id: .: (0.000265) test_enzymes_as_strings: .: (0.000234) test_genes_as_hash: .: (0.000235) test_genes_as_strings: .: (0.000229) test_keggclass: .: (0.000259) test_ko_pathway: .: (0.000528) test_modules_as_hash: .: (0.000822) test_modules_as_strings: .: (0.000385) test_name: .: (0.000304) test_new: .: (0.000309) test_organism: .: (0.000319) test_orthologs_as_hash: .: (0.000290) test_orthologs_as_strings: .: (0.000284) test_pathways_as_hash: .: (0.000312) test_pathways_as_strings: .: (0.000536) test_reactions_as_hash: .: (0.000452) test_reactions_as_strings: .: (0.000255) test_references: .: (0.001016) test_rel_pathways_as_hash: .: (0.000359) test_rel_pathways_as_strings: .: (0.000278) Bio::TestBioKeggDRUG: test_activity: .: (0.000539) test_comment: .: (0.000800) test_dblinks_as_hash: .: (0.000456) test_dblinks_as_strings: .: (0.000338) test_entry_id: .: (0.000356) test_formula: .: (0.000330) test_kcf: .: (0.000280) test_mass: .: (0.000302) test_name: .: (0.000327) test_names: .: (0.000389) test_pathways_as_hash: .: (0.000587) test_pathways_as_strings: .: (0.000285) test_products: .: (0.006544) test_remark: .: (0.000355) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000850) test_composition: .: (0.000355) test_compounds: .: (0.000344) test_dblinks_as_hash: .: (0.000711) test_dblinks_as_strings: .: (0.000937) test_entry_id: .: (0.000298) test_enzymes: .: (0.000543) test_kcf: .: (0.000269) test_keggclass: .: (0.000286) test_mass: .: (0.000281) test_name: .: (0.000318) test_orthologs_as_hash: .: (0.000520) test_orthologs_as_strings: .: (0.000824) test_pathways_as_hash: .: (0.000297) test_pathways_as_strings: .: (0.000250) test_reactions: .: (0.000575) test_references: .: (0.000411) test_remark: .: (0.000322) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000498) test_composition: .: (0.000691) test_compounds: .: (0.000297) test_dblinks_as_hash: .: (0.000283) test_dblinks_as_strings: .: (0.000219) test_entry_id: .: (0.000236) test_enzymes: .: (0.000588) test_kcf: .: (0.000228) test_keggclass: .: (0.000270) test_mass: .: (0.000280) test_name: .: (0.000256) test_orthologs_as_hash: .: (0.000569) test_orthologs_as_strings: .: (0.000248) test_pathways_as_hash: .: (0.000240) test_pathways_as_strings: .: (0.000216) test_reactions: .: (0.000251) test_references: .: (0.000229) test_remark: .: (0.000284) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000731) test_compounds_as_strings: .: (0.000788) test_dblinks_as_hash: .: (0.000364) test_dblinks_as_strings: .: (0.000253) test_description: .: (0.000289) test_diseases_as_hash: .: (0.000290) test_diseases_as_strings: .: (0.000562) test_entry_id: .: (0.000310) test_enzymes_as_strings: .: (0.000260) test_genes_as_hash: .: (0.000258) test_genes_as_strings: .: (0.000642) test_keggclass: .: (0.000395) test_ko_pathway: .: (0.000315) test_modules_as_hash: .: (0.000445) test_modules_as_strings: .: (0.000373) test_name: .: (0.000542) test_new: .: (0.000299) test_organism: .: (0.000285) test_orthologs_as_hash: .: (0.000266) test_orthologs_as_strings: .: (0.000685) test_pathways_as_hash: .: (0.000282) test_pathways_as_strings: .: (0.000255) test_reactions_as_hash: .: (0.000647) test_reactions_as_strings: .: (0.000462) test_references: .: (0.001483) test_rel_pathways_as_hash: .: (0.000567) test_rel_pathways_as_strings: .: (0.000366) Bio::TestBioLITDB: test_author: .: (0.000455) test_entry_id: .: (0.000216) test_field: .: (0.000220) test_journal: .: (0.000214) test_keyword: .: (0.000843) test_reference: .: (0.000472) test_title: .: (0.000247) test_volume: .: (0.000214) Bio::TestBioNBRF: test_aalen: .: (0.000427) test_aaseq: .: (0.000200) test_entry: .: (0.000184) test_length: .: (0.000188) test_nalen: .: (0.000289) test_naseq: .: (0.000810) test_seq: .: (0.000230) test_seq_class: .: (0.000161) test_to_nbrf: .: (0.000201) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000458) test_to_newick_format_leaf: .: (0.000388) test_to_newick_format_leaf_NHX: .: (0.000223) Bio::TestBl2seqReport: test_db_len: .: (0.000850) test_db_num: .: (0.001191) test_new: .: (0.000462) test_undefed_methods: .: (0.001599) test_undefed_methods_for_iteration: .: (0.001608) Bio::TestBl2seqReportConstants: test_rs: .: (0.000301) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000502) test_hits: .: (0.000691) Bio::TestBlast: test_blast_reports_format0: .: (0.008806) test_blast_reports_format0_with_block: .: (0.001361) test_blast_reports_format7: .: (0.045500) test_blast_reports_format7_with_block: .: (0.100529) test_blast_reports_format7_with_parser: .: (0.143817) test_blast_reports_format7_with_parser_with_block: .: (0.030920) test_blast_reports_format8: .: (0.001162) test_blast_reports_format8_with_block: .: (0.000919) test_blast_reports_format8_with_parser: .: (0.000459) test_blast_reports_format8_with_parser_with_block: .: (0.000837) test_blast_reports_xml: .: (0.026145) test_blast_reports_xml_with_block: .: (0.026537) test_blastll: .: (0.000298) test_db: .: (0.000183) test_exec_genomenet: .: (0.000519) test_exec_local: .: (0.000189) test_exec_ncbi: .: (0.000181) test_filter: .: (0.000205) test_format: .: (0.000228) test_make_command_line: .: (0.001000) test_make_command_line_2: .: (0.001292) test_matrix: .: (0.000529) test_new: .: (0.000470) test_new_opt_string: .: (0.000413) test_option: .: (0.000251) test_option_set: .: (0.000399) test_option_set_m0: .: (0.000348) test_options: .: (0.000493) test_output: .: (0.000219) test_parse_result: .: (0.029360) test_parser: .: (0.000325) test_program: .: (0.000526) test_query: .: (0.000176) test_self_local: .: (0.000352) test_self_remote: .: (0.003428) test_server: .: (0.000331) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000887) test_delete: .: (0.000941) test_equal_equal: .: (0.000619) test_get: .: (0.000630) test_make_command_line_options: .: (0.000767) test_normalize!: .: (0.000367) test_parse: .: (0.000398) test_set: .: (0.001009) Bio::TestBlastReport: test_db: .: (0.026913) test_db_len: .: (0.026662) test_db_num: .: (0.026589) test_each_hit: .: (0.027342) test_each_iteration: .: (0.030408) test_eff_space: .: (0.032641) test_entrez_query: .: (0.026006) test_entropy: .: (0.027082) test_expect: .: (0.027942) test_filter: .: (0.027924) test_gap_extend: .: (0.026519) test_gap_open: .: (0.025783) test_hits: .: (0.027482) test_hsp_len: .: (0.026315) test_inclusion: .: (0.029050) test_iterations: .: (0.027258) test_kappa: .: (0.027173) test_lambda: .: (0.026633) test_matrix: .: (0.032011) test_message: .: (0.028620) test_parameters: .: (0.027691) test_pattern: .: (0.032377) test_program: .: (0.040250) test_query_def: .: (0.032136) test_query_id: .: (0.027278) test_query_len: .: (0.026524) test_reference: .: (0.026861) test_sc_match: .: (0.026708) test_sc_mismatch: .: (0.029400) test_statistics: .: (0.026867) test_version: .: (0.026771) Bio::TestBlastReportDefault: test_db: .: (0.001520) test_db_len: .: (0.000711) test_db_num: .: (0.000622) test_each_hit: .: (0.004959) test_each_iteration: .: (0.000696) test_eff_space: .: (0.000775) test_entropy: .: (0.000654) test_expect: .: (0.000747) test_gap_extend: .: (0.002868) test_gap_open: .: (0.000743) test_gapped_entropy: .: (0.000647) test_gapped_kappa: .: (0.000595) test_gapped_lambda: .: (0.000581) test_hits: .: (0.000718) test_iterations: .: (0.000603) test_kappa: .: (0.000684) test_lambda: .: (0.001067) test_matrix: .: (0.000780) test_message: .: (0.000545) test_pattern: .: (0.000541) test_program: .: (0.000575) test_query_def: .: (0.000949) test_query_len: .: (0.000660) test_reference: .: (0.000676) test_sc_match: .: (0.000877) test_sc_mismatch: .: (0.000702) test_version: .: (0.000893) Bio::TestBlastReportHit: test_Hit_accession: .: (0.026414) test_Hit_bit_score: .: (0.029992) test_Hit_definition: .: (0.026661) test_Hit_evalue: .: (0.026962) test_Hit_hit_id: .: (0.027156) test_Hit_hsps: .: (0.027025) test_Hit_identity: .: (0.028983) test_Hit_lap_at: .: (0.028836) test_Hit_len: .: (0.026816) test_Hit_midline: .: (0.026969) test_Hit_num: .: (0.027225) test_Hit_overlap: .: (0.028947) test_Hit_query_def: .: (0.027027) test_Hit_query_end: .: (0.026745) test_Hit_query_id: .: (0.026403) test_Hit_query_len: .: (0.028612) test_Hit_query_seq: .: (0.028136) test_Hit_query_start: .: (0.026885) test_Hit_taeget_def: .: (0.027882) test_Hit_target_end: .: (0.026906) test_Hit_target_id: .: (0.029013) test_Hit_target_len: .: (0.027327) test_Hit_target_seq: .: (0.026183) test_Hit_target_start: .: (0.026966) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001548) test_Hit_definition: .: (0.000646) test_Hit_evalue: .: (0.000633) test_Hit_hsps: .: (0.000581) test_Hit_identity: .: (0.001090) test_Hit_lap_at: .: (0.001068) test_Hit_len: .: (0.000785) test_Hit_midline: .: (0.000925) test_Hit_overlap: .: (0.000872) test_Hit_query_end: .: (0.000841) test_Hit_query_seq: .: (0.001159) test_Hit_query_start: .: (0.000968) test_Hit_taeget_def: .: (0.000918) test_Hit_target_end: .: (0.000861) test_Hit_target_id: .: (0.000596) test_Hit_target_len: .: (0.000571) test_Hit_target_seq: .: (0.000834) test_Hit_target_start: .: (0.001038) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.082232) test_Hit_bit_score: .: (0.087420) test_Hit_definition: .: (0.091654) test_Hit_evalue: .: (0.152189) test_Hit_hit_id: .: (0.083265) test_Hit_hsps: .: (0.080021) test_Hit_identity: .: (0.078862) test_Hit_lap_at: .: (0.082135) test_Hit_len: .: (0.081332) test_Hit_midline: .: (0.081594) test_Hit_num: .: (0.081397) test_Hit_overlap: .: (0.086638) test_Hit_query_def: .: (0.079489) test_Hit_query_end: .: (0.080452) test_Hit_query_id: .: (0.081336) test_Hit_query_len: .: (0.081238) test_Hit_query_seq: .: (0.078534) test_Hit_query_start: .: (0.085860) test_Hit_taeget_def: .: (0.079291) test_Hit_target_end: .: (0.075499) test_Hit_target_id: .: (0.082973) test_Hit_target_len: .: (0.089502) test_Hit_target_seq: .: (0.080270) test_Hit_target_start: .: (0.078156) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.076175) test_Hit_bit_score: .: (0.074567) test_Hit_definition: .: (0.074188) test_Hit_evalue: .: (0.083544) test_Hit_hit_id: .: (0.073997) test_Hit_hsps: .: (0.072895) test_Hit_identity: .: (0.080481) test_Hit_lap_at: .: (0.081206) test_Hit_len: .: (0.074821) test_Hit_midline: .: (0.083129) test_Hit_num: .: (0.076704) test_Hit_overlap: .: (0.093165) test_Hit_query_def: .: (0.142260) test_Hit_query_end: .: (0.082840) test_Hit_query_id: .: (0.079325) test_Hit_query_len: .: (0.079161) test_Hit_query_seq: .: (0.084595) test_Hit_query_start: .: (0.085932) test_Hit_taeget_def: .: (0.082349) test_Hit_target_end: .: (0.101777) test_Hit_target_id: .: (0.080697) test_Hit_target_len: .: (0.072125) test_Hit_target_seq: .: (0.085017) test_Hit_target_start: .: (0.085369) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.025802) test_Hit_bit_score: .: (0.024861) test_Hit_definition: .: (0.027408) test_Hit_evalue: .: (0.025602) test_Hit_hit_id: .: (0.024888) test_Hit_hsps: .: (0.025752) test_Hit_identity: .: (0.024902) test_Hit_lap_at: .: (0.027110) test_Hit_len: .: (0.022303) test_Hit_midline: .: (0.024862) test_Hit_num: .: (0.031265) test_Hit_overlap: .: (0.025066) test_Hit_query_def: .: (0.022515) test_Hit_query_end: .: (0.025029) test_Hit_query_id: .: (0.027372) test_Hit_query_len: .: (0.027614) test_Hit_query_seq: .: (0.028988) test_Hit_query_start: .: (0.026780) test_Hit_taeget_def: .: (0.026724) test_Hit_target_end: .: (0.027362) test_Hit_target_id: .: (0.029877) test_Hit_target_len: .: (0.026829) test_Hit_target_seq: .: (0.023947) test_Hit_target_start: .: (0.023649) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000645) test_Hit_bit_score: .: (0.000229) test_Hit_definition: .: (0.000198) test_Hit_evalue: .: (0.000237) test_Hit_hit_id: .: (0.000205) test_Hit_hsps: .: (0.000201) test_Hit_identity: .: (0.000202) test_Hit_lap_at: .: (0.000247) test_Hit_len: .: (0.000220) test_Hit_midline: .: (0.000232) test_Hit_num: .: (0.000519) test_Hit_overlap: .: (0.000252) test_Hit_query_def: .: (0.000243) test_Hit_query_end: .: (0.000244) test_Hit_query_id: .: (0.000234) test_Hit_query_len: .: (0.000294) test_Hit_query_seq: .: (0.000224) test_Hit_query_start: .: (0.000244) test_Hit_taeget_def: .: (0.000203) test_Hit_target_end: .: (0.000200) test_Hit_target_id: .: (0.000201) test_Hit_target_len: .: (0.000206) test_Hit_target_seq: .: (0.000428) test_Hit_target_start: .: (0.000222) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.029414) test_Hsp_bit_score: .: (0.027413) test_Hsp_density: .: (0.026039) test_Hsp_evalue: .: (0.026976) test_Hsp_gaps: .: (0.024651) test_Hsp_hit_frame: .: (0.026702) test_Hsp_hit_from: .: (0.024456) test_Hsp_hit_to: .: (0.024142) test_Hsp_hseq: .: (0.023990) test_Hsp_identity: .: (0.026721) test_Hsp_midline: .: (0.024202) test_Hsp_mismatch_count: .: (0.024224) test_Hsp_num: .: (0.023987) test_Hsp_pattern_from: .: (0.026412) test_Hsp_pattern_to: .: (0.028910) test_Hsp_percent_identity: .: (0.028138) test_Hsp_positive: .: (0.026861) test_Hsp_qseq: .: (0.027031) test_Hsp_query_frame: .: (0.028955) test_Hsp_query_from: .: (0.026681) test_Hsp_query_to: .: (0.028513) test_Hsp_score: .: (0.026692) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.001241) test_Hsp_bit_score: .: (0.000675) test_Hsp_evalue: .: (0.000703) test_Hsp_gaps: .: (0.001321) test_Hsp_hit_frame: .: (0.000662) test_Hsp_hit_from: .: (0.000848) test_Hsp_hit_to: .: (0.000821) test_Hsp_hseq: .: (0.001160) test_Hsp_identity: .: (0.000667) test_Hsp_midline: .: (0.001131) test_Hsp_percent_identity: .: (0.000630) test_Hsp_positive: .: (0.000592) test_Hsp_qseq: .: (0.001216) test_Hsp_query_frame: .: (0.000681) test_Hsp_query_from: .: (0.000957) test_Hsp_query_to: .: (0.000922) test_Hsp_score: .: (0.001153) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.083183) test_Hsp_bit_score: .: (0.157214) test_Hsp_density: .: (0.086963) test_Hsp_evalue: .: (0.183062) test_Hsp_gaps: .: (0.133427) test_Hsp_hit_frame: .: (0.078184) test_Hsp_hit_from: .: (0.080322) test_Hsp_hit_to: .: (0.125398) test_Hsp_hseq: .: (0.087369) test_Hsp_identity: .: (0.075980) test_Hsp_midline: .: (0.075956) test_Hsp_mismatch_count: .: (0.078484) test_Hsp_num: .: (0.135446) test_Hsp_pattern_from: .: (0.072353) test_Hsp_pattern_to: .: (0.074235) test_Hsp_percent_identity: .: (0.138502) test_Hsp_positive: .: (0.160157) test_Hsp_qseq: .: (0.172968) test_Hsp_query_frame: .: (0.127331) test_Hsp_query_from: .: (0.080314) test_Hsp_query_to: .: (0.082320) test_Hsp_score: .: (0.079452) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.077168) test_Hsp_bit_score: .: (0.080905) test_Hsp_density: .: (0.081708) test_Hsp_evalue: .: (0.079973) test_Hsp_gaps: .: (0.088428) test_Hsp_hit_frame: .: (0.081398) test_Hsp_hit_from: .: (0.079696) test_Hsp_hit_to: .: (0.084335) test_Hsp_hseq: .: (0.167399) test_Hsp_identity: .: (0.086053) test_Hsp_midline: .: (0.080666) test_Hsp_mismatch_count: .: (0.076815) test_Hsp_num: .: (0.080691) test_Hsp_pattern_from: .: (0.079816) test_Hsp_pattern_to: .: (0.076951) test_Hsp_percent_identity: .: (0.094714) test_Hsp_positive: .: (0.059555) test_Hsp_qseq: .: (0.058319) test_Hsp_query_frame: .: (0.058540) test_Hsp_query_from: .: (0.056318) test_Hsp_query_to: .: (0.057160) test_Hsp_score: .: (0.058353) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.020704) test_Hsp_bit_score: .: (0.018875) test_Hsp_density: .: (0.019204) test_Hsp_evalue: .: (0.020608) test_Hsp_gaps: .: (0.019506) test_Hsp_hit_frame: .: (0.018864) test_Hsp_hit_from: .: (0.019190) test_Hsp_hit_to: .: (0.019773) test_Hsp_hseq: .: (0.021315) test_Hsp_identity: .: (0.018950) test_Hsp_midline: .: (0.018834) test_Hsp_mismatch_count: .: (0.018639) test_Hsp_num: .: (0.019362) test_Hsp_pattern_from: .: (0.020981) test_Hsp_pattern_to: .: (0.019384) test_Hsp_percent_identity: .: (0.020177) test_Hsp_positive: .: (0.022220) test_Hsp_qseq: .: (0.018759) test_Hsp_query_frame: .: (0.020423) test_Hsp_query_from: .: (0.019213) test_Hsp_query_to: .: (0.019303) test_Hsp_score: .: (0.018992) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000889) test_Hsp_bit_score: .: (0.000203) test_Hsp_density: .: (0.000147) test_Hsp_evalue: .: (0.000148) test_Hsp_gaps: .: (0.000146) test_Hsp_hit_frame: .: (0.000137) test_Hsp_hit_from: .: (0.000138) test_Hsp_hit_to: .: (0.000239) test_Hsp_hseq: .: (0.000167) test_Hsp_identity: .: (0.000174) test_Hsp_midline: .: (0.000163) test_Hsp_mismatch_count: .: (0.000157) test_Hsp_num: .: (0.000162) test_Hsp_pattern_from: .: (0.000167) test_Hsp_pattern_to: .: (0.000159) test_Hsp_percent_identity: .: (0.000387) test_Hsp_positive: .: (0.000344) test_Hsp_qseq: .: (0.000159) test_Hsp_query_frame: .: (0.000160) test_Hsp_query_from: .: (0.000140) test_Hsp_query_to: .: (0.000139) test_Hsp_score: .: (0.000146) Bio::TestBlastReportIteration: test_hits: .: (0.022021) test_message: .: (0.020451) test_num: .: (0.019449) test_statistics: .: (0.019126) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000783) test_message: .: (0.000460) test_num: .: (0.000434) Bio::TestBlastReportIterationMulti: test_each: .: (0.062932) test_hits: .: (0.057238) test_message: .: (0.057504) test_num: .: (0.059503) test_query_def: .: (0.056952) test_query_id: .: (0.058408) test_query_len: .: (0.059138) test_statistics: .: (0.057575) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.060897) test_hits: .: (0.058559) test_message: .: (0.055716) test_num: .: (0.058606) test_query_def: .: (0.059968) test_query_id: .: (0.062324) test_query_len: .: (0.057663) test_statistics: .: (0.063786) Bio::TestBlastReportIterationREXML: test_hits: .: (0.019066) test_message: .: (0.020124) test_num: .: (0.019246) test_statistics: .: (0.020223) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000494) test_message: .: (0.000174) test_num: .: (0.000167) test_statistics: .: (0.000171) Bio::TestBlastReportMulti: test_db: .: (0.056500) test_db_len: .: (0.059043) test_db_num: .: (0.056056) test_each_hit: .: (0.056966) test_each_iteration: .: (0.060047) test_eff_space: .: (0.055350) test_entropy: .: (0.058850) test_expect: .: (0.058279) test_filter: .: (0.056055) test_gap_extend: .: (0.058535) test_gap_open: .: (0.058259) test_hits: .: (0.056134) test_hsp_len: .: (0.059433) test_iterations: .: (0.059011) test_kappa: .: (0.058530) test_lambda: .: (0.056434) test_matrix: .: (0.062748) test_message: .: (0.059787) test_parameters: .: (0.056523) test_pattern: .: (0.059870) test_program: .: (0.089068) test_query_def: .: (0.082861) test_query_id: .: (0.146942) test_query_len: .: (0.166600) test_reference: .: (0.076372) test_reports: .: (0.081606) test_statistics: .: (0.086834) test_version: .: (0.076799) Bio::TestBlastReportMultiREXML: test_db: .: (0.095922) test_db_len: .: (0.082250) test_db_num: .: (0.081492) test_each_hit: .: (0.077851) test_each_iteration: .: (0.091615) test_eff_space: .: (0.080602) test_entropy: .: (0.075176) test_expect: .: (0.077717) test_filter: .: (0.079155) test_gap_extend: .: (0.075592) test_gap_open: .: (0.111165) test_hits: .: (0.083075) test_hsp_len: .: (0.075296) test_iterations: .: (0.067565) test_kappa: .: (0.086925) test_lambda: .: (0.082497) test_matrix: .: (0.081345) test_message: .: (0.085416) test_parameters: .: (0.084624) test_pattern: .: (0.082227) test_program: .: (0.077096) test_query_def: .: (0.081160) test_query_id: .: (0.081438) test_query_len: .: (0.076202) test_reference: .: (0.075283) test_reports: .: (0.095170) test_statistics: .: (0.077651) test_version: .: (0.075410) Bio::TestBlastReportREXML: test_db: .: (0.029905) test_db_len: .: (0.026623) test_db_num: .: (0.025312) test_each_hit: .: (0.024968) test_each_iteration: .: (0.027441) test_eff_space: .: (0.026289) test_entrez_query: .: (0.025795) test_entropy: .: (0.024321) test_expect: .: (0.026725) test_filter: .: (0.028194) test_gap_extend: .: (0.025353) test_gap_open: .: (0.025763) test_hits: .: (0.025354) test_hsp_len: .: (0.027402) test_inclusion: .: (0.025483) test_iterations: .: (0.025643) test_kappa: .: (0.025075) test_lambda: .: (0.027256) test_matrix: .: (0.028688) test_message: .: (0.025308) test_parameters: .: (0.025366) test_pattern: .: (0.029783) test_program: .: (0.027337) test_query_def: .: (0.027271) test_query_id: .: (0.025142) test_query_len: .: (0.024334) test_reference: .: (0.028199) test_sc_match: .: (0.024055) test_sc_mismatch: .: (0.028623) test_statistics: .: (0.024705) test_version: .: (0.026264) Bio::TestBlastReportTabular: test_db: .: (0.000547) test_db_len: .: (0.000185) test_db_num: .: (0.000187) test_each_hit: .: (0.000196) test_each_iteration: .: (0.000180) test_eff_space: .: (0.000181) test_entrez_query: .: (0.000218) test_entropy: .: (0.000205) test_expect: .: (0.000206) test_filter: .: (0.000428) test_gap_extend: .: (0.000230) test_gap_open: .: (0.000196) test_hits: .: (0.000493) test_hsp_len: .: (0.000186) test_inclusion: .: (0.000189) test_iterations: .: (0.000180) test_kappa: .: (0.000177) test_lambda: .: (0.000181) test_matrix: .: (0.000182) test_message: .: (0.000199) test_parameters: .: (0.000189) test_pattern: .: (0.000191) test_program: .: (0.000185) test_query_def: .: (0.000553) test_query_id: .: (0.000256) test_query_len: .: (0.000187) test_reference: .: (0.000223) test_sc_match: .: (0.000199) test_sc_mismatch: .: (0.000217) test_statistics: .: (0.000219) test_version: .: (0.000203) Bio::TestChain: test_aaseq: .: (0.000589) test_addLigand: .: (0.000180) test_addResidue: .: (0.000174) test_atom_seq: .: (0.000179) test_comp: .: (0.000528) test_each: .: (0.000476) test_each_heterogen: .: (0.000159) test_each_residue: .: (0.000150) test_get_heterogen_by_id: .: (0.000156) test_get_residue_by_id: .: (0.000145) test_inspect: .: (0.000227) test_rehash: .: (0.000162) test_rehash_heterogens: .: (0.000137) test_rehash_residues: .: (0.000140) test_square_brace: .: (0.000151) test_to_s: .: (0.000179) Bio::TestChainFinder: test_chains: .: (0.000443) test_each_chain: .: (0.000228) test_find_chain: .: (0.000443) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.015073) test_header: .: (0.001573) test_match_line: .: (0.000826) test_sequence0: .: (0.000883) test_sequence1: .: (0.001358) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.015802) test_header: .: (0.001619) test_match_line: .: (0.001323) test_sequence0: .: (0.001473) test_sequence1: .: (0.001481) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.019498) test_header: .: (0.001041) test_match_line: .: (0.001153) test_sequence0: .: (0.001251) test_sequence1: .: (0.001024) Bio::TestCodonTable: test_Tables: .: (0.000320) test_accessor: .: (0.000369) test_definition: .: (0.000117) test_each: .: (0.000137) test_revtrans: .: (0.000222) test_self_accessor: .: (0.000118) test_self_copy: .: (0.001356) test_set_accessor: .: (0.226731) test_start: .: (0.000190) test_start_codon?: .: (0.000178) test_stop: .: (0.000144) test_stop_codon?: .: (0.000166) test_table: .: (0.000139) Bio::TestCodonTableConstants: test_Definitions: .: (0.000349) test_Starts: .: (0.000144) test_Tables: .: (0.000114) test_stops: .: (0.000138) Bio::TestColorScheme: test_buried: .: (0.002027) Bio::TestCommand: test_command_constants: .: (0.000306) test_escape_shell: .: (0.000195) test_escape_shell_unix: .: (0.000187) test_escape_shell_windows: .: (0.000190) test_make_cgi_params_by_array_of_array: .: (0.000489) test_make_cgi_params_by_array_of_hash: .: (0.000491) test_make_cgi_params_by_array_of_string: .: (0.000439) test_make_cgi_params_by_hash_in_string: .: (0.000644) test_make_cgi_params_by_hash_in_symbol: .: (0.000602) test_make_cgi_params_by_string: .: (0.000229) test_make_command_line: .: (0.000167) test_make_command_line_unix: .: (0.000152) test_make_command_line_windows: .: (0.000162) test_safe_command_line_array: .: (0.000170) test_safe_command_line_array_passthrough: .: (0.000353) Bio::TestContingencyTable: test_lite_example: .: (0.236534) Bio::TestDB: test_entry_id: .: (0.000467) test_exists: .: (0.000317) test_fetch: .: (0.000221) test_get: .: (0.000136) test_open: .: (0.000129) test_tags: .: (0.000138) Bio::TestDataType: test_const_like_method: .: (0.000695) test_pdb_achar: .: (0.000257) test_pdb_atom: .: (0.000231) test_pdb_character: .: (0.000227) test_pdb_date: .: (0.000258) test_pdb_idcode: .: (0.000226) test_pdb_integer: .: (0.000121) test_pdb_list: .: (0.000137) test_pdb_lstring: .: (0.000432) test_pdb_real: .: (0.000203) test_pdb_resudue_name: .: (0.000263) test_pdb_slist: .: (0.000146) test_pdb_string: .: (0.000272) test_pdb_stringrj: .: (0.000143) test_pdb_symop: .: (0.000252) test_specification_list: .: (0.000165) Bio::TestEMBL: test_ac: .: (0.001083) test_accession: .: (0.000683) test_cc: .: (0.000524) test_de: .: (0.000501) test_division: .: (0.000516) test_dr: .: (0.000461) test_dt: .: (0.000908) test_dt_created: .: (0.000533) test_dt_iterator: .: (0.000496) test_dt_updated: .: (0.000477) test_each_cds: .: (0.000982) test_each_gene: .: (0.000938) test_entry: .: (0.000585) test_fh: .: (0.000532) test_ft: .: (0.001006) test_ft_accessor: .: (0.000798) test_ft_iterator: .: (0.001056) test_id_line: .: (0.000524) test_id_line_data_class: .: (0.000624) test_id_line_division: .: (0.000491) test_id_line_entry_name: .: (0.000522) test_id_line_iterator: .: (0.000633) test_id_line_molecule_type: .: (0.001047) test_id_line_sequence_length: .: (0.000613) test_kw: .: (0.000554) test_molecule: .: (0.000557) test_oc: .: (0.000774) test_og: .: (0.000659) test_os: .: (0.000584) test_ref: .: (0.000785) test_references: .: (0.001253) test_seq: .: (0.001105) test_sequence_length: .: (0.000573) test_sq: .: (0.000529) test_sq_get: .: (0.000664) test_sv: .: (0.000545) test_version: .: (0.000566) Bio::TestEMBL89: test_ac: .: (0.001073) test_accession: .: (0.000678) test_cc: .: (0.000460) test_de: .: (0.000514) test_division: .: (0.000535) test_dr: .: (0.000464) test_dt: .: (0.001611) test_dt_created: .: (0.000555) test_dt_iterator: .: (0.000483) test_dt_updated: .: (0.000479) test_each_cds: .: (0.000774) test_each_gene: .: (0.001035) test_entry: .: (0.000641) test_fh: .: (0.000555) test_ft: .: (0.000833) test_ft_accessor: .: (0.000925) test_ft_iterator: .: (0.000779) test_id_line: .: (0.000532) test_id_line_data_class: .: (0.000781) test_id_line_division: .: (0.000516) test_id_line_entry_name: .: (0.000581) test_id_line_iterator: .: (0.000878) test_id_line_molecule_type: .: (0.000594) test_id_line_sequence_length: .: (0.000682) test_id_line_sequence_version: .: (0.000513) test_kw: .: (0.000470) test_molecule: .: (0.000594) test_oc: .: (0.009193) test_og: .: (0.000562) test_os: .: (0.000544) test_ref: .: (0.000687) test_references: .: (0.001019) test_seq: .: (0.001085) test_sequence_length: .: (0.000542) test_sq: .: (0.000706) test_sq_get: .: (0.000519) test_sv: .: (0.000590) test_version: .: (0.000906) Bio::TestEMBLAPI: test_ac: .: (0.000456) test_accessions: .: (0.000397) Bio::TestEMBLCommon: test_ac: .: (0.000285) test_accession: .: (0.000122) test_accessions: .: (0.000119) test_de: .: (0.000114) test_definition: .: (0.000130) test_description: .: (0.000138) test_dr: .: (0.000116) test_keywords: .: (0.000116) test_kw: .: (0.000117) test_oc: .: (0.000206) test_og: .: (0.000153) test_os: .: (0.000148) test_ref: .: (0.000147) test_references: .: (0.000138) Bio::TestEMBLDB: test_fetch: .: (0.000678) test_p_entry2hash: .: (0.000135) Bio::TestEMBLToBioSequence: test_classification: .: (0.005581) test_date_created: .: (0.001070) test_date_modified: .: (0.000628) test_definition: .: (0.000780) test_division: .: (0.000567) test_entry_id: .: (0.000580) test_entry_version: .: (0.000909) test_features: .: (0.001018) test_keywords: .: (0.000577) test_molecule_type: .: (0.000545) test_primary_accession: .: (0.005620) test_references: .: (0.001041) test_release_created: .: (0.000580) test_release_modified: .: (0.000883) test_secondary_accessions: .: (0.000911) test_sequence_version: .: (0.000708) test_species: .: (0.000575) test_topology: .: (0.000782) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.005457) test_date_created: .: (0.004977) test_date_modified: .: (0.005263) test_definition: .: (0.005344) test_division: .: (0.005307) test_entry_id: .: (0.005240) test_entry_version: .: (0.005490) test_features: .: (0.005625) test_keywords: .: (0.005444) test_molecule_type: .: (0.005193) test_primary_accession: .: (0.005156) test_references: .: (0.005717) test_release_created: .: (0.005102) test_release_modified: .: (0.004935) test_secondary_accessions: .: (0.005104) test_sequence_version: .: (0.005724) test_species: .: (0.004932) test_topology: .: (0.009740) Bio::TestFasta: test_db: .: (0.000343) test_format: .: (0.000128) test_format_arg_integer: .: (0.000160) test_format_arg_str: .: (0.000132) test_ktup: .: (0.000132) test_matrix: .: (0.000167) test_option: .: (0.000222) test_options: .: (0.000168) test_output: .: (0.000131) test_program: .: (0.000146) test_server: .: (0.000150) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000362) test_accession: .: (0.000472) test_accessions: .: (0.000162) test_description: .: (0.000153) test_descriptions: .: (0.000154) test_entry_id: .: (0.000153) test_get_all_by_type: .: (0.000158) test_gi: .: (0.000152) test_id_strings: .: (0.000216) test_list_ids: .: (0.000147) test_locus: .: (0.000158) test_words: .: (0.000217) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000620) test_accession: .: (0.000189) test_accessions: .: (0.000202) test_description: .: (0.000432) test_descriptions: .: (0.000188) test_emb: .: (0.000204) test_entry_id: .: (0.000179) test_get_all_by_type: .: (0.000180) test_get_emb: .: (0.000200) test_gi: .: (0.000164) test_id_strings: .: (0.000233) test_list_ids: .: (0.000161) test_locus: .: (0.000161) test_words: .: (0.000443) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000297) test_accession: .: (0.000160) test_accessions: .: (0.000429) test_description: .: (0.000154) test_descriptions: .: (0.000146) test_entry_id: .: (0.000133) test_get_all_by_type: .: (0.000149) test_gi: .: (0.000171) test_id_strings: .: (0.000223) test_list_ids: .: (0.000162) test_locus: .: (0.000169) test_sp: .: (0.000193) test_words: .: (0.000467) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000428) test_accession: .: (0.000207) test_accessions: .: (0.000220) test_description: .: (0.000414) test_descriptions: .: (0.000196) test_entry_id: .: (0.000193) test_get_all_by_type: .: (0.000200) test_gi: .: (0.000195) test_id_strings: .: (0.000727) test_list_ids: .: (0.000220) test_locus: .: (0.000212) test_words: .: (0.000437) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000383) test_accession: .: (0.000413) test_accessions: .: (0.000216) test_description: .: (0.000194) test_descriptions: .: (0.000195) test_entry_id: .: (0.000201) test_get_all_by_type: .: (0.000175) test_gi: .: (0.000513) test_id_strings: .: (0.000301) test_list_ids: .: (0.000173) test_locus: .: (0.000171) test_words: .: (0.000286) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000288) test_accession: .: (0.000128) test_accessions: .: (0.000314) test_description: .: (0.000127) test_descriptions: .: (0.000129) test_entry_id: .: (0.000128) test_get_all_by_type: .: (0.000571) test_gi: .: (0.000143) test_id_strings: .: (0.000180) test_list_ids: .: (0.000142) test_locus: .: (0.000146) test_words: .: (0.000188) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000322) test_accession: .: (0.000170) test_accessions: .: (0.000156) test_description: .: (0.000145) test_descriptions: .: (0.000146) test_entry_id: .: (0.000336) test_get: .: (0.000163) test_get_all_by_type: .: (0.000140) test_id_strings: .: (0.000242) test_list_ids: .: (0.000455) test_locus: .: (0.000140) test_sp: .: (0.000179) test_words: .: (0.000247) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000321) test_accession: .: (0.000174) test_accessions: .: (0.000170) test_description: .: (0.000147) test_descriptions: .: (0.000160) test_entry_id: .: (0.000159) test_get: .: (0.000469) test_get_all_by_type: .: (0.000169) test_id_strings: .: (0.000326) test_list_ids: .: (0.000147) test_locus: .: (0.000149) test_tr: .: (0.000161) test_words: .: (0.000308) Bio::TestFastaFirstName: test_first_name1: .: (0.000309) test_first_name_multi_identifier: .: (0.000142) test_first_name_single_worded_defintion: .: (0.000134) test_no_definition: .: (0.000131) test_space_before_first_name: .: (0.000139) test_tabbed_defintion: .: (0.000137) Bio::TestFastaFormat: test_aalen: .: (0.000546) test_aaseq: .: (0.000180) test_acc_version: .: (0.000569) test_accession: .: (0.000298) test_accessions: .: (0.000227) test_data: .: (0.000165) test_definition: .: (0.000160) test_entry: .: (0.000165) test_entry_id: .: (0.000231) test_entry_overrun: .: (0.000159) test_first_name: .: (0.000159) test_gi: .: (0.000198) test_identifiers: .: (0.000198) test_length: .: (0.003983) test_query: .: (0.000347) test_seq: .: (0.000177) Bio::TestFastaFormatConst: test_delimiter: .: (0.000744) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000407) test_data: .: (0.000153) test_definition: .: (0.000153) test_entry: .: (0.000156) test_entry_id: .: (0.000214) test_first_name: .: (0.000158) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000314) test_naseq: .: (0.000181) test_naseq_class: .: (0.000196) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000406) Bio::TestFastaInitialize: test_new_1: .: (0.001294) test_option: .: (0.000131) test_option_backward_compatibility: .: (0.000168) Bio::TestFastaNumericFormat: test_arg: .: (0.000351) test_data: .: (0.000190) test_definition: .: (0.000441) test_each: .: (0.000196) test_entry: .: (0.000138) test_entry_id: .: (0.000164) test_length: .: (0.000188) test_to_biosequence: .: (0.001633) Bio::TestFastaQuery: test_query: .: (0.000268) test_self_local: .: (0.000102) test_self_parser: .: (0.000101) test_self_remote: .: (0.000095) Bio::TestFastacmd: test_database: .: (0.000513) test_fastacmd: .: (0.000112) test_methods: .: (0.000164) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000858) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.001134) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000637) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000734) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000899) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000740) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000873) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000661) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001001) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000799) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000920) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000618) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000835) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.002181) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.002188) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000701) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000841) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000729) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.009749) test_error_probabilities_as_sanger: .: (0.010366) test_error_probabilities_as_solexa: .: (0.016291) test_quality_scores_as_illumina: .: (0.000683) test_quality_scores_as_sanger: .: (0.000404) test_quality_scores_as_solexa: .: (0.000523) test_validate_format: .: (0.000859) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.002261) test_entry_id: .: (0.001981) test_error_probabilities: .: (0.357858) test_nalen: .: (0.001817) test_naseq: .: (0.002366) test_quality_scores: .: (0.003308) test_quality_string: .: (0.001690) test_roundtrip: .: (0.288535) test_seq: .: (0.002356) test_sequence_string: .: (0.002105) test_to_biosequence: .: (0.281457) test_to_biosequence_and_output: .: (0.008301) test_to_s: .: (0.002113) test_validate_format: .: (0.001832) test_validate_format_with_array: .: (0.002102) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000954) test_mask_20_with_empty_string: .: (0.000583) test_mask_20_with_longer_string: .: (0.000533) test_mask_20_with_x: .: (0.000502) test_mask_60: .: (0.001220) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.014704) test_error_probabilities_as_sanger: .: (0.014873) test_error_probabilities_as_solexa: .: (0.015197) test_quality_scores_as_illumina: .: (0.000715) test_quality_scores_as_sanger: .: (0.000401) test_quality_scores_as_solexa: .: (0.000584) test_validate_format: .: (0.001224) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.012962) test_error_probabilities_as_sanger: .: (0.011260) test_error_probabilities_as_solexa: .: (0.011547) test_quality_scores_as_illumina: .: (0.001053) test_quality_scores_as_sanger: .: (0.000551) test_quality_scores_as_solexa: .: (0.000492) test_validate_format: .: (0.001305) Bio::TestFeature: test_append: .: (0.000379) test_append_nil: .: (0.000144) test_assoc: .: (0.000158) test_each: .: (0.000122) test_feature: .: (0.000116) test_locations: .: (0.000222) test_new: .: (0.000122) test_position: .: (0.000120) test_qualifiers: .: (0.000123) Bio::TestFeatures: test_append: .: (0.000685) test_arg: .: (0.000156) test_each: .: (0.000144) test_features: .: (0.000155) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.001577) test_aaindex2: .: (0.000318) test_blast: .: (0.000252) test_blastxml: .: (0.000959) test_embl: .: (0.000353) test_embl_oldrelease: .: (0.000554) test_fastaformat: .: (0.000654) test_fastanumericformat: .: (0.000230) test_fastq: .: (0.000268) test_genbank: .: (0.000337) test_genpept: .: (0.000358) test_hmmer: .: (0.000324) test_maxml_cluster: .: (0.009667) test_maxml_sequence: .: (0.000224) test_medline: .: (0.000272) test_prosite: .: (0.004150) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.004344) test_transfac: .: (0.003224) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000435) test_auto_1arg_filename: .: (0.000547) test_auto_1arg_io: .: (0.000667) test_auto_1arg_io_with_block: .: (0.000987) test_auto_1arg_with_block: .: (0.001192) test_auto_2arg_filename_mode: .: (0.000550) test_auto_2arg_filename_mode_with_block: .: (0.001251) test_auto_3arg: .: (0.000455) test_auto_3arg_with_block: .: (0.000890) test_foreach: .: (0.000991) test_new_2arg_class: .: (0.000256) test_new_2arg_nil: .: (0.000449) test_open_0arg: .: (0.000481) test_open_1arg_class: .: (0.000179) test_open_1arg_filename: .: (0.000515) test_open_1arg_io: .: (0.000436) test_open_1arg_io_with_block: .: (0.001180) test_open_1arg_nil: .: (0.000205) test_open_1arg_with_block: .: (0.001130) test_open_2arg_autodetect: .: (0.000526) test_open_2arg_autodetect_io: .: (0.000492) test_open_2arg_autodetect_io_with_block: .: (0.001382) test_open_2arg_autodetect_with_block: .: (0.001233) test_open_2arg_class: .: (0.000281) test_open_2arg_class_io: .: (0.000259) test_open_2arg_class_io_with_block: .: (0.000818) test_open_2arg_class_with_block: .: (0.000836) test_open_2arg_filename_mode: .: (0.000609) test_open_2arg_filename_mode_with_block: .: (0.001272) test_open_3arg: .: (0.000969) test_open_3arg_with_block: .: (0.003354) test_open_4arg: .: (0.002215) test_to_a: .: (0.001035) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000686) test_close: .: (0.000217) test_dbclass: .: (0.000202) test_dbclass_eq: .: (0.000262) test_dbclass_nil: .: (0.000342) test_each: .: (0.000462) test_each_entry: .: (0.001054) test_ended_pos: .: (0.000404) test_entry_pos_flag: .: (0.000229) test_entry_raw: .: (0.000441) test_eof?: .: (0.000381) test_next_entry: .: (0.000537) test_path: .: (0.000209) test_pos: .: (0.000315) test_raw: .: (0.001040) test_rewind: .: (0.000353) test_start_pos: .: (0.000328) test_start_pos_ended_pos_not_recorded: .: (0.000359) test_to_io: .: (0.000203) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000438) test_simpleformat2: .: (0.000247) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000271) test_eof_false_after_prefetch: .: (0.000272) test_eof_false_first: .: (0.000439) test_eof_true: .: (0.000328) test_getc: .: (0.000177) test_getc_after_prefetch: .: (0.000165) test_gets: .: (0.000167) test_gets_equal_prefetch_gets: .: (0.000191) test_gets_paragraph_mode: .: (0.000237) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000406) test_gets_paragraph_mode_within_buffer: .: (0.000476) test_gets_rs: .: (0.000186) test_gets_rs_equal_prefetch_gets: .: (0.000202) test_gets_rs_within_buffer: .: (0.000838) test_pos: .: (0.000174) test_pos=: .: (0.000172) test_prefetch_buffer: .: (0.000179) test_prefetch_gets: .: (0.000172) test_prefetch_gets_with_arg: .: (0.000221) test_rewind: .: (0.000159) test_skip_spaces: .: (0.000209) test_to_io: .: (0.000196) test_ungetc: .: (0.000179) test_ungetc_after_prefetch: .: (0.000198) test_ungets: .: (0.000251) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000662) test_self_open_file: .: (0.000198) test_self_open_file_with_block: .: (0.000227) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000347) test_parse_file_open_arg_int_perm: .: (0.000341) test_parse_file_open_arg_int_perm_opt: .: (0.000136) test_parse_file_open_arg_integer: .: (0.000130) test_parse_file_open_arg_nil: .: (0.000121) test_parse_file_open_arg_opt: .: (0.000218) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000156) test_parse_file_open_arg_str: .: (0.000156) test_parse_file_open_arg_str_opt: .: (0.000181) test_parse_file_open_arg_str_perm: .: (0.000169) test_parse_file_open_arg_str_perm_opt: .: (0.000174) test_parse_file_open_arg_str_with_enc: .: (0.000186) test_parse_file_open_arg_str_with_ext_enc: .: (0.000191) test_parse_file_open_mode_integer: .: (0.000151) test_parse_file_open_mode_nil: .: (0.000168) test_parse_file_open_mode_str: .: (0.000160) test_parse_file_open_mode_str_with_enc: .: (0.000163) test_parse_file_open_mode_str_with_ext_enc: .: (0.000161) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000647) test_entry: .: (0.000159) test_entry_ended_pos: .: (0.000129) test_entry_pos_flag: .: (0.000172) test_entry_start_pos: .: (0.000128) test_get_entry: .: (0.000204) test_rewind: .: (0.000170) test_skip_leader: .: (0.000421) test_stream: .: (0.000161) test_stream_pos: .: (0.000206) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000374) test_delimiter_overrun: .: (0.000159) test_entry: .: (0.000229) test_entry_ended_pos: .: (0.000202) test_entry_ended_pos_default_nil: .: (0.000188) test_entry_start_pos: .: (0.000452) test_entry_start_pos_default_nil: .: (0.000146) test_get_entry: .: (0.000307) test_get_parsed_entry: .: (0.000364) test_header: .: (0.000400) test_skip_leader: .: (0.000213) test_skip_leader_without_header: .: (0.000204) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000496) test_entry_ended_pos: .: (0.000375) test_entry_start_pos: .: (0.000648) test_flag_to_fetch_header: .: (0.000341) test_get_entry: .: (0.000558) test_get_parsed_entry: .: (0.000767) test_rewind: .: (0.000338) test_skip_leader: .: (0.000197) Bio::TestGCGMsf: test_alignment: .: (0.001847) test_checksum: .: (0.000397) test_compcheck: .: (0.000382) test_date: .: (0.000354) test_description: .: (0.000533) test_entry_id: .: (0.000308) test_gap_length_weight: .: (0.000323) test_gap_weight: .: (0.000322) test_heading: .: (0.000302) test_length: .: (0.000298) test_seq_type: .: (0.000302) test_symbol_comparison_table: .: (0.000792) test_validate_checksum: .: (0.002579) Bio::TestGFF: test_record_class: .: (0.000967) test_records: .: (0.010226) Bio::TestGFF2: test_const_version: .: (0.009011) test_gff_version: .: (0.000844) test_metadata: .: (0.001032) test_metadata_size: .: (0.000564) test_records_size: .: (0.000563) test_to_s: .: (0.001600) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000421) test_attributes_case2: .: (0.000265) test_attributes_incompatible_backslash_semicolon: .: (0.000287) Bio::TestGFF2MetaData: test_data: .: (0.000242) test_directive: .: (0.000118) test_parse: .: (0.000138) Bio::TestGFF2Record: test_attribute: .: (0.009404) test_attribute_nonexistent: .: (0.000460) test_attributes: .: (0.000424) test_attributes_to_hash: .: (0.000444) test_comment_only?: .: (0.000348) test_delete_attribute: .: (0.000608) test_delete_attribute_multiple: .: (0.000407) test_delete_attribute_multiple2: .: (0.000450) test_delete_attribute_multiple_nil: .: (0.000379) test_delete_attribute_nil: .: (0.000334) test_delete_attribute_nonexistent: .: (0.000546) test_delete_attributes: .: (0.000424) test_delete_attributes_multiple: .: (0.000415) test_delete_attributes_nonexistent: .: (0.000424) test_end: .: (0.000486) test_eqeq: .: (0.001448) test_eqeq_false: .: (0.000935) test_feature: .: (0.000396) test_frame: .: (0.000390) test_get_attribute: .: (0.000939) test_get_attribute_nonexistent: .: (0.000338) test_get_attributes: .: (0.000510) test_get_attributes_nonexistent: .: (0.000431) test_replace_attributes: .: (0.000431) test_replace_attributes_multiple_multiple_over: .: (0.000443) test_replace_attributes_multiple_multiple_same: .: (0.000697) test_replace_attributes_multiple_multiple_two: .: (0.008863) test_replace_attributes_multiple_single: .: (0.000441) test_replace_attributes_nonexistent: .: (0.000373) test_replace_attributes_nonexistent_multiple: .: (0.000396) test_replace_attributes_single_multiple: .: (0.000720) test_score: .: (0.000377) test_self_parse: .: (0.001100) test_seqname: .: (0.000362) test_set_attribute: .: (0.000460) test_set_attribute_multiple: .: (0.000695) test_set_attribute_nonexistent: .: (0.000398) test_sort_attributes_by_tag!: .: (0.000523) test_sort_attributes_by_tag_bang_test2: .: (0.000503) test_sort_attributes_by_tag_bang_with_block: .: (0.008961) test_source: .: (0.000931) test_start: .: (0.000331) test_strand: .: (0.000341) test_to_s: .: (0.000661) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000956) test_comment_eq: .: (0.000163) test_comment_only?: .: (0.000161) test_comment_only_false: .: (0.000151) test_to_s: .: (0.000160) test_to_s_not_empty: .: (0.000254) Bio::TestGFF3: test_const_version: .: (0.001107) test_gff_version: .: (0.009665) test_records: .: (0.001218) test_sequence_regions: .: (0.001048) test_sequences: .: (0.001045) test_to_s: .: (0.002124) Bio::TestGFF3MetaData: test_data: .: (0.000354) test_directive: .: (0.000134) test_parse: .: (0.000146) Bio::TestGFF3Record: test_attributes: .: (0.000781) test_end: .: (0.000342) test_feature: .: (0.000705) test_frame: .: (0.000359) test_id: .: (0.000332) test_score: .: (0.000338) test_seqname: .: (0.000359) test_source: .: (0.000386) test_start: .: (0.000635) test_strand: .: (0.000328) test_to_s: .: (0.000697) test_to_s_attr_order_changed: .: (0.000805) Bio::TestGFF3RecordEscape: test_escape: .: (0.009029) test_escape_attribute: .: (0.000299) test_escape_seqid: .: (0.000201) test_unescape: .: (0.000222) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000545) test_eqeq: .: (0.000344) test_new_from_sequences_na: .: (0.000337) test_new_from_sequences_na_aa: .: (0.000464) test_new_from_sequences_na_aa_boundary_gap: .: (0.000854) test_new_from_sequences_na_aa_example: .: (0.000541) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000510) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000385) test_process_sequences_na: .: (0.000431) test_process_sequences_na_aa: .: (0.000345) test_process_sequences_na_aa_reverse_frameshift: .: (0.008979) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000467) test_process_sequences_na_aa_tooshort: .: (0.000464) test_process_sequences_na_tooshort: .: (0.000360) test_to_s: .: (0.000283) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000426) test_attributes_one: .: (0.000180) test_attributes_with_escaping: .: (0.000539) test_id_multiple: .: (0.000510) test_id_multiple2: .: (0.000382) test_id_replace: .: (0.000246) test_id_set: .: (0.000263) test_initialize_9: .: (0.000136) test_phase: .: (0.000238) test_score: .: (0.000211) test_to_s_void: .: (0.000170) Bio::TestGFF3RecordTarget: test_end: .: (0.000348) test_parse: .: (0.000578) test_start: .: (0.000170) test_strand: .: (0.000172) test_target_id: .: (0.000421) test_to_s: .: (0.000296) Bio::TestGFF3SequenceRegion: test_end: .: (0.000354) test_parse: .: (0.000258) test_seqid: .: (0.000146) test_start: .: (0.000142) test_to_s: .: (0.000231) Bio::TestGFFRecord: test_attributes: .: (0.000363) test_comment: .: (0.000190) test_end: .: (0.000276) test_feature: .: (0.000199) test_frame: .: (0.000188) test_score: .: (0.000190) test_seqname: .: (0.000179) test_source: .: (0.000164) test_start: .: (0.000171) test_strand: .: (0.000165) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000345) Bio::TestGeneAssociation: test_aspect: .: (0.000342) test_assigned_by: .: (0.000168) test_date: .: (0.000164) test_db: .: (0.000421) test_db_object_id: .: (0.004452) test_db_object_name: .: (0.000238) test_db_object_symbol: .: (0.000152) test_db_object_synonym: .: (0.000172) test_db_object_type: .: (0.000198) test_db_reference: .: (0.000179) test_evidence: .: (0.000185) test_goid: .: (0.000234) test_parser: .: (0.000962) test_qualifier: .: (0.000443) test_taxon: .: (0.000156) test_to_str: .: (0.008564) test_with: .: (0.000219) Bio::TestGenscanReport: test_date_run: .: (0.001644) test_gccontent: .: (0.001526) test_genscan_version: .: (0.001100) test_isochore: .: (0.001154) test_length: .: (0.006175) test_matrix: .: (0.001168) test_predictions_size: .: (0.001463) test_query_name: .: (0.009600) test_time: .: (0.001095) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.001493) test_donor_score: .: (0.000975) test_exon_type: .: (0.001280) test_exon_type_long: .: (0.009419) test_first: .: (0.015305) test_initiation_score: .: (0.001376) test_last: .: (0.001530) test_number: .: (0.001359) test_p_value: .: (0.001365) test_phase: .: (0.000961) test_range: .: (0.009520) test_score: .: (0.001663) test_strand: .: (0.001346) test_t_score: .: (0.001351) test_termination_score: .: (0.000939) Bio::TestGenscanReportGene: test_aaseq: .: (0.010080) test_naseq: .: (0.001447) test_number: .: (0.000859) test_polyA: .: (0.001382) test_promoter: .: (0.001070) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.001434) test_reports_ary_contents: .: (0.005354) Bio::TestHMMERReportConstants: test_rs: .: (0.000322) Bio::TestHMMERReportHit: test_accession: .: (0.001161) test_append_hsp: .: (0.009496) test_bit_score: .: (0.001109) test_definition: .: (0.000925) test_description: .: (0.001293) test_each: .: (0.001380) test_each_hsp: .: (0.001032) test_entry_id: .: (0.000951) test_evalue: .: (0.002743) test_hit: .: (0.001062) test_hit_id: .: (0.001014) test_hsps: .: (0.000943) test_num: .: (0.001305) test_score: .: (0.001224) test_target_def: .: (0.000987) test_target_id: .: (0.000994) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.001395) test_each: .: (0.001105) test_each_hit: .: (0.000980) test_histogram: .: (0.001195) test_hits: .: (0.001121) test_hsps: .: (0.001024) test_parameter: .: (0.001092) test_program: .: (0.001700) test_query_info: .: (0.001084) test_statistical_detail: .: (0.000914) test_total_seq_searched: .: (0.001297) test_whole_seq_top_hits: .: (0.001427) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.001357) test_histogram: .: (0.001222) test_statistical_detail: .: (0.001846) test_total_seq_searched: .: (0.001071) test_whole_seq_top_hit: .: (0.001223) Bio::TestHMMERReportHsp: test_accession: .: (0.001500) test_bit_score: .: (0.001061) test_csline: .: (0.001085) test_domain: .: (0.000927) test_evalue: .: (0.001316) test_flatseq: .: (0.001269) test_hmm_f: .: (0.001122) test_hmm_t: .: (0.001350) test_hmmseq: .: (0.001269) test_hsp: .: (0.001116) test_midline: .: (0.001095) test_query_frame: .: (0.001625) test_query_from: .: (0.001258) test_query_seq: .: (0.001008) test_query_to: .: (0.001399) test_rfline: .: (0.001537) test_score: .: (0.001189) test_seq_f: .: (0.001356) test_seq_ft: .: (0.001207) test_seq_t: .: (0.001577) test_set_alignment: .: (0.001391) test_targat_to: .: (0.000997) test_target_frame: .: (0.001096) test_target_from: .: (0.001803) test_target_seq: .: (0.000926) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000754) test_find_hetatm: .: (0.001054) test_hetatms: .: (0.000563) Bio::TestHeterogen: test_addAtom: .: (0.000645) test_each: .: (0.000331) test_each_hetatm: .: (0.000320) test_get_residue_id_from_atom: .: (0.000242) test_het_atom: .: (0.000223) test_iCode: .: (0.006435) test_inspect: .: (0.000278) test_resSeq: .: (0.007971) test_sort: .: (0.000359) test_square_bracket: .: (0.008436) test_to_s: .: (0.000450) test_update_resudue_id: .: (0.005459) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000491) test_find_heterogen: .: (0.000185) test_heterogens: .: (0.006631) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000518) test_match_description: .: (0.006928) test_match_evalue: .: (0.000287) test_match_ipr_description: .: (0.007572) test_match_ipr_id: .: (0.000371) test_match_match_end: .: (0.000232) test_match_match_start: .: (0.006987) test_match_method: .: (0.000275) test_matches_size: .: (0.006426) test_query_id: .: (0.000349) test_query_length: .: (0.005444) Bio::TestIprscanRawReport: test_entry_id: .: (0.019241) test_match_accession: .: (0.003856) test_match_crc64: .: (0.004372) test_match_date: .: (0.004122) test_match_description: .: (0.003866) test_match_evalue: .: (0.004246) test_match_go_terms: .: (0.004219) test_match_ipr_description: .: (0.003880) test_match_ipr_id: .: (0.004983) test_match_match_end: .: (0.004115) test_match_match_start: .: (0.003990) test_match_method: .: (0.004600) test_match_query_id: .: (0.003983) test_match_query_length: .: (0.006293) test_match_status: .: (0.005006) test_obj: .: (0.003820) test_query_id: .: (0.003793) test_query_length: .: (0.003943) test_self_reports_in_raw: .: (0.007248) Bio::TestIprscanReport: test_output_raw: .: (0.001058) test_to_raw: .: (0.000833) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.001139) test_match_accession: .: (0.000962) test_match_date: .: (0.000787) test_match_description: .: (0.000763) test_match_evalue: .: (0.001004) test_match_go_terms: .: (0.005057) test_match_ipr_description: .: (0.000731) test_match_ipr_id: .: (0.000590) test_match_match_end: .: (0.000851) test_match_match_start: .: (0.000610) test_match_method: .: (0.008975) test_match_status: .: (0.000707) test_matches_size: .: (0.000773) test_query_id: .: (0.000595) test_query_length: .: (0.000567) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.001043) test_to_hash_match?: .: (0.001235) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.010092) Bio::TestKeggCompound: test_comment: .: (0.001096) test_dblinks_as_hash: .: (0.000550) test_dblinks_as_strings: .: (0.000333) test_entry_id: .: (0.000321) test_enzymes: .: (0.000703) test_formula: .: (0.000594) test_kcf: .: (0.000342) test_mass: .: (0.000308) test_name: .: (0.000335) test_names: .: (0.000333) test_pathways_as_hash: .: (0.000682) test_pathways_as_strings: .: (0.000774) test_reactions: .: (0.009299) test_remark: .: (0.000401) test_rpairs: .: (0.000314) Bio::TestKeggEnzyme: test_all_reac: .: (0.000977) test_classes: .: (0.000650) test_cofactors: .: (0.000685) test_comment: .: (0.000615) test_dblinks_as_hash: .: (0.000732) test_dblinks_as_strings: .: (0.000561) test_diseases: .: (0.000519) test_entry: .: (0.009101) test_entry_id: .: (0.001031) test_genes: .: (0.042958) test_genes_as_hash: .: (0.023463) test_genes_as_strings: .: (0.007493) test_inhibitors: .: (0.000828) test_iubmb_reactions: .: (0.000748) test_kegg_reactions: .: (0.000741) test_motifs: .: (0.001206) test_name: .: (0.000841) test_names: .: (0.000720) test_obsolete?: .: (0.000703) test_orthologs_as_hash: .: (0.000780) test_orthologs_as_strings: .: (0.000997) test_pathways_as_hash: .: (0.001217) test_pathways_as_strings: .: (0.000752) test_products: .: (0.000681) test_reaction: .: (0.001052) test_structures: .: (0.001105) test_substrates: .: (0.000782) test_sysname: .: (0.000739) Bio::TestKeggGenesDblinks: test_data: .: (0.000694) test_dblinks_0: .: (0.000188) test_dblinks_1: .: (0.000170) test_dblinks_2: .: (0.000165) Bio::TestKeggGenesStructure: test_data: .: (0.000342) test_ids: .: (0.000267) test_ids_in_array: .: (0.000224) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.020122) test_graphics__size: .: (0.015349) test_id: .: (0.015180) test_link: .: (0.016670) test_name: .: (0.091931) test_reaction: .: (0.014855) test_type: .: (0.016211) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.016211) test_graphics__size: .: (0.015975) test_id: .: (0.016733) test_link: .: (0.016088) test_name: .: (0.015492) test_reaction: .: (0.015334) test_type: .: (0.015618) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.016146) test_category: .: (0.015389) test_entry_id: .: (0.014266) test_fgcolor=: .: (0.015274) test_height=: .: (0.016314) test_label=: .: (0.017773) test_shape=: .: (0.015927) test_width=: .: (0.016367) test_x=: .: (0.016394) test_y=: .: (0.014320) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.013388) test_graphics__size: .: (0.013239) test_id: .: (0.016830) test_link: .: (0.015715) test_name: .: (0.015510) test_reaction: .: (0.015834) test_type: .: (0.015883) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000383) test_graphics=: .: (0.000157) test_id=: .: (0.000203) test_link=: .: (0.000195) test_name=: .: (0.000206) test_reaction=: .: (0.000183) test_type=: .: (0.000193) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000802) test_category=: .: (0.000552) test_entry_id=: .: (0.000278) test_fgcolor=: .: (0.000330) test_height=: .: (0.000192) test_label=: .: (0.000236) test_pathway=: .: (0.000200) test_shape=: .: (0.000263) test_width=: .: (0.000232) test_x=: .: (0.000245) test_y=: .: (0.000504) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.016051) test_coords: .: (0.016012) test_fgcolor: .: (0.017679) test_height: .: (0.015959) test_name: .: (0.015039) test_type: .: (0.015279) test_width: .: (0.015819) test_x: .: (0.016237) test_y: .: (0.015082) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.017773) test_coords: .: (0.015977) test_fgcolor: .: (0.015998) test_height: .: (0.015913) test_name: .: (0.016138) test_type: .: (0.015821) test_width: .: (0.015865) test_x: .: (0.018043) test_y: .: (0.016026) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000419) test_coords=: .: (0.000196) test_fgcolor=: .: (0.000195) test_height=: .: (0.000186) test_name=: .: (0.000191) test_type=: .: (0.000201) test_width=: .: (0.000187) test_x=: .: (0.000197) test_y=: .: (0.000515) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.016017) test_entries__size: .: (0.015514) test_image: .: (0.015405) test_link: .: (0.015771) test_name: .: (0.015726) test_number: .: (0.017801) test_org: .: (0.016187) test_reactions=: .: (0.015234) test_reactions__size: .: (0.015172) test_relations=: .: (0.014919) test_relations__size: .: (0.015975) test_title: .: (0.015933) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.032778) test_name: .: (0.032162) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000496) test_initialize_0: .: (0.000159) test_initialize_1: .: (0.000159) test_initialize_2: .: (0.000156) test_name=: .: (0.000216) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.016634) test_name: .: (0.016123) test_products: .: (0.016660) test_substrates: .: (0.017364) test_type: .: (0.017076) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000800) test_name=: .: (0.000244) test_products=: .: (0.000230) test_substraces=: .: (0.000228) test_type=: .: (0.000248) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000496) test_entry_id=: .: (0.000300) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.016780) test_entry2: .: (0.017395) test_name: .: (0.016199) test_type: .: (0.016289) test_value: .: (0.016097) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000377) test_node1=: .: (0.000270) test_node2=: .: (0.000544) test_rel=: .: (0.000260) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000372) test_entry2=: .: (0.000205) test_name=: .: (0.000207) test_type=: .: (0.000218) test_value=: .: (0.000214) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.034138) test_name: .: (0.031548) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000454) test_initialize_0: .: (0.000135) test_initialize_1: .: (0.000212) test_initialize_2: .: (0.000154) test_name=: .: (0.000219) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000586) test_initialize_0: .: (0.000155) test_initialize_1: .: (0.000169) test_initialize_2: .: (0.000158) test_name=: .: (0.000246) Bio::TestKeggModule: test_compounds: .: (0.000720) test_compounds_as_hash: .: (0.000439) test_compounds_as_strings: .: (0.000348) test_definition: .: (0.000375) test_entry_id: .: (0.000460) test_keggclass: .: (0.000327) test_name: .: (0.000561) test_new: .: (0.000327) test_orthologs: .: (0.000580) test_orthologs_as_array: .: (0.000638) test_orthologs_as_hash: .: (0.000516) test_orthologs_as_strings: .: (0.000404) test_pathways: .: (0.000310) test_pathways_as_hash: .: (0.000957) test_pathways_as_strings: .: (0.000284) test_reactions: .: (0.000440) test_reactions_as_hash: .: (0.000430) test_reactions_as_strings: .: (0.000369) Bio::TestKeggOrthology: test_dblinks: .: (0.000881) test_dblinks_as_hash: .: (0.000938) test_dblinks_as_strings: .: (0.001106) test_definition: .: (0.000599) test_entry_id: .: (0.000464) test_genes_as_hash: .: (0.024257) test_genes_as_strings: .: (0.007708) test_keggclass: .: (0.001639) test_keggclasses: .: (0.000855) test_modules: .: (0.000568) test_modules_as_hash: .: (0.000550) test_modules_as_strings: .: (0.000550) test_name: .: (0.000906) test_names: .: (0.000642) test_pathways_as_strings: .: (0.000883) test_pathways_in_keggclass: .: (0.000791) test_references: .: (0.000790) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000570) test_compounds_as_strings: .: (0.000297) test_dblinks_as_hash: .: (0.000286) test_dblinks_as_strings: .: (0.000342) test_description: .: (0.000365) test_diseases_as_hash: .: (0.000512) test_diseases_as_strings: .: (0.000360) test_entry_id: .: (0.000642) test_enzymes_as_strings: .: (0.000320) test_genes_as_hash: .: (0.000282) test_genes_as_strings: .: (0.000277) test_keggclass: .: (0.000327) test_ko_pathway: .: (0.000308) test_modules_as_hash: .: (0.000415) test_modules_as_strings: .: (0.000534) test_name: .: (0.000352) test_organism: .: (0.000314) test_orthologs_as_hash: .: (0.000350) test_orthologs_as_strings: .: (0.000329) test_pathways_as_hash: .: (0.000370) test_pathways_as_strings: .: (0.000351) test_reactions_as_hash: .: (0.000319) test_reactions_as_strings: .: (0.000332) test_references: .: (0.000291) test_rel_pathways_as_hash: .: (0.000739) test_rel_pathways_as_strings: .: (0.000698) Bio::TestKeggReaction: test_definition: .: (0.000660) test_entry_id: .: (0.000370) test_enzymes: .: (0.000373) test_equation: .: (0.000381) test_name: .: (0.000412) test_orthologs_as_hash: .: (0.000493) test_orthologs_as_strings: .: (0.001052) test_pathways_as_hash: .: (0.000375) test_pathways_as_strings: .: (0.000322) test_rpairs_as_hash: .: (0.000423) test_rpairs_as_strings: .: (0.000341) test_rpairs_as_tokens: .: (0.000409) Bio::TestLasergene: test_methods: .: (0.012897) Bio::TestLocations: test_complement: .: (0.000581) test_hat: .: (0.000252) test_normal: .: (0.000231) test_replace_single_base: .: (0.000190) test_should_not_modify_argument: .: (0.000190) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.006816) test_locations_to_s: .: (0.003312) Bio::TestMEDLINE: test_authors: .: (0.001269) test_authors_with_last_name_all_caps: .: (0.000169) test_authors_with_suffix: .: (0.000557) Bio::TestMEDLINE_20146148: test_ab: .: (0.001176) test_ad: .: (0.000637) test_au: .: (0.000593) test_authors: .: (0.000919) test_doi: .: (0.001087) test_dp: .: (0.000682) test_ip: .: (0.000628) test_mh: .: (0.001291) test_pages: .: (0.000605) test_pg: .: (0.000842) test_pii: .: (0.000661) test_pmid: .: (0.001066) test_pt: .: (0.000788) test_reference: .: (0.001366) test_self_new: .: (0.000659) test_so: .: (0.001129) test_ta: .: (0.000710) test_ti: .: (0.000945) test_ui: .: (0.000667) test_vi: .: (0.000974) test_year: .: (0.000637) Bio::TestMapSimple: test_attributes: .: (0.000533) Bio::TestMapping: test_add_mapping_as_map: .: (0.000525) test_add_mapping_as_marker: .: (0.000261) test_contains_marker?: .: (0.000199) test_mapped_to?: .: (0.000193) test_mapping_location_comparison: .: (0.001100) test_mappings_as_map_each: .: (0.000205) test_mappings_as_marker_each: .: (0.000283) test_mappings_on: .: (0.000283) test_multiple_mappings_between_same_marker_and_map: .: (0.000906) test_positions_on: .: (0.000289) test_raise_error_kind_of: .: (0.000602) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000580) test_check_options_with_invalid_opts: .: (0.000281) test_check_options_with_valid_opts: .: (0.000598) test_command_to_be_run: .: (0.000300) test_config_defaults: .: (0.000268) test_minimal_config: .: (0.000271) test_more_config: .: (0.000244) test_run: .: (0.000168) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000817) test_report_has_motifs: .: (0.000369) Bio::TestModel: test_addChain: .: (0.000317) test_comp: .: (0.000186) test_each: .: (0.000188) test_each_chain: .: (0.000754) test_inspect: .: (0.000164) test_rehash: .: (0.000148) test_square_brace: .: (0.000155) test_to_s: .: (0.000157) Bio::TestModelFinder: test_find_model: .: (0.000458) Bio::TestMotif: test_creation_and_attributes: .: (0.000463) test_length: .: (0.000156) Bio::TestMyGraph: test_cliquishness: .: (0.001241) Bio::TestNA: test_accessor: .: (0.000401) test_na: .: (0.000136) test_name: .: (0.000132) test_names: .: (0.000120) test_to_re: .: (0.000357) test_weight: .: (0.000173) test_weight_rna: .: (0.000160) Bio::TestNAConstants: test_NAMES: .: (0.000297) test_NAMES_1_to_name: .: (0.000134) test_WEIGHT: .: (0.000156) Bio::TestNATranslate: test_translate: .: (0.000801) test_translate_1: .: (0.000192) test_translate_2: .: (0.000166) test_translate_3: .: (0.000166) test_translate_4: .: (0.000289) test_translate_5: .: (0.000169) test_translate_6: .: (0.000162) Bio::TestNCBIDB: test_fetch: .: (0.000361) test_p_entry2hash: .: (0.000117) test_p_subtag2array: .: (0.000102) test_p_toptag2array: .: (0.000101) Bio::TestNewick: test_reparse: .: (0.008713) test_reparse_before_lazy_parsing: .: (0.000732) test_string_tree: .: (0.001790) Bio::TestNewick2: test_string_tree: .: (0.001495) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000514) test_parse_newick_leaf: .: (0.000329) test_parse_newick_tokenize: .: (0.000607) Bio::TestNexus: test_nexus: .: (0.022611) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000621) test_uncapitalized_letter_Q32725_9POAL: .: (0.000223) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000431) test_load_parameters: .: (0.000203) test_parameters: .: (0.000162) test_set_default_parameters: .: (0.000178) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000882) test_expected_parameters_set_in_control_file: .: (0.001478) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000522) test_new_with_parameters: .: (0.000224) test_new_with_two_argument: .: (0.000208) test_new_without_argument: .: (0.000191) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.003324) test_rates_hundred_and_fiftieth_position: .: (0.002883) test_rates_last_position: .: (0.002621) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.012081) test_tree: .: (0.011622) test_tree_length: .: (0.011740) test_tree_log_likelihood: .: (0.011586) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000858) test_parameters_should_be_loaded_from_control: .: (0.001050) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001837) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000477) test_dN_dS: .: (0.000842) test_kappa: .: (0.000306) test_lnL: .: (0.000257) test_m3_classes: .: (0.000458) test_m3_lnL: .: (0.000239) test_m3_to_s: .: (0.000238) test_m3_tree: .: (0.000810) test_omega: .: (0.000548) test_to_s: .: (0.000237) test_tree: .: (0.000744) test_tree_length: .: (0.000261) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000931) test_p: .: (0.000549) test_position: .: (0.001224) test_probability: .: (0.000558) test_w: .: (0.000514) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.001382) test_graph_omega: .: (0.001234) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000524) test_footer: .: (0.000236) test_header: .: (0.000229) test_initialize: .: (0.000247) test_models: .: (0.000279) test_nb_sites: .: (0.001817) test_num_codons: .: (0.000290) test_num_sequences: .: (0.000250) test_significant: .: (0.000297) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000561) test_nb_sites: .: (0.000440) test_significant: .: (0.000281) test_sites: .: (0.002586) Bio::TestPDB: test_accession: .: (0.002919) test_addModel: .: (0.001731) test_authors: .: (0.002005) test_bracket: .: (0.001464) test_classification: .: (0.002233) test_dbref: .: (0.001424) test_definition: .: (0.001833) test_each: .: (0.001557) test_each_model: .: (0.001617) test_entry_id: .: (0.001623) test_helix: .: (0.008523) test_inspect: .: (0.022058) test_jrnl: .: (0.018852) test_keywords: .: (0.019711) test_record: .: (0.013822) test_remark: .: (0.013744) test_seqres: .: (0.002779) test_sheet: .: (0.002080) test_ssbond: .: (0.002300) test_to_s: .: (0.002297) test_turn: .: (0.002346) test_version: .: (0.001737) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000497) test_U12: .: (0.000253) test_U13: .: (0.000248) test_U22: .: (0.000234) test_U23: .: (0.000251) test_U33: .: (0.000596) test_altLoc: .: (0.000242) test_chainID: .: (0.000489) test_charge: .: (0.000225) test_element: .: (0.000212) test_iCode: .: (0.000214) test_name: .: (0.000167) test_resName: .: (0.000215) test_resSeq: .: (0.000204) test_segID: .: (0.000229) test_serial: .: (0.000216) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000434) test_anisou: .: (0.000178) test_chainID: .: (0.000969) test_charge: .: (0.000182) test_comparable: .: (0.000263) test_do_parse: .: (0.000193) test_element: .: (0.000157) test_iCode: .: (0.000149) test_name: .: (0.000148) test_occupancy: .: (0.000266) test_original_data: .: (0.000165) test_record_name: .: (0.000155) test_resName: .: (0.000156) test_resSeq: .: (0.000156) test_residue: .: (0.000154) test_segID: .: (0.000156) test_serial: .: (0.000154) test_sigatm: .: (0.000673) test_tempFactor: .: (0.000233) test_ter: .: (0.000160) test_to_a: .: (0.000179) test_to_s: .: (0.000242) test_x: .: (0.000227) test_xyz: .: (0.000246) test_y: .: (0.000316) test_z: .: (0.000234) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000406) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000328) test_idcode: .: (0.000171) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000421) test_chainID2: .: (0.000198) test_icode1: .: (0.000196) test_icode2: .: (0.000210) test_measure: .: (0.000201) test_modNum: .: (0.000207) test_pep1: .: (0.000244) test_pep2: .: (0.000222) test_seqNum1: .: (0.000227) test_seqNum2: .: (0.000238) test_serNum: .: (0.000487) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000423) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000434) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000354) test_alpha: .: (0.000165) test_b: .: (0.000158) test_beta: .: (0.000168) test_c: .: (0.000170) test_gamma: .: (0.000164) test_sGroup: .: (0.000178) test_z: .: (0.000189) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000478) test_database: .: (0.000262) test_dbAccession: .: (0.000271) test_dbIdCode: .: (0.000656) test_dbseqBegin: .: (0.000262) test_dbseqEnd: .: (0.000234) test_idCode: .: (0.000227) test_idbnsBeg: .: (0.000231) test_insertBegin: .: (0.000471) test_insertEnd: .: (0.000235) test_seqBegin: .: (0.000247) test_seqEnd: .: (0.000225) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000450) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000319) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000848) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000655) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000401) test_depDate: .: (0.000186) test_idCode: .: (0.000173) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000380) test_hetID: .: (0.000189) test_iCode: .: (0.000181) test_numHetAtoms: .: (0.000190) test_seqNum: .: (0.000189) test_text: .: (0.000176) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000908) test_anisou: .: (0.000200) test_chainID: .: (0.000175) test_charge: .: (0.000169) test_comparable: .: (0.000234) test_do_parse: .: (0.000179) test_element: .: (0.000175) test_iCode: .: (0.000175) test_name: .: (0.000170) test_occupancy: .: (0.000291) test_original_data: .: (0.000189) test_record_name: .: (0.000161) test_resName: .: (0.000170) test_resSeq: .: (0.000168) test_residue: .: (0.000865) test_segID: .: (0.000179) test_serial: .: (0.000162) test_sigatm: .: (0.000162) test_tempFactor: .: (0.000235) test_ter: .: (0.000151) test_to_a: .: (0.000175) test_to_s: .: (0.000227) test_x: .: (0.000221) test_xyz: .: (0.000202) test_y: .: (0.000217) test_z: .: (0.000221) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000911) test_ChainH: .: (0.000660) test_ICode1: .: (0.000259) test_altLoc1: .: (0.000257) test_altLoc2: .: (0.000259) test_altLocH: .: (0.000256) test_chainID2: .: (0.000261) test_iCode2: .: (0.000274) test_iCodeH: .: (0.000270) test_name1: .: (0.000257) test_name2: .: (0.000547) test_nameH: .: (0.000213) test_resName1: .: (0.000258) test_resName2: .: (0.000600) test_resSeq1: .: (0.000275) test_resSeq2: .: (0.000317) test_resSeqH: .: (0.000296) test_sym1: .: (0.000271) test_sym2: .: (0.000261) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000715) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000406) test_altLoc2: .: (0.000229) test_chainID1: .: (0.000480) test_chainID2: .: (0.000223) test_iCode1: .: (0.000216) test_iCode2: .: (0.000212) test_name1: .: (0.000237) test_name2: .: (0.000242) test_resName1: .: (0.000252) test_resName2: .: (0.000555) test_resSeq1: .: (0.000263) test_resSeq2: .: (0.000246) test_sym1: .: (0.000256) test_sym2: .: (0.000223) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000734) test_numCoord: .: (0.000168) test_numHelix: .: (0.000165) test_numHet: .: (0.000169) test_numRemark: .: (0.000165) test_numSeq: .: (0.000166) test_numSheet: .: (0.000236) test_numSite: .: (0.000160) test_numTer: .: (0.000153) test_numTurn: .: (0.000160) test_numXform: .: (0.000156) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000324) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000377) test_comment: .: (0.000194) test_iCode: .: (0.000542) test_idCode: .: (0.000189) test_resName: .: (0.000189) test_seqNum: .: (0.000182) test_stdRes: .: (0.000192) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000330) test_Mn2: .: (0.000158) test_Mn3: .: (0.000155) test_Vn: .: (0.000160) test_iGiven: .: (0.000160) test_serial: .: (0.000155) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000303) test_Mn2: .: (0.000157) test_Mn3: .: (0.000157) test_Vn: .: (0.000160) test_iGiven: .: (0.000502) test_serial: .: (0.000166) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000665) test_Mn2: .: (0.000167) test_Mn3: .: (0.000181) test_Vn: .: (0.000176) test_iGiven: .: (0.000187) test_serial: .: (0.000183) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000392) test_rIdCode: .: (0.000179) test_repDate: .: (0.000182) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000338) test_On2: .: (0.000152) test_On3: .: (0.000833) test_Tn: .: (0.000156) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000330) test_modId: .: (0.000153) test_modNum: .: (0.000163) test_modType: .: (0.000163) test_record: .: (0.000173) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000313) test_text: .: (0.000171) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000364) test_Sn2: .: (0.000174) test_Sn3: .: (0.000181) test_Un: .: (0.000485) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000634) test_Sn2: .: (0.000150) test_Sn3: .: (0.000137) test_Un: .: (0.000143) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000353) test_Sn2: .: (0.000154) test_Sn3: .: (0.000153) test_Un: .: (0.000154) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000396) test_conflict: .: (0.000920) test_database: .: (0.000252) test_dbIdCode: .: (0.000244) test_dbRes: .: (0.000242) test_dbSeq: .: (0.000467) test_iCode: .: (0.000252) test_idCode: .: (0.000229) test_resName: .: (0.000229) test_seqNum: .: (0.000196) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000426) test_numRes: .: (0.000232) test_resName: .: (0.000209) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000450) test_curChainId: .: (0.000251) test_curICode: .: (0.000600) test_curResName: .: (0.000255) test_curResSeq: .: (0.000285) test_endChainID: .: (0.000292) test_endICode: .: (0.000299) test_endResName: .: (0.000596) test_endSeqNum: .: (0.000313) test_initChainID: .: (0.000293) test_initICode: .: (0.000248) test_initResName: .: (0.000252) test_initSeqNum: .: (0.000338) test_numStrands: .: (0.000259) test_prevAtom: .: (0.000271) test_prevChainId: .: (0.000254) test_prevICode: .: (0.000260) test_prevResName: .: (0.000544) test_prevResSeq: .: (0.000441) test_sense: .: (0.000309) test_sheetID: .: (0.000303) test_strand: .: (0.000305) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000518) test_chainID: .: (0.000571) test_charge: .: (0.000213) test_element: .: (0.000213) test_iCode: .: (0.000440) test_name: .: (0.000260) test_resName: .: (0.000218) test_resSeq: .: (0.000213) test_segID: .: (0.000220) test_serial: .: (0.000221) test_sigOcc: .: (0.000222) test_sigTemp: .: (0.000215) test_sigX: .: (0.000210) test_sigY: .: (0.000274) test_sigZ: .: (0.000210) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.009337) test_SigmaU12: .: (0.000247) test_SigmaU13: .: (0.000204) test_SigmaU22: .: (0.000204) test_SigmaU23: .: (0.000217) test_SigmaU33: .: (0.000218) test_altLoc: .: (0.000243) test_chainID: .: (0.000223) test_charge: .: (0.000217) test_element: .: (0.000213) test_iCode: .: (0.000247) test_name: .: (0.000225) test_resName: .: (0.000206) test_resSeq: .: (0.000495) test_segID: .: (0.000210) test_serial: .: (0.000209) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000517) test_chainID2: .: (0.000261) test_chainID3: .: (0.000253) test_chainID4: .: (0.000267) test_iCode1: .: (0.000266) test_iCode2: .: (0.008626) test_iCode3: .: (0.000258) test_iCode4: .: (0.000238) test_numRes: .: (0.000246) test_resName1: .: (0.000597) test_resName2: .: (0.000248) test_resName3: .: (0.000257) test_resName4: .: (0.000235) test_seq1: .: (0.000263) test_seq2: .: (0.000257) test_seq3: .: (0.000291) test_seq4: .: (0.015186) test_seqNum: .: (0.000281) test_siteID: .: (0.000273) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000534) test_altLoc2: .: (0.000238) test_atom1: .: (0.000237) test_atom2: .: (0.000243) test_chainID1: .: (0.000251) test_chainID2: .: (0.000224) test_iCode1: .: (0.000224) test_iCode2: .: (0.000208) test_resName1: .: (0.000227) test_resName2: .: (0.000205) test_resSeq1: .: (0.008967) test_resSeq2: .: (0.000241) test_sym1: .: (0.000204) test_sym2: .: (0.000205) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000478) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000422) test_sIdCode: .: (0.000205) test_sprsdeDate: .: (0.000206) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000444) test_iCode: .: (0.000202) test_resName: .: (0.000182) test_resSeq: .: (0.000522) test_serial: .: (0.000179) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000331) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000333) test_t1: .: (0.000172) test_t2: .: (0.000171) test_t3: .: (0.000168) test_text: .: (0.000170) Bio::TestPROSITE: test_ac: .: (0.011531) test_cc: .: (0.003242) test_de: .: (0.011376) test_division: .: (0.003058) test_dr: .: (0.050444) test_dt: .: (0.007030) test_false_neg: .: (0.011319) test_false_pos: .: (0.003032) test_false_positive_sequences: .: (0.011169) test_list_falsenegative: .: (0.158526) test_list_falsepositive: .: (0.028048) test_list_potentialhit: .: (0.043690) test_list_truepositive: .: (0.033383) test_list_unknown: .: (0.029349) test_list_xref: .: (0.028299) test_ma: .: (0.002976) test_max_repeat: .: (0.002768) test_name: .: (0.002880) test_nr: .: (0.002835) test_pa: .: (0.002777) test_pa2re: .: (0.002859) test_partial: .: (0.002669) test_pdb_xref: .: (0.002870) test_pdoc_xref: .: (0.002750) test_positive: .: (0.002976) test_positive_hits: .: (0.002623) test_positive_sequences: .: (0.002967) test_release: .: (0.002666) test_ru: .: (0.002721) test_self_pa2re: .: (0.002729) test_site: .: (0.002727) test_skip_flag: .: (0.002704) test_swissprot_release_number: .: (0.002726) test_swissprot_release_sequences: .: (0.003146) test_taxon_range: .: (0.002719) test_total: .: (0.002998) test_total_hits: .: (0.002753) test_total_sequences: .: (0.003043) test_unknown: .: (0.002806) test_unknown_hits: .: (0.002933) test_unknown_sequences: .: (0.002732) Bio::TestPROSITEConst: test_delimiter: .: (0.000357) test_tagsize: .: (0.000121) Bio::TestPTS1: test_function_set: .: (0.000379) test_function_set_number_1: .: (0.000179) test_function_set_number_2: .: (0.000286) test_function_set_number_3: .: (0.000178) test_function_show: .: (0.000156) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000359) Bio::TestPTS1New: test_fungi: .: (0.000311) test_general: .: (0.000141) test_metazoa: .: (0.000145) Bio::TestQualifier: test_qualifier: .: (0.000288) test_value: .: (0.000118) Bio::TestREBASE: test_methods: .: (0.001401) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001472) test_bit_score: .: (0.000938) test_evalue: .: (0.000821) test_gaps: .: (0.000886) test_hit_from: .: (0.000918) test_hit_to: .: (0.000972) test_hseq: .: (0.001021) test_identity: .: (0.001014) test_midline: .: (0.000935) test_percent_identity: .: (0.000863) test_positive: .: (0.000789) test_qseq: .: (0.000949) test_query_from: .: (0.000937) test_query_to: .: (0.000996) test_score: .: (0.000981) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000988) test_hits_size: .: (0.001910) test_iterations_size: .: (0.002100) test_program: .: (0.000807) test_query_def: .: (0.001819) test_query_len: .: (0.002093) test_version: .: (0.000806) test_version_date: .: (0.000751) test_version_number: .: (0.000755) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.001151) test_definition: .: (0.000899) test_evalue: .: (0.001047) test_hsps_size: .: (0.000937) test_identity: .: (0.000916) test_lap_at: .: (0.000962) test_len: .: (0.000997) test_midline: .: (0.001023) test_overlap: .: (0.001006) test_query_end: .: (0.001082) test_query_seq: .: (0.000967) test_query_start: .: (0.007068) test_target_def: .: (0.000971) test_target_end: .: (0.001007) test_target_len: .: (0.000992) test_target_seq: .: (0.001642) test_target_start: .: (0.001074) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000818) test_get_entry: .: (0.000793) test_rewind: .: (0.000185) test_skip_leader: .: (0.000475) Bio::TestReference: test_abstract: .: (0.000444) test_affiliations: .: (0.000141) test_authors: .: (0.000134) test_format_bibitem: .: (0.000224) test_format_bibtex: .: (0.000329) test_format_bibtex_with_arguments: .: (0.000303) test_format_cell: .: (0.000179) test_format_current: .: (0.000170) test_format_endnote: .: (0.000206) test_format_general: .: (0.000204) test_format_genome_biol: .: (0.000201) test_format_genome_res: .: (0.000204) test_format_nar: .: (0.000210) test_format_nature: .: (0.000249) test_format_rd: .: (0.000213) test_format_science: .: (0.000304) test_format_trends: .: (0.000175) test_issue: .: (0.000153) test_journal: .: (0.000151) test_mesh: .: (0.000162) test_pages: .: (0.000134) test_pubmed: .: (0.000118) test_pubmed_url: .: (0.000709) test_url: .: (0.000163) test_volume: .: (0.000139) test_year: .: (0.000129) Bio::TestReference_noURL: test_format_endnote: .: (0.000420) test_url: .: (0.000188) Bio::TestReferences: test_append: .: (0.000367) test_each: .: (0.000162) Bio::TestRelation: test_comparison_operator: .: (0.000360) test_uniq: .: (0.000227) Bio::TestResidue: test_addAtom: .: (0.000722) test_each: .: (0.000328) test_each_atom: .: (0.000292) test_get_residue_id_from_atom: .: (0.000268) test_het_atom: .: (0.000236) test_iCode: .: (0.000224) test_inspect: .: (0.000254) test_resSeq: .: (0.000980) test_sort: .: (0.000290) test_square_bracket: .: (0.000277) test_to_s: .: (0.000422) test_update_resudue_id: .: (0.000268) Bio::TestResidueFinder: test_each_residue: .: (0.000451) test_find_residue: .: (0.000197) test_residues: .: (0.000216) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.238387) test_cut_from_bio_sequence_na: .: (0.060415) test_cut_without_permutations: .: (0.037821) test_view_ranges: .: (0.037971) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.002689) test_cuts_after_remove_incomplete_cuts: .: (0.001233) test_strands_for_display: .: (0.004778) test_strands_for_display_current: .: (0.001542) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000975) test_fragments_for_display_1: .: (0.001507) test_fragments_for_display_10: .: (0.001700) test_fragments_for_display_2: .: (0.001302) test_fragments_for_display_3: .: (0.001909) test_fragments_for_display_4: .: (0.001436) test_fragments_for_display_5: .: (0.001031) test_fragments_for_display_6: .: (0.001360) test_fragments_for_display_7: .: (0.001057) test_fragments_for_display_8: .: (0.004093) test_fragments_for_display_9: .: (0.000887) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000720) test_obj_3: .: (0.000476) test_obj_7: .: (0.000784) test_obj_z: .: (0.000379) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000606) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000461) test_bracket_eq: .: (0.000348) test_concat: .: (0.000231) test_delete: .: (0.000194) test_dup: .: (0.000281) test_each: .: (0.000466) test_eqeq: .: (0.000155) test_eqeq_false: .: (0.000136) test_eqeq_other: .: (0.000125) test_eqeq_self: .: (0.000127) test_include?: .: (0.000148) test_internal_data: .: (0.000139) test_internal_data_eq: .: (0.000157) test_length: .: (0.000133) test_ltlt: .: (0.000152) test_ltlt_larger: .: (0.000151) test_ltlt_middle: .: (0.000154) test_plus: .: (0.000217) test_plus_error: .: (0.000252) test_push: .: (0.000195) test_reverse_each: .: (0.000488) test_self_bracket: .: (0.000144) test_self_new: .: (0.000202) test_size: .: (0.000163) test_sort!: .: (0.000156) test_to_a: .: (0.000159) test_uniq!: .: (0.000153) test_unshift: .: (0.000248) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.007493) test_complement: .: (0.007097) test_complement_with_cut_symbols: .: (0.007018) test_cut_locations: .: (0.006489) test_cut_locations_in_enzyme_notation: .: (0.006707) test_primary: .: (0.006602) test_primary_with_cut_symbols: .: (0.006123) test_to_re: .: (0.006364) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.001766) test_align_with_cuts: .: (0.001212) test_argument_error: .: (0.001446) test_ds: .: (0.001400) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000792) test_complement: .: (0.000307) test_contents: .: (0.000442) test_primary: .: (0.000308) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000556) test_complement: .: (0.000300) test_contents: .: (0.000293) test_primary: .: (0.000297) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000430) test_contents: .: (0.000401) test_primary: .: (0.000211) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000398) test_complement_to_array_index: .: (0.000355) test_complement_to_array_index_class: .: (0.000293) test_contents: .: (0.000230) test_primary: .: (0.000212) test_primary_to_array_index: .: (0.000326) test_primary_to_array_index_class: .: (0.000375) test_to_array_index: .: (0.000771) test_to_array_index_class: .: (0.000629) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000711) test_rebase: .: (0.000220) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001753) test_creation_with_no_cuts: .: (0.001272) test_cut_locations: .: (0.000792) test_cut_locations_in_enzyme_notation: .: (0.000802) test_orientation: .: (0.000948) test_pattern: .: (0.000830) test_pattern_palindromic?: .: (0.001012) test_stripped: .: (0.000789) test_to_re: .: (0.000923) test_with_cut_symbols: .: (0.000859) test_with_spaces: .: (0.000987) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.001871) test_creation_with_no_cuts: .: (0.000828) test_cut_locations: .: (0.000845) test_cut_locations_in_enzyme_notation: .: (0.001043) test_orientation: .: (0.000786) test_pattern: .: (0.000836) test_pattern_palindromic?: .: (0.001048) test_stripped: .: (0.000603) test_to_re: .: (0.000532) test_with_cut_symbols: .: (0.000950) test_with_spaces: .: (0.001322) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000870) test_initialize_with_pattern: .: (0.000546) test_max: .: (0.003576) test_min: .: (0.000392) test_to_array_index: .: (0.000358) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000675) test_bracket_eq: .: (0.000272) test_concat: .: (0.000182) test_delete: .: (0.000147) test_dup: .: (0.000214) test_each: .: (0.000276) test_eqeq: .: (0.000149) test_eqeq_false: .: (0.000131) test_eqeq_other: .: (0.000123) test_eqeq_self: .: (0.000126) test_include?: .: (0.000143) test_internal_data_hash: .: (0.000134) test_internal_data_hash_eq: .: (0.000257) test_length: .: (0.000145) test_ltlt: .: (0.000319) test_ltlt_noeffect: .: (0.000166) test_plus: .: (0.000161) test_plus_error: .: (0.000247) test_private_push_element: .: (0.000157) test_private_push_element_intermediate: .: (0.000170) test_private_push_element_last: .: (0.000169) test_private_push_element_noeffect: .: (0.000172) test_private_sorted_keys: .: (0.000167) test_private_unshift_element: .: (0.000183) test_private_unshift_element_first: .: (0.000190) test_private_unshift_element_intermediate: .: (0.000187) test_private_unshift_element_noeffect: .: (0.000184) test_push: .: (0.000196) test_reverse_each: .: (0.000358) test_self_bracket: .: (0.000161) test_self_new: .: (0.000313) test_size: .: (0.000124) test_sort!: .: (0.000134) test_to_a: .: (0.000141) test_uniq!: .: (0.000136) test_unshift: .: (0.000165) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000380) test_left_padding: .: (0.000203) test_right_padding: .: (0.000207) test_strip_padding: .: (0.000213) Bio::TestSOFT: test_dataset: .: (0.019302) test_series: .: (0.014954) Bio::TestSOSUIReport: test_entry_id: .: (0.000483) test_prediction: .: (0.000556) test_tmh: .: (0.000218) test_tmhs: .: (0.000240) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000339) test_rs: .: (0.000120) Bio::TestSOSUITMH: test_grade: .: (0.000385) test_range: .: (0.000231) test_sequence: .: (0.000242) Bio::TestSampleGraph: test_bellman_ford: .: (0.000758) test_bfs_shortest_path: .: (0.000326) test_breadth_first_search: .: (0.000297) test_depth_first_search: .: (0.000632) test_dijkstra: .: (0.000370) test_dump_list: .: (0.000349) test_dump_matrix: .: (0.000511) test_extract_subgraph_by_label: .: (0.000695) test_extract_subgraph_by_list: .: (0.000336) test_extract_subgraph_retains_disconnected_nodes: .: (0.000250) test_small_world_aka_node_degree_histogram: .: (0.000243) test_to_matrix: .: (0.000750) test_to_matrix_fixed_index: .: (0.000454) test_undirected_cliquishness: .: (0.000599) Bio::TestScf_version_2: test_complement: .: (0.017665) test_seq: .: (0.016541) test_to_biosequence: .: (0.016608) Bio::TestScf_version_3: test_complement: .: (0.049391) test_seq: .: (0.047983) test_to_biosequence: .: (0.055733) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000346) test_AA_new_sequence_all_legal_symbols: .: (0.000141) test_AA_new_sequence_removes_whitespace: .: (0.000129) test_AA_new_sequence_upcases_symbols: .: (0.000133) test_DNA_new_blank_sequence: .: (0.000127) test_DNA_new_sequence_downcases_symbols: .: (0.000133) test_DNA_new_sequence_removes_whitespace: .: (0.000338) test_NA_randomize_with_counts: .: (0.001600) test_NA_randomize_with_counts_and_block: .: (0.001884) test_RNA_new_sequence: .: (0.000151) test_ambiguous_dna_sequence_complement: .: (0.000190) test_ambiguous_rna_sequence_complement: .: (0.000152) test_amino_acid_codes: .: (0.000211) test_amino_acid_molecular_weight: .: (0.000360) test_amino_acid_names: .: (0.000195) test_amino_acid_randomize_can_be_chained: .: (0.002327) test_amino_acid_randomize_has_same_composition: .: (0.001353) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.001050) test_dna_composition: .: (0.000199) test_dna_gc_percent: .: (0.000460) test_dna_molecular_weight: .: (0.000297) test_dna_pikachu: .: (0.000163) test_dna_sequence_complement: .: (0.000137) test_dna_sequence_translate: .: (0.000688) test_dna_to_re: .: (0.000240) test_element_reference_operator_with_one_argument: .: (0.000131) test_element_reference_operator_with_two_arguments: .: (0.000138) test_invalid_nucleic_acid_illegal_bases: .: (0.000198) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000225) test_nucleic_acid_names: .: (0.000181) test_randomize_dna_can_be_chained: .: (0.000933) test_randomize_dna_retains_composition: .: (0.000723) test_randomize_dna_with_block: .: (0.000517) test_rna_composition: .: (0.000170) test_rna_gc_percent: .: (0.000199) test_rna_molecular_weight: .: (0.000308) test_rna_pikachu: .: (0.000154) test_rna_sequence_complement: .: (0.000395) test_rna_sequence_translate: .: (0.000549) test_rna_to_re: .: (0.000242) test_total: .: (0.000149) test_two_consecutive_dna_randomizations_not_equal: .: (0.000830) test_valid_dna_sequence_illegal_bases: .: (0.000162) Bio::TestSequenceAA: test_codes: .: (0.000400) test_molecular_weight: .: (0.000295) test_names: .: (0.000186) test_to_re: .: (0.000488) test_to_s: .: (0.000120) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000375) Bio::TestSequenceAANew: test_new: .: (0.000233) test_new_n: .: (0.000120) test_new_r: .: (0.000345) test_new_t: .: (0.000118) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000327) test_concat: .: (0.000128) test_push: .: (0.000120) test_seq: .: (0.000117) test_splicing: .: (0.000244) test_sum: .: (0.000119) test_to_s: .: (0.000117) test_to_str: .: (0.000119) test_total: .: (0.000154) test_window_search: .: (0.000493) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000263) test_normalize_A: .: (0.000148) test_normalize_a: .: (0.000361) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.001926) test_randomize_with_block: .: (0.007925) test_randomize_with_hash: .: (0.002765) test_randomize_with_hash_block: .: (0.088731) 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' =============================================================================== : (0.013279) 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' =============================================================================== : (0.001767) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000418) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000144) test_subseq_returns_subsequence: .: (0.000134) test_to_s_returns_self_as_string: .: (0.000158) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000291) test_window_search_with_width_3_step_two_with_residual: .: (0.000149) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000324) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000276) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000774) test_na_self_randomize: .: (0.000353) Bio::TestSequenceDBLink: test_database: .: (0.000242) test_id: .: (0.000110) test_secondary_ids: .: (0.000116) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000298) test_parse_uniprot_DR_line: .: (0.000174) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.001816) test_output_width_35: .: (0.000473) test_output_width_nil: .: (0.000705) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000758) test_output_after_adding_sequence: .: (0.000822) test_output_after_truncating_sequence: .: (0.000288) test_output_from_error_probabilities: .: (0.005704) test_output_width45: .: (0.000782) test_output_with_converting_score_phred2solexa: .: (0.001251) test_output_with_converting_score_solexa2phred: .: (0.000498) test_output_with_default_score: .: (0.000394) Bio::TestSequenceMasker: test_mask: .: (0.000505) test_mask_with_enumerator: .: (0.000539) test_mask_with_enumerator_empty_mask_char: .: (0.000266) test_mask_with_enumerator_excess: .: (0.001194) test_mask_with_enumerator_longer_mask_char: .: (0.000231) test_mask_with_enumerator_shorter: .: (0.000321) test_mask_with_error_probability: .: (0.000219) test_mask_with_quality_score: .: (0.000277) Bio::TestSequenceNA: test_at_content: .: (0.000693) test_at_skew: .: (0.000483) test_codon_usage: .: (0.000215) test_complement: .: (0.000668) test_dna: .: (0.000177) test_dna!: .: (0.000160) test_forward_complement: .: (0.000269) test_gc_content: .: (0.000473) test_gc_percent: .: (0.000299) test_gc_skew: .: (0.000583) test_iliegal_bases: .: (0.000139) test_molecular_weight: .: (0.000352) test_names: .: (0.000204) test_reverse_complement: .: (0.000218) test_rna: .: (0.000427) test_rna!: .: (0.000138) test_splicing: .: (0.000220) test_to_re: .: (0.000272) test_to_s: .: (0.000134) Bio::TestSequenceNACommon: test_composition: .: (0.000427) test_concat: .: (0.000144) test_push: .: (0.000131) test_seq: .: (0.000133) test_splicing: .: (0.000229) test_sum: .: (0.000393) test_to_s: .: (0.000138) test_to_str: .: (0.000119) test_total: .: (0.000139) test_window_search: .: (0.000713) Bio::TestSequenceNANew: test_new: .: (0.000307) test_new_n: .: (0.000124) test_new_r: .: (0.000116) test_new_t: .: (0.000117) Bio::TestSequenceNATranslation: test_translate: .: (0.000592) test_translate_0: .: (0.001437) test_translate_1: .: (0.000401) test_translate_2: .: (0.000319) test_translate_3: .: (0.000318) test_translate_4: .: (0.000334) test_translate_5: .: (0.000290) test_translate_6: .: (0.000309) test_translate_7: .: (0.000713) test_translate_given_codon_table: .: (0.088849) test_translate_n1: .: (0.000978) test_translate_n2: .: (0.001081) test_translate_n3: .: (0.000714) test_translate_unknown_o: .: (0.000346) test_translate_unknown_x: .: (0.000731) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000332) test_convert_scores_from_phred_to_solexa: .: (0.000734) test_convert_scores_from_solexa_to_phred: .: (0.000280) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000296) test_convert_scores_from_phred: .: (0.000460) test_convert_scores_from_phred_to_solexa: .: (0.001117) test_convert_scores_from_solexa: .: (0.000348) test_convert_scores_from_solexa_to_phred: .: (0.000388) test_convert_scores_to_phred: .: (0.000127) test_convert_scores_to_solexa: .: (0.000729) test_p2q: .: (0.000258) test_phred_p2q: .: (0.000269) test_phred_q2p: .: (0.010813) test_q2p: .: (0.010072) test_quality_score_type: .: (0.000181) test_self_convert_scores_to_solexa: .: (0.000827) test_self_p2q: .: (0.000240) test_self_q2p: .: (0.011545) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000401) test_convert_scores_from_phred: .: (0.000779) test_convert_scores_from_phred_to_solexa: .: (0.000739) test_convert_scores_from_solexa: .: (0.000127) test_convert_scores_from_solexa_to_phred: .: (0.000573) test_convert_scores_to_phred: .: (0.000253) test_convert_scores_to_solexa: .: (0.000130) test_p2q: .: (0.000358) test_q2p: .: (0.015472) test_quality_score_type: .: (0.000164) test_self_convert_scores_to_phred: .: (0.000630) test_self_p2q: .: (0.000653) test_self_q2p: .: (0.009932) test_solexa_p2q: .: (0.000479) test_solexa_q2p: .: (0.009586) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000383) test_center: .: (0.000146) test_chomp: .: (0.000180) test_chop: .: (0.000176) test_delete: .: (0.000440) test_delete_prefix: .: (0.000154) test_delete_suffix: .: (0.000436) test_downcase: .: (0.000162) test_each_char: .: (0.000302) test_each_char_enum: .: (0.000273) test_each_grapheme_cluster: .: (0.000565) test_each_grapheme_cluster_enum: .: (0.000221) test_each_line: .: (0.000230) test_each_line_enum: .: (0.000192) test_gsub: .: (0.000759) test_gsub_with_block: .: (0.000717) test_ljust: .: (0.000138) test_lstrip: .: (0.000134) test_multiply: .: (0.000132) test_next: .: (0.000137) test_reverse: .: (0.000137) test_rjust: .: (0.000130) test_rstrip: .: (0.000128) test_slice: .: (0.000135) test_slice2: .: (0.000132) test_split: .: (0.000241) test_squeeze: .: (0.000381) test_strip: .: (0.000156) test_sub: .: (0.000456) test_sub_with_block: .: (0.000434) test_succ: .: (0.000160) test_swapcase: .: (0.000161) test_tr: .: (0.000152) test_tr_s: .: (0.000147) test_upcase: .: (0.000149) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000411) test_partition_nomatch: .: (0.000200) test_partition_sep_TSeq: .: (0.000195) test_partition_sep_regexp: .: (0.000328) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000318) test_rpartition_nomatch: .: (0.000473) test_rpartition_sep_TSeq: .: (0.000192) test_rpartition_sep_regexp: .: (0.000187) Bio::TestShRNA: test_blocK_it: .: (0.044366) test_blocK_it_: .: (0.047533) test_blocK_it_BLOCK_IT: .: (0.048447) test_blocK_it_BLOCK_iT: .: (0.039047) test_blocK_it_piGene: .: (0.048748) test_bottom_strand: .: (0.048416) test_bottom_strand_class: .: (0.048626) test_bottom_strand_nil: .: (0.051190) test_design: .: (0.047063) test_design_BLOCK_IT: .: (0.049952) test_report: .: (0.048687) test_report_before_design: .: (0.047112) test_top_strand: .: (0.050116) test_top_strand_class: .: (0.048051) test_top_strand_nil: .: (0.046839) Bio::TestShRNANew: test_new: .: (0.000803) Bio::TestSiRNA: test_antisense_size: .: (0.000361) test_design: .: (0.051532) test_design_reynolds: .: (0.058083) test_design_uitei: .: (0.050029) test_max_gc_percent: .: (0.000195) test_min_gc_percent: .: (0.000146) test_reynolds: .: (0.060019) test_reynolds?: .: (0.000252) test_uitei: .: (0.053706) test_uitei?: .: (0.000271) Bio::TestSiRNANew: test_new: .: (0.001855) Bio::TestSiRNAPair: test_antisense: .: (0.089076) test_gc_percent: .: (0.088625) test_report: .: (0.093980) test_rule: .: (0.090893) test_sense: .: (0.089262) test_start: .: (0.091130) test_stop: .: (0.081845) test_target: .: (0.058861) Bio::TestSiRNAPairNew: test_new: .: (0.001048) Bio::TestSim4Report: test_all_hits: .: (0.000656) test_each: .: (0.000334) test_each_hit: .: (0.000416) test_hits: .: (0.000410) test_num_hits: .: (0.000296) test_query_def: .: (0.000321) test_query_id: .: (0.000274) test_query_len: .: (0.000265) test_seq1: .: (0.000630) Bio::TestSim4Report2: test_all_hits: .: (0.000615) test_each: .: (0.000961) test_each_hit: .: (0.000361) test_hits: .: (0.000341) test_num_hits: .: (0.000271) test_query_def: .: (0.000289) test_query_id: .: (0.000317) test_query_len: .: (0.000301) test_seq1: .: (0.000830) Bio::TestSim4Report4: test_all_hits: .: (0.000741) test_each: .: (0.000319) test_each_hit: .: (0.000399) test_hits: .: (0.000332) test_num_hits: .: (0.000265) test_query_def: .: (0.000263) test_query_id: .: (0.000263) test_query_len: .: (0.000234) test_seq1: .: (0.000661) Bio::TestSim4ReportHit: test_align: .: (0.000863) test_complement?: .: (0.000278) test_definition: .: (0.000284) test_each: .: (0.000589) test_exons: .: (0.000504) test_hit_id: .: (0.000572) test_hsps: .: (0.000519) test_introns: .: (0.000922) test_len: .: (0.000251) test_query_def: .: (0.000277) test_query_id: .: (0.000288) test_query_len: .: (0.000297) test_segmentpairs: .: (0.000992) test_seq1: .: (0.000401) test_seq2: .: (0.000332) test_target_def: .: (0.000229) test_target_id: .: (0.000331) test_target_len: .: (0.000250) Bio::TestSim4ReportHit2: test_align: .: (0.000619) test_complement?: .: (0.000264) test_definition: .: (0.000565) test_each: .: (0.000595) test_exons: .: (0.000550) test_hit_id: .: (0.000286) test_hsps: .: (0.000893) test_introns: .: (0.000461) test_len: .: (0.000242) test_query_def: .: (0.000610) test_query_id: .: (0.000257) test_query_len: .: (0.000255) test_segmentpairs: .: (0.000566) test_seq1: .: (0.000634) test_seq2: .: (0.000430) test_target_def: .: (0.000300) test_target_id: .: (0.000301) test_target_len: .: (0.000593) Bio::TestSim4ReportHit4: test_align: .: (0.000882) test_complement?: .: (0.000309) test_definition: .: (0.000286) test_each: .: (0.001021) test_exons: .: (0.001154) test_hit_id: .: (0.000330) test_hsps: .: (0.000779) test_introns: .: (0.000742) test_len: .: (0.000334) test_query_def: .: (0.000305) test_query_id: .: (0.000729) test_query_len: .: (0.000286) test_segmentpairs: .: (0.000756) test_seq1: .: (0.000370) test_seq2: .: (0.000372) test_target_def: .: (0.000265) test_target_id: .: (0.000257) test_target_len: .: (0.000286) Bio::TestSim4ReportSegment: test_from: .: (0.000496) test_self_new: .: (0.000227) test_seq: .: (0.000160) test_to: .: (0.000158) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000670) test_direction: .: (0.000415) test_hit_from: .: (0.000416) test_hit_to: .: (0.000697) test_hseq: .: (0.000662) test_midline: .: (0.000428) test_percent_identity: .: (0.000475) test_qseq: .: (0.000437) test_query_from: .: (0.000451) test_query_to: .: (0.000425) test_seq1: .: (0.001085) test_seq2: .: (0.000546) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000612) test_direction: .: (0.000399) test_hit_from: .: (0.000375) test_hit_to: .: (0.000387) test_hseq: .: (0.000914) test_midline: .: (0.000414) test_percent_identity: .: (0.000375) test_qseq: .: (0.000432) test_query_from: .: (0.000424) test_query_to: .: (0.000433) test_seq1: .: (0.000539) test_seq2: .: (0.001231) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000775) test_direction: .: (0.000511) test_hit_from: .: (0.000528) test_hit_to: .: (0.000697) test_hseq: .: (0.001018) test_midline: .: (0.000595) test_percent_identity: .: (0.000561) test_qseq: .: (0.000587) test_query_from: .: (0.000723) test_query_to: .: (0.000903) test_seq1: .: (0.000644) test_seq2: .: (0.000680) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000978) test_direction: .: (0.000551) test_hit_from: .: (0.000628) test_hit_to: .: (0.000546) test_hseq: .: (0.000519) test_midline: .: (0.000687) test_percent_identity: .: (0.000523) test_qseq: .: (0.000869) test_query_from: .: (0.000522) test_query_to: .: (0.000437) test_seq1: .: (0.000714) test_seq2: .: (0.000673) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.001169) test_direction: .: (0.000520) test_hit_from: .: (0.000769) test_hit_to: .: (0.000534) test_hseq: .: (0.000480) test_midline: .: (0.000523) test_percent_identity: .: (0.000777) test_qseq: .: (0.000784) test_query_from: .: (0.000617) test_query_to: .: (0.000562) test_seq1: .: (0.000660) test_seq2: .: (0.001223) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000670) test_direction: .: (0.000418) test_hit_from: .: (0.000411) test_hit_to: .: (0.000416) test_hseq: .: (0.000359) test_midline: .: (0.000368) test_percent_identity: .: (0.000614) test_qseq: .: (0.000401) test_query_from: .: (0.000360) test_query_to: .: (0.000362) test_seq1: .: (0.000447) test_seq2: .: (0.000494) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.001113) test_direction: .: (0.000361) test_hit_from: .: (0.000344) test_hit_to: .: (0.000337) test_hseq: .: (0.000377) test_midline: .: (0.000398) test_percent_identity: .: (0.000524) test_qseq: .: (0.000678) test_query_from: .: (0.000481) test_query_to: .: (0.000365) test_seq1: .: (0.000444) test_seq2: .: (0.000431) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000364) test_entry_id: .: (0.000141) test_filename: .: (0.000141) test_len: .: (0.008546) test_self_new: .: (0.000237) test_self_parse: .: (0.000466) Bio::TestTMHMMReport: test_entry_id: .: (0.000805) test_exp_aas_in_tmhs: .: (0.000444) test_exp_first_60aa: .: (0.000394) test_helix: .: (0.000583) test_predicted_tmhs: .: (0.000687) test_query_len: .: (0.000465) test_tmhs: .: (0.000520) test_to_s: .: (0.000725) test_total_prob_of_N_in: .: (0.000559) Bio::TestTMHMMReport_reports: test_reports: .: (0.009216) Bio::TestTMHMMTMH: test_entry_id: .: (0.000865) test_pos: .: (0.000564) test_range: .: (0.000529) test_status: .: (0.000562) test_version: .: (0.000778) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000560) test_cutoff: .: (0.000308) test_entry_id: .: (0.000307) test_length: .: (0.000316) test_loc: .: (0.000303) test_name: .: (0.000307) test_networks: .: (0.000343) test_prediction: .: (0.008810) test_query_len: .: (0.000541) test_query_sequences: .: (0.000313) test_rc: .: (0.000319) test_version: .: (0.000317) Bio::TestTargetPReportConst: test_delimiter: .: (0.000358) test_rs: .: (0.000148) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000323) test_togows_access_wait: .: (2.008613) Bio::TestTogoWSREST: test_debug: .: (0.000897) test_debug_default: .: (0.000469) test_internal_http: .: (0.000318) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000301) test_entry: .: (0.000123) test_entry_database_list: .: (0.000124) test_new: .: (0.000273) test_new_with_uri_object: .: (0.000498) test_new_with_uri_string: .: (0.000278) test_retrieve: .: (0.000132) test_search: .: (0.000124) test_search_database_list: .: (0.000121) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000763) test_prepare_return_value: .: (0.000303) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000567) Bio::TestTree: test_get_edge_distance: .: (0.000330) test_get_edge_distance_string: .: (0.008548) test_get_node_name: .: (0.000202) test_initialize: .: (0.000162) test_options: .: (0.000136) test_root: .: (0.000143) test_root=: .: (0.000189) Bio::TestTree2: test_add_edge: .: (0.000542) test_add_node: .: (0.000355) test_adjacency_matrix: .: (0.000327) test_adjacency_matrix_with_block: .: (0.000303) test_adjacent_nodes: .: (0.000635) test_adjacent_nodes_nonexistent: .: (0.000225) test_ancestors: .: (0.000319) test_children: .: (0.000271) test_clear: .: (0.000292) test_clear_node: .: (0.000369) test_clear_node_nonexistent: .: (0.000336) test_collect_edge!: .: (0.000460) test_collect_node!: .: (0.000391) test_concat: .: (0.009360) test_descendents: .: (0.000345) test_distance_matrix: .: (0.001031) test_each_edge: .: (0.000426) test_each_node: .: (0.000381) test_each_out_edge: .: (0.000361) test_each_out_edge_chimpanzee: .: (0.000486) test_each_out_edge_human: .: (0.000258) test_each_out_edge_mammals: .: (0.000303) test_each_out_edge_nonexistent: .: (0.000219) test_each_out_edge_primates: .: (0.000340) test_each_out_edge_rat: .: (0.000251) test_each_out_edge_rodents: .: (0.000340) test_edges: .: (0.000233) test_get_edge: .: (0.000889) test_get_edge_indirect: .: (0.000454) test_get_edge_merged: .: (0.000270) test_get_edge_nonexistent: .: (0.000226) test_get_node_bootstrap: .: (0.000233) test_get_node_bootstrap_string=: .: (0.000249) test_get_node_by_name: .: (0.000444) test_get_node_by_name_noexistent: .: (0.000275) test_include?: .: (0.000391) test_include_nonexistent: .: (0.000295) test_insert_node: .: (0.005804) test_leaves: .: (0.000526) test_leaves_noargs: .: (0.000250) test_lowest_common_ancestor: .: (0.000266) test_nodes: .: (0.000226) test_number_of_edges: .: (0.000218) test_number_of_nodes: .: (0.000216) test_out_degree: .: (0.000336) test_out_degree_nonexistent: .: (0.000849) test_out_edges: .: (0.000269) test_out_edges_mammals: .: (0.000318) test_out_edges_nonexistent: .: (0.000201) test_out_edges_primates: .: (0.000415) test_out_edges_rodents: .: (0.000402) test_parent: .: (0.000299) test_path: .: (0.000276) test_remove_edge: .: (0.000298) test_remove_edge_if: .: (0.000301) test_remove_edge_if_nothing_removed: .: (0.000313) test_remove_edge_nonexistent: .: (0.000556) test_remove_node: .: (0.000313) test_remove_node_if: .: (0.000479) test_remove_node_if_false: .: (0.000314) test_remove_node_nonexistent: .: (0.000315) test_remove_nonsense_nodes: .: (0.000280) test_subtree: .: (0.000699) test_subtree_with_all_paths: .: (0.000623) test_total_distance: .: (0.000288) Bio::TestTreeEdge: test_distance: .: (0.000383) test_distance=: .: (0.000217) test_distance_string: .: (0.000128) test_distance_string=: .: (0.000200) test_initialize: .: (0.000183) test_inspect: .: (0.000136) test_to_s: .: (0.000195) Bio::TestTreeNode: test_bootstrap: .: (0.008031) test_bootstrap=: .: (0.000276) test_bootstrap_string: .: (0.000128) test_bootstrap_string=: .: (0.000254) test_initialize: .: (0.000192) test_inspect: .: (0.000186) test_name: .: (0.000151) test_to_s: .: (0.000134) Bio::TestUniProt: test_gene_name: .: (0.009965) Bio::TestUniProtKB: test_ac: .: (0.009099) test_accession: .: (0.009340) test_cc: .: (0.011764) test_cc_alternative_products: .: (0.012069) test_cc_database: .: (0.011285) test_cc_mass_spectrometry: .: (0.011387) test_de: .: (0.008502) test_dr: .: (0.013119) test_dr_with_key: .: (0.010993) test_dr_with_key_empty: .: (0.105663) test_dt: .: (0.009676) test_dt_annotation: .: (0.009851) test_dt_created: .: (0.009286) test_dt_sequence: .: (0.009594) test_entry: .: (0.009946) test_ft: .: (0.022857) test_gene_name: .: (0.008871) test_gene_names: .: (0.008746) test_gn: .: (0.008907) test_gn_old_parser: .: (0.008574) test_gn_uniprot_parser: .: (0.009115) test_id_line: .: (0.008511) test_id_line_data_class: .: (0.011609) test_id_line_entry_name: .: (0.009581) test_id_line_molecule_type: .: (0.008685) test_id_line_sequence_length: .: (0.008250) test_kw: .: (0.009614) test_molecule: .: (0.009844) test_oc: .: (0.009442) test_og_1: .: (0.008507) test_og_2: .: (0.008521) test_og_3: .: (0.008689) test_og_4: .: (0.008638) test_og_5: .: (0.008600) test_og_6: .: (0.008922) test_os: .: (0.009966) test_os_access: .: (0.009078) test_os_access2: .: (0.008854) test_ox: .: (0.008884) test_protein_name: .: (0.009281) test_ref: .: (0.019842) test_seq: .: (0.009391) test_sequence_length: .: (0.008239) test_sq: .: (0.008459) test_sq_crc64: .: (0.009035) test_sq_len: .: (0.009188) test_sq_mw: .: (0.008311) test_synonyms: .: (0.012223) Bio::TestUniProtKB_CC: test_allergen: .: (0.000529) test_alternative_products_access_as_hash: .: (0.000356) test_alternative_products_ai: .: (0.000938) test_alternative_products_apu: .: (0.001266) test_alternative_products_as: .: (0.000439) test_alternative_products_rf: .: (0.000120) test_biophysicochemical_properties: .: (0.000584) test_biotechnology: .: (0.000297) test_catalytic_activity: .: (0.000243) test_caution: .: (0.000604) test_cofactor: .: (0.000725) test_developmental_stage: .: (0.000299) test_disease: .: (0.000505) test_domain: .: (0.000501) test_enzyme_regulation: .: (0.000314) test_function: .: (0.000331) test_induction: .: (0.000294) test_interaction: .: (0.000729) test_mass_spectrometry: .: (0.000684) test_miscellaneous: .: (0.000225) test_pathway: .: (0.000293) test_pharmaceutical: .: (0.000314) test_polymorphism: .: (0.000398) test_ptm: .: (0.000264) test_rna_editing: .: (0.000416) test_similarity: .: (0.000745) test_subcellular_location: .: (0.000468) test_subunit: .: (0.000984) test_tissue_specificity: .: (0.000308) test_toxic_dose: .: (0.000220) test_web_resource: .: (0.000406) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000674) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.001137) test_protein_name: .: (0.001041) test_synonyms: .: (0.000702) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000880) test_entry: .: (0.000161) test_entry_id: .: (0.000149) test_entry_name: .: (0.000151) test_id_line: .: (0.000167) test_molecule: .: (0.000150) test_sequence_length: .: (0.000243) Bio::TestUniProtKB_P28907: test_ac: .: (0.004256) test_accession: .: (0.003571) test_cc: .: (0.004637) test_cc_alternative_products: .: (0.004463) test_cc_database: .: (0.004924) test_cc_mass_spectrometry: .: (0.004291) test_de: .: (0.003774) test_dr: .: (0.009295) test_dr_with_key: .: (0.009986) test_dr_with_key_empty: .: (0.008341) test_dt: .: (0.004141) test_dt_annotation: .: (0.003417) test_dt_created: .: (0.002783) test_dt_sequence: .: (0.003132) test_entry: .: (0.003330) test_ft: .: (0.005725) test_gene_name: .: (0.003201) test_gene_names: .: (0.003442) test_gn: .: (0.003028) test_gn_old_parser: .: (0.005214) test_gn_uniprot_parser: .: (0.003270) test_id_line: .: (0.003416) test_id_line_data_class: .: (0.002974) test_id_line_entry_name: .: (0.002687) test_id_line_sequence_length: .: (0.003209) test_kw: .: (0.002948) test_oc: .: (0.007388) test_os: .: (0.010367) test_os_access: .: (0.006828) test_os_access2: .: (0.003821) test_ox: .: (0.003301) test_protein_name: .: (0.003473) test_protein_name_after_calling_de: .: (0.009504) test_ref: .: (0.004002) test_seq: .: (0.010836) test_sequence_length: .: (0.002122) test_sq: .: (0.002818) test_sq_crc64: .: (0.010975) test_sq_len: .: (0.007240) test_sq_mw: .: (0.003345) test_synonyms: .: (0.004852) test_synonyms_after_calling_de: .: (0.004041) Bio::TestUniProtKB_Ref: test_RA: .: (0.000602) test_RC: .: (0.001053) test_RG: .: (0.000365) test_RL: .: (0.000370) test_RN: .: (0.000414) test_RP: .: (0.000813) test_RT: .: (0.000412) test_RX: .: (0.000415) test_ref: .: (0.000770) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000461) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.001444) test_alternative_products_with_ft: .: (0.001485) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000610) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000778) test_RL_lines: .: (0.000232) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000893) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000585) test_RG_line: .: (0.000227) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.001322) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000484) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000329) test_RL_line: .: (0.000239) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.001111) test_RP_line: .: (0.000649) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000236) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000399) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000288) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000266) test_CC_interaction_isoform: .: (0.000516) test_CC_interaction_no_gene_name: .: (0.000272) test_CC_interaction_self_association: .: (0.000356) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000526) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000487) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000605) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000739) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000409) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000529) test_DT_line: .: (0.000265) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.006771) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.001477) test_CC_web_resource: .: (0.000124) test_FT_VER_SEQ: .: (0.000244) test_OH_line_exception: .: (0.000440) test_OH_lines: .: (0.000530) Bio::TestUtils: test_centreOfGravity: .: (0.001097) test_dihedral_angle: .: (0.000650) test_distance: .: (0.000602) test_geometricCentre: .: (0.000867) test_rad2deg: .: (0.000302) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000701) test_dijkstra_on_weighted_graph: .: (0.000195) Finished in 30.559969983 seconds. ------------------------------------------------------------------------------- 3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 126.21 tests/s, 703.08 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_amd64.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.4-1_amd64.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/828210 and its subdirectories I: Current time: Sat Apr 22 19:18:52 -12 2023 I: pbuilder-time-stamp: 1682234332 Sun Apr 23 07:18:53 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Apr 23 07:18:53 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Apr 23 07:21:55 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Apr 23 07:21:56 UTC 2023 I: ruby-bio_2.0.4-1_amd64.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 5014ca620b420c84ce096677ef203a2f0a64cf1a 8366 ruby-bio_2.0.4-1_amd64.buildinfo Checksums-Sha256: 3e8f9547e50199c92950c8a83142c34d210c7b675d54697c53707646cb0ac50e 654676 ruby-bio_2.0.4-1_all.deb 88f7d57a428efefa4a82f9c607f8cc86c9d6540f95807bd0798f3e8b8746e234 8366 ruby-bio_2.0.4-1_amd64.buildinfo Files: 2e4e47c285c3625b3a158fdc12e29110 654676 ruby optional ruby-bio_2.0.4-1_all.deb f94cf0a7250ef12bd1bfd34cf7c0d7e4 8366 ruby optional ruby-bio_2.0.4-1_amd64.buildinfo Sun Apr 23 07:21:57 UTC 2023 I: diffoscope 241 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.0lFmHjuG/ruby-bio_2.0.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/ruby-bio_2.0.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/ruby-bio_2.0.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/b1/ruby-bio_2.0.4-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/b2/ruby-bio_2.0.4-1_amd64.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: 0.381s) 0.381s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sun Apr 23 07:21:58 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 23 07:21:58 UTC 2023 I: ruby-bio from bookworm built successfully and reproducibly on amd64. Sun Apr 23 07:22:00 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Apr 23 07:22:00 UTC 2023 I: Submitting 12K b1/ruby-bio_2.0.4-1_amd64.buildinfo.asc Sun Apr 23 07:22:02 UTC 2023 I: Submitting 12K b2/ruby-bio_2.0.4-1_amd64.buildinfo.asc Sun Apr 23 07:22:02 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 23 07:22:02 UTC 2023 I: Done submitting .buildinfo files. Sun Apr 23 07:22:02 UTC 2023 I: Removing signed ruby-bio_2.0.4-1_amd64.buildinfo.asc files: removed './b1/ruby-bio_2.0.4-1_amd64.buildinfo.asc' removed './b2/ruby-bio_2.0.4-1_amd64.buildinfo.asc'