I: pbuilder: network access will be disabled during build I: Current time: Sun May 26 03:41:57 +14 2024 I: pbuilder-time-stamp: 1716644517 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 Sun Oct 9 22:31:23 2022 +14 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/3004191/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 26 03:42 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3004191/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3004191/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=e90951066aad4cf0a8c351c0af69e419 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3004191 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/pbuilderrc_LVnQ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0lFmHjuG/b2 --logfile b2/build.log --extrapackages usrmerge ruby-bio_2.0.4-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 May 26 03:42 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3004191/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 1s (57.4 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. Preparing to unpack .../045-gpg_2.2.40-1.1_amd64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../046-pinentry-curses_1.2.1-1_amd64.deb ... Unpacking pinentry-curses (1.2.1-1) ... Selecting previously unselected package gpg-agent. Preparing to unpack .../047-gpg-agent_2.2.40-1.1_amd64.deb ... Unpacking gpg-agent (2.2.40-1.1) ... Selecting previously unselected package gpg-wks-client. Preparing to unpack .../048-gpg-wks-client_2.2.40-1.1_amd64.deb ... Unpacking gpg-wks-client (2.2.40-1.1) ... Selecting previously unselected package gpg-wks-server. Preparing to unpack .../049-gpg-wks-server_2.2.40-1.1_amd64.deb ... Unpacking gpg-wks-server (2.2.40-1.1) ... Selecting previously unselected package gpgsm. Preparing to unpack .../050-gpgsm_2.2.40-1.1_amd64.deb ... Unpacking gpgsm (2.2.40-1.1) ... Selecting previously unselected package gnupg. Preparing to unpack .../051-gnupg_2.2.40-1.1_all.deb ... Unpacking gnupg (2.2.40-1.1) ... Selecting previously unselected package libfile-dirlist-perl. Preparing to unpack .../052-libfile-dirlist-perl_0.05-3_all.deb ... Unpacking libfile-dirlist-perl (0.05-3) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../053-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../054-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libfile-touch-perl. Preparing to unpack .../055-libfile-touch-perl_0.12-2_all.deb ... Unpacking libfile-touch-perl (0.12-2) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../056-libio-pty-perl_1%3a1.17-1_amd64.deb ... Unpacking libio-pty-perl (1:1.17-1) ... Selecting previously unselected package libipc-run-perl. 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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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3004191/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3004191/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/ruby-bio-2.0.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ruby-bio_2.0.4-1_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: .: (0.000814) test_dbs: .: (0.000277) test_go_ids: .: (0.000220) test_go_terms: .: (0.000508) test_parser: .: (0.000477) test_set_date: .: (0.000227) test_set_desc: .: (0.000221) test_to_str: .: (0.000242) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000758) test_mktmpdir_without_block: .: (0.000889) test_remove_entry_secure: .: (0.000503) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.035217) test_call_command_fork: .: (0.000209) test_call_command_open3: .: (0.035343) test_call_command_popen: .: (0.027915) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.031906) test_call_command_fork: .: (0.000200) test_call_command_open3: .: (0.039461) test_call_command_popen: .: (0.031988) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.031809) test_call_command_fork: .: (0.000199) test_call_command_open3: .: (0.035544) test_call_command_popen: .: (0.027988) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.016069) test_call_command_fork_chdir: .: (0.000398) test_call_command_popen_chdir: .: (0.015162) test_query_command_chdir: .: (0.015900) test_query_command_fork_chdir: .: (0.000380) test_query_command_popen_chdir: .: (0.015539) Bio::FuncTestCommandQuery: test_query_command: .: (0.067784) test_query_command_fork: .: (0.015843) test_query_command_open3: .: (0.055782) test_query_command_popen: .: (0.031984) Bio::FuncTestCommandTmpdir: test_close!: .: (0.002059) test_initialize: .: (0.000351) test_path: .: (0.000224) test_path_after_close: .: (0.000491) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.030000) test_output_fasta: .: (0.085016) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000800) test_accession: .: (0.000236) test_accessions: .: (0.000218) test_comment: .: (0.000189) test_common_name: .: (0.000272) test_definition: .: (0.000257) test_features: .: (0.000479) test_gi: .: (0.000806) test_keywords: .: (0.000206) test_locus: .: (0.000142) test_nid: .: (0.000964) test_organism: .: (0.000262) test_origin: .: (0.000201) test_references: .: (0.000922) test_segment: .: (0.000230) test_source: .: (0.002120) test_taxonomy: .: (0.000404) test_version: .: (0.000243) test_versions: .: (0.000219) Bio::TestAA: test_13: .: (0.000376) test_1n: .: (0.000136) test_name2one: .: (0.000197) test_name2three: .: (0.000180) test_one2name: .: (0.000186) test_one2three: .: (0.000140) test_three2name: .: (0.000156) test_three2one: .: (0.000327) test_to_1_1: .: (0.000167) test_to_1_3: .: (0.000179) test_to_1_name: .: (0.000177) test_to_3_1: .: (0.000687) test_to_3_3: .: (0.000116) test_to_3_name: .: (0.000219) test_to_re: .: (0.000203) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000318) Bio::TestAAindex: test_api: .: (0.000240) test_auto_aax1: .: (0.000405) test_auto_aax2: .: (0.000414) Bio::TestAAindex1: test_author: .: (0.000509) test_comment: .: (0.000313) test_correlation_coefficient: .: (0.001425) test_dblinks: .: (0.000518) test_definition: .: (0.000274) test_entry_id: .: (0.000418) test_index: .: (0.000418) test_journal: .: (0.000335) test_title: .: (0.000305) Bio::TestAAindex2: test_access_A_R: .: (0.002528) test_access_R_A: .: (0.001154) test_author: .: (0.000298) test_cols: .: (0.000219) test_comment: .: (0.000213) test_dblinks: .: (0.000353) test_definition: .: (0.000418) test_entry_id: .: (0.002084) test_journal: .: (0.000477) test_matrix: .: (0.001148) test_matrix_1_2: .: (0.001193) test_matrix_2_2: .: (0.001482) test_matrix_A_R: .: (0.001046) test_matrix_R_A: .: (0.001076) test_matrix_determinant: .: (0.006652) test_matrix_rank: .: (0.005543) test_matrix_transpose: .: (0.002005) test_rows: .: (0.000298) test_title: .: (0.000310) Bio::TestAAindexConstant: test_delimiter: .: (0.000508) test_tagsize: .: (0.000155) Bio::TestAbif: test_complement: .: (0.017489) test_seq: .: (0.015872) test_to_biosequence: .: (0.017254) Bio::TestActsLikeMap: test_mixin: .: (0.000658) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000442) Bio::TestActsLikeMarker: test_mixin: .: (0.000312) Bio::TestAlignment: test_add_seq_no_key: .: (0.000465) test_add_seq_using_seq_with_aaseq_method: .: (0.000185) test_add_seq_using_seq_with_definition_method: .: (0.000148) test_add_seq_using_seq_with_entry_id_method: .: (0.000221) test_add_seq_using_seq_with_naseq_method: .: (0.000190) test_add_seq_using_seq_with_seq_method: .: (0.000179) test_consensus_iupac_gap_modes: .: (0.000643) test_consensus_iupac_missing_char: .: (0.000289) test_consensus_iupac_missing_char_option: .: (0.000367) test_consensus_iupac_no_gaps: .: (0.000458) test_consensus_iupac_of_ambiguous_bases: .: (0.000520) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.009870) test_consensus_opt_gap_mode: .: (0.001064) test_consensus_opt_missing_char: .: (0.000324) test_consensus_string_no_gaps: .: (0.000348) test_consensus_threshold_four_sequences: .: (0.000501) test_consensus_threshold_two_sequences: .: (0.000607) test_convert_match: .: (0.000355) test_convert_unmatch: .: (0.000426) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000224) test_convert_unmatch_different_match_char: .: (0.000239) test_convert_unmatch_multiple_sequences: .: (0.000329) test_default_gap_char: .: (0.000110) test_default_gap_regexp_matches_default_gap_char: .: (0.000121) test_default_missing_char: .: (0.000152) test_each_site_equal_length: .: (0.000221) test_each_site_unequal_length: .: (0.000255) test_equals: .: (0.000252) test_match_line_protein: .: (0.000727) test_normalizebang_extends_sequences_with_gaps: .: (0.000185) test_seq_length_is_max_seq_length: .: (0.000122) test_seq_length_when_one_sequence: .: (0.000372) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000171) test_seqclass_when_seqclass_set: .: (0.000167) test_seqclass_when_sequence_used: .: (0.000212) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000167) test_set_and_get_gap_char: .: (0.000155) test_store_cannot_override_key: .: (0.000183) test_store_with_default_keys_and_user_defined_keys: .: (0.000235) test_store_with_nil_key_uses_next_number_for_key: .: (0.000179) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000446) test_alignment_concat: .: (0.000218) test_alignment_length: .: (0.000183) test_alignment_lstrip!: .: (0.000261) test_alignment_lstrip_nil: .: (0.000317) test_alignment_normalize!: .: (0.000181) test_alignment_rstrip!: .: (0.000258) test_alignment_rstrip_nil: .: (0.000212) test_alignment_site: .: (0.000153) test_alignment_slice: .: (0.000141) test_alignment_strip!: .: (0.000381) test_alignment_strip_nil: .: (0.000221) test_alignment_subseq: .: (0.000295) test_alignment_window: .: (0.000161) test_collect_each_site: .: (0.000237) test_consensus_each_site_default: .: (0.000324) test_consensus_each_site_gap_mode_1: .: (0.000256) test_consensus_each_site_gap_mode_minus1: .: (0.000441) test_consensus_iupac: .: (0.000530) test_consensus_string_default: .: (0.000193) test_consensus_string_half: .: (0.000226) test_convert_match: .: (0.000151) test_convert_unmatch: .: (0.000186) test_each_seq: .: (0.000142) test_each_site: .: (0.000267) test_each_site_step: .: (0.000159) test_each_window: .: (0.000242) test_match_line: .: (0.001492) test_match_line_amino: .: (0.002050) test_match_line_nuc: .: (0.000235) test_private_alignment_site: .: (0.000143) test_remove_all_gaps!: .: (0.000242) test_seqclass: .: (0.000124) test_seqclass=: .: (0.000211) test_seqclass_default: .: (0.000096) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.006474) test_determine_seq_method: .: (0.003303) test_entries: .: (0.000568) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000424) test_avoid_same_name_numbering: .: (0.000174) test_clustal_have_same_name_true: .: (0.000125) test_have_same_name_false: .: (0.000304) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000264) test_gap_char_default: .: (0.000173) test_gap_char_never_nil: .: (0.000121) test_gap_regexp: .: (0.000115) test_gap_regexp=: .: (0.000185) test_gap_regexp_never_nil: .: (0.000133) test_get_all_property_default: .: (0.000132) test_get_all_property_nodefault: .: (0.000150) test_is_gap_default_false: .: (0.000148) test_is_gap_default_true: .: (0.000188) test_is_gap_nodefault_false: .: (0.000140) test_is_gap_nodefault_true: .: (0.000135) test_missing_char=: .: (0.000191) test_missing_char_default: .: (0.000161) test_missing_char_never_nil: .: (0.000129) test_seqclass=: .: (0.000127) test_seqclass_default: .: (0.000269) test_seqclass_never_nil: .: (0.000133) test_set_all_property: .: (0.000161) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001092) test_consensus_string_50percent: .: (0.000177) test_consensus_string_50percent_nil: .: (0.000209) test_consensus_string_default: .: (0.000153) test_consensus_string_default_nil: .: (0.000155) test_has_gap_false: .: (0.000218) test_has_gap_true: .: (0.000156) test_match_line_amino_100percent: .: (0.000228) test_match_line_amino_missing: .: (0.000593) test_match_line_amino_strong: .: (0.000231) test_match_line_amino_weak: .: (0.000312) test_match_line_nuc_100percent: .: (0.000188) test_match_line_nuc_missing: .: (0.000237) test_remove_gaps!: .: (0.000153) test_remove_gaps_bang_not_removed: .: (0.000130) Bio::TestAtomFinder: test_atoms: .: (0.032133) test_each_atom: .: (0.000454) test_find_atom: .: (0.000434) Bio::TestBioFastaDefline: test_acc_version: .: (0.000899) test_accession: .: (0.000668) test_accessions: .: (0.000501) test_description: .: (0.000493) test_descriptions: .: (0.000491) test_entry_id: .: (0.000493) test_get: .: (0.000821) test_get_all_by_type: .: (0.000461) test_get_by_type: .: (0.000437) test_gi: .: (0.000392) test_id_strings: .: (0.000924) test_locus: .: (0.012185) test_method_missing: .: (0.000534) test_to_s: .: (0.000749) test_words: .: (0.001963) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.001532) test_goid2term: .: (0.000607) test_parse_goids: .: (0.000584) Bio::TestBioGenBank: test_basecount: .: (0.001077) test_circular: .: (0.000532) test_classification: .: (0.000757) test_date: .: (0.000412) test_date_modified: .: (0.001236) test_division: .: (0.000425) test_each_cds_feature: .: (0.002121) test_each_cds_qualifiers: .: (0.001136) test_each_gene: .: (0.001722) test_entry_id: .: (0.000448) test_length: .: (0.000381) test_locus_circular: .: (0.000488) test_locus_class: .: (0.000473) test_locus_date: .: (0.000464) test_locus_division: .: (0.000556) test_locus_entry_id: .: (0.000435) test_locus_length: .: (0.001077) test_locus_natype: .: (0.000588) test_locus_strand: .: (0.000430) test_natype: .: (0.000392) test_seq: .: (0.000541) test_seq_len: .: (0.000510) test_strand: .: (0.000652) test_strandedness: .: (0.000483) test_to_biosequence: .: (0.004456) Bio::TestBioGenPept: test_circular: .: (0.001003) test_date: .: (0.000262) test_dbsource: .: (0.000265) test_division: .: (0.000257) test_entry_id: .: (0.000397) test_length: .: (0.000296) test_locus: .: (0.000274) test_seq: .: (0.000295) test_seq_len: .: (0.000270) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000968) test_aaseq: .: (0.000376) test_chromosome: .: (0.000321) test_codon_usage: .: (0.000680) test_cu_list: .: (0.000285) test_dblinks_as_hash: .: (0.000378) test_dblinks_as_strings: .: (0.000317) test_definition: .: (0.000347) test_division: .: (0.000300) test_eclinks: .: (0.000359) test_entry: .: (0.000290) test_entry_id: .: (0.000299) test_gbposition: .: (0.000475) test_gene: .: (0.000397) test_genes: .: (0.000358) test_keggclass: .: (0.000392) test_keggclasses: .: (0.000408) test_locations: .: (0.000853) test_motifs_as_hash: .: (0.000429) test_motifs_as_strings: .: (0.000286) test_name: .: (0.000430) test_names_as_array: .: (0.000343) test_new: .: (0.000292) test_ntlen: .: (0.000432) test_ntseq: .: (0.000494) test_organism: .: (0.000294) test_orthologs_as_hash: .: (0.000568) test_orthologs_as_strings: .: (0.000309) test_pathway: .: (0.000339) test_pathway_after_pathways_as_strings: .: (0.000531) test_pathway_before_pathways_as_strings: .: (0.000379) test_pathways_as_hash: .: (0.000305) test_pathways_as_strings: .: (0.000342) test_position: .: (0.000263) test_structure: .: (0.000275) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.002143) test_comment: .: (0.000624) test_data_source: .: (0.000627) test_definition: .: (0.000510) test_disease: .: (0.000512) test_entry_id: .: (0.000522) test_lineage: .: (0.000827) test_nalen: .: (0.000724) test_name: .: (0.000599) test_new: .: (0.000570) test_num_gene: .: (0.000632) test_num_rna: .: (0.000506) test_original_databases: .: (0.000701) test_original_db: .: (0.000697) test_plasmids: .: (0.000569) test_references: .: (0.004494) test_statistics: .: (0.000969) test_taxid: .: (0.000885) test_taxonomy: .: (0.000855) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000700) test_comment: .: (0.000391) test_data_source: .: (0.000521) test_definition: .: (0.000360) test_disease: .: (0.000523) test_entry_id: .: (0.000370) test_lineage: .: (0.000451) test_nalen: .: (0.000387) test_name: .: (0.000403) test_new: .: (0.000381) test_num_gene: .: (0.000394) test_num_rna: .: (0.000501) test_original_databases: .: (0.000482) test_original_db: .: (0.000311) test_plasmids: .: (0.000441) test_references: .: (0.000512) test_statistics: .: (0.000312) test_taxid: .: (0.000376) test_taxonomy: .: (0.000537) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000727) test_compounds_as_strings: .: (0.000311) test_dblinks_as_hash: .: (0.000256) test_dblinks_as_strings: .: (0.000220) test_description: .: (0.000265) test_diseases_as_hash: .: (0.000227) test_diseases_as_strings: .: (0.000220) test_entry_id: .: (0.000250) test_enzymes_as_strings: .: (0.000254) test_genes_as_hash: .: (0.000454) test_genes_as_strings: .: (0.000227) test_keggclass: .: (0.000315) test_ko_pathway: .: (0.000420) test_modules_as_hash: .: (0.000327) test_modules_as_strings: .: (0.000299) test_name: .: (0.000310) test_new: .: (0.000319) test_organism: .: (0.000292) test_orthologs_as_hash: .: (0.000271) test_orthologs_as_strings: .: (0.000252) test_pathways_as_hash: .: (0.000285) test_pathways_as_strings: .: (0.000572) test_reactions_as_hash: .: (0.000453) test_reactions_as_strings: .: (0.000275) test_references: .: (0.000253) test_rel_pathways_as_hash: .: (0.000413) test_rel_pathways_as_strings: .: (0.000312) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000915) test_compounds_as_strings: .: (0.000886) test_dblinks_as_hash: .: (0.000491) test_dblinks_as_strings: .: (0.000249) test_description: .: (0.000294) test_diseases_as_hash: .: (0.000269) test_diseases_as_strings: .: (0.000255) test_entry_id: .: (0.000284) test_enzymes_as_strings: .: (0.000258) test_genes_as_hash: .: (0.000407) test_genes_as_strings: .: (0.000626) test_keggclass: .: (0.000369) test_ko_pathway: .: (0.000470) test_modules_as_hash: .: (0.000337) test_modules_as_strings: .: (0.000323) test_name: .: (0.000278) test_new: .: (0.000296) test_organism: .: (0.000310) test_orthologs_as_hash: .: (0.000268) test_orthologs_as_strings: .: (0.000264) test_pathways_as_hash: .: (0.000515) test_pathways_as_strings: .: (0.000287) test_reactions_as_hash: .: (0.001230) test_reactions_as_strings: .: (0.000394) test_references: .: (0.000380) test_rel_pathways_as_hash: .: (0.000410) test_rel_pathways_as_strings: .: (0.000362) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000523) test_compounds_as_strings: .: (0.000271) test_dblinks_as_hash: .: (0.000289) test_dblinks_as_strings: .: (0.000412) test_description: .: (0.000279) test_diseases_as_hash: .: (0.000242) test_diseases_as_strings: .: (0.000275) test_entry_id: .: (0.000302) test_enzymes_as_strings: .: (0.000282) test_genes_as_hash: .: (0.000289) test_genes_as_strings: .: (0.000280) test_keggclass: .: (0.000328) test_ko_pathway: .: (0.000433) test_modules_as_hash: .: (0.000281) test_modules_as_strings: .: (0.000206) test_name: .: (0.000571) test_new: .: (0.000271) test_organism: .: (0.000223) test_orthologs_as_hash: .: (0.000306) test_orthologs_as_strings: .: (0.000249) test_pathways_as_hash: .: (0.000227) test_pathways_as_strings: .: (0.000234) test_reactions_as_hash: .: (0.000258) test_reactions_as_strings: .: (0.000229) test_references: .: (0.000397) test_rel_pathways_as_hash: .: (0.000563) test_rel_pathways_as_strings: .: (0.000302) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000489) test_compounds_as_strings: .: (0.000254) test_dblinks_as_hash: .: (0.000274) test_dblinks_as_strings: .: (0.000252) test_description: .: (0.000478) test_diseases_as_hash: .: (0.000304) test_diseases_as_strings: .: (0.000429) test_entry_id: .: (0.000824) test_enzymes_as_strings: .: (0.000329) test_genes_as_hash: .: (0.000329) test_genes_as_strings: .: (0.000322) test_keggclass: .: (0.000358) test_ko_pathway: .: (0.000352) test_modules_as_hash: .: (0.000526) test_modules_as_strings: .: (0.000448) test_name: .: (0.000788) test_new: .: (0.000383) test_organism: .: (0.000321) test_orthologs_as_hash: .: (0.000291) test_orthologs_as_strings: .: (0.000290) test_pathways_as_hash: .: (0.000393) test_pathways_as_strings: .: (0.000381) test_reactions_as_hash: .: (0.000349) test_reactions_as_strings: .: (0.000472) test_references: .: (0.001183) test_rel_pathways_as_hash: .: (0.000361) test_rel_pathways_as_strings: .: (0.000295) Bio::TestBioKeggDRUG: test_activity: .: (0.000583) test_comment: .: (0.000322) test_dblinks_as_hash: .: (0.000861) test_dblinks_as_strings: .: (0.000437) test_entry_id: .: (0.000462) test_formula: .: (0.000328) test_kcf: .: (0.000335) test_mass: .: (0.000324) test_name: .: (0.000354) test_names: .: (0.000348) test_pathways_as_hash: .: (0.000359) test_pathways_as_strings: .: (0.000545) test_products: .: (0.000387) test_remark: .: (0.000395) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000629) test_composition: .: (0.006431) test_compounds: .: (0.000339) test_dblinks_as_hash: .: (0.000816) test_dblinks_as_strings: .: (0.000455) test_entry_id: .: (0.000374) test_enzymes: .: (0.000380) test_kcf: .: (0.000307) test_keggclass: .: (0.000391) test_mass: .: (0.000325) test_name: .: (0.000344) test_orthologs_as_hash: .: (0.000515) test_orthologs_as_strings: .: (0.000420) test_pathways_as_hash: .: (0.000382) test_pathways_as_strings: .: (0.000343) test_reactions: .: (0.000921) test_references: .: (0.000493) test_remark: .: (0.000448) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000487) test_composition: .: (0.000286) test_compounds: .: (0.000260) test_dblinks_as_hash: .: (0.000385) test_dblinks_as_strings: .: (0.000298) test_entry_id: .: (0.000480) test_enzymes: .: (0.000736) test_kcf: .: (0.000332) test_keggclass: .: (0.000272) test_mass: .: (0.000276) test_name: .: (0.000267) test_orthologs_as_hash: .: (0.000264) test_orthologs_as_strings: .: (0.000244) test_pathways_as_hash: .: (0.000253) test_pathways_as_strings: .: (0.000248) test_reactions: .: (0.000438) test_references: .: (0.000246) test_remark: .: (0.000347) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000813) test_compounds_as_strings: .: (0.000457) test_dblinks_as_hash: .: (0.000423) test_dblinks_as_strings: .: (0.000295) test_description: .: (0.000462) test_diseases_as_hash: .: (0.000948) test_diseases_as_strings: .: (0.000322) test_entry_id: .: (0.000315) test_enzymes_as_strings: .: (0.000291) test_genes_as_hash: .: (0.000310) test_genes_as_strings: .: (0.000304) test_keggclass: .: (0.000346) test_ko_pathway: .: (0.000345) test_modules_as_hash: .: (0.000701) test_modules_as_strings: .: (0.000437) test_name: .: (0.000353) test_new: .: (0.000332) test_organism: .: (0.000322) test_orthologs_as_hash: .: (0.000303) test_orthologs_as_strings: .: (0.000305) test_pathways_as_hash: .: (0.000341) test_pathways_as_strings: .: (0.000504) test_reactions_as_hash: .: (0.001335) test_reactions_as_strings: .: (0.000558) test_references: .: (0.000741) test_rel_pathways_as_hash: .: (0.001068) test_rel_pathways_as_strings: .: (0.000492) Bio::TestBioLITDB: test_author: .: (0.000500) test_entry_id: .: (0.000276) test_field: .: (0.000280) test_journal: .: (0.000282) test_keyword: .: (0.000349) test_reference: .: (0.000575) test_title: .: (0.000864) test_volume: .: (0.000322) Bio::TestBioNBRF: test_aalen: .: (0.000451) test_aaseq: .: (0.000196) test_entry: .: (0.000173) test_length: .: (0.000179) test_nalen: .: (0.000286) test_naseq: .: (0.000233) test_seq: .: (0.000318) test_seq_class: .: (0.000213) test_to_nbrf: .: (0.000246) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000895) test_to_newick_format_leaf: .: (0.000527) test_to_newick_format_leaf_NHX: .: (0.000251) Bio::TestBl2seqReport: test_db_len: .: (0.001039) test_db_num: .: (0.000835) test_new: .: (0.000496) test_undefed_methods: .: (0.002216) test_undefed_methods_for_iteration: .: (0.001745) Bio::TestBl2seqReportConstants: test_rs: .: (0.000445) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000603) test_hits: .: (0.000436) Bio::TestBlast: test_blast_reports_format0: .: (0.009989) test_blast_reports_format0_with_block: .: (0.001325) test_blast_reports_format7: .: (0.026198) test_blast_reports_format7_with_block: .: (0.040279) test_blast_reports_format7_with_parser: .: (0.083721) test_blast_reports_format7_with_parser_with_block: .: (0.027319) test_blast_reports_format8: .: (0.001297) test_blast_reports_format8_with_block: .: (0.001308) test_blast_reports_format8_with_parser: .: (0.000441) test_blast_reports_format8_with_parser_with_block: .: (0.000755) test_blast_reports_xml: .: (0.025805) test_blast_reports_xml_with_block: .: (0.025070) test_blastll: .: (0.000294) test_db: .: (0.000606) test_exec_genomenet: .: (0.000202) test_exec_local: .: (0.000197) test_exec_ncbi: .: (0.000188) test_filter: .: (0.000502) test_format: .: (0.000246) test_make_command_line: .: (0.000879) test_make_command_line_2: .: (0.000619) test_matrix: .: (0.000520) test_new: .: (0.000395) test_new_opt_string: .: (0.000662) test_option: .: (0.000249) test_option_set: .: (0.000393) test_option_set_m0: .: (0.000342) test_options: .: (0.000230) test_output: .: (0.000233) test_parse_result: .: (0.027445) test_parser: .: (0.000312) test_program: .: (0.000228) test_query: .: (0.000210) test_self_local: .: (0.000654) test_self_remote: .: (0.002904) test_server: .: (0.000989) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000633) test_delete: .: (0.000579) test_equal_equal: .: (0.000565) test_get: .: (0.000878) test_make_command_line_options: .: (0.000806) test_normalize!: .: (0.000356) test_parse: .: (0.000402) test_set: .: (0.000816) Bio::TestBlastReport: test_db: .: (0.026648) test_db_len: .: (0.025455) test_db_num: .: (0.024065) test_each_hit: .: (0.024472) test_each_iteration: .: (0.029054) test_eff_space: .: (0.023738) test_entrez_query: .: (0.024125) test_entropy: .: (0.022939) test_expect: .: (0.024364) test_filter: .: (0.026288) test_gap_extend: .: (0.024185) test_gap_open: .: (0.024380) test_hits: .: (0.023820) test_hsp_len: .: (0.025833) test_inclusion: .: (0.028002) test_iterations: .: (0.025264) test_kappa: .: (0.023460) test_lambda: .: (0.024372) test_matrix: .: (0.024704) test_message: .: (0.026580) test_parameters: .: (0.025132) test_pattern: .: (0.024094) test_program: .: (0.024289) test_query_def: .: (0.025841) test_query_id: .: (0.025048) test_query_len: .: (0.026087) test_reference: .: (0.023402) test_sc_match: .: (0.024154) test_sc_mismatch: .: (0.028452) test_statistics: .: (0.024816) test_version: .: (0.023885) Bio::TestBlastReportDefault: test_db: .: (0.001414) test_db_len: .: (0.000634) test_db_num: .: (0.000586) test_each_hit: .: (0.000559) test_each_iteration: .: (0.000452) test_eff_space: .: (0.001033) test_entropy: .: (0.000568) test_expect: .: (0.000718) test_gap_extend: .: (0.000607) test_gap_open: .: (0.000610) test_gapped_entropy: .: (0.000532) test_gapped_kappa: .: (0.000742) test_gapped_lambda: .: (0.000493) test_hits: .: (0.000616) test_iterations: .: (0.000430) test_kappa: .: (0.000547) test_lambda: .: (0.000564) test_matrix: .: (0.000946) test_message: .: (0.000513) test_pattern: .: (0.000450) test_program: .: (0.000464) test_query_def: .: (0.000706) test_query_len: .: (0.000657) test_reference: .: (0.000538) test_sc_match: .: (0.001038) test_sc_mismatch: .: (0.000664) test_version: .: (0.000543) Bio::TestBlastReportHit: test_Hit_accession: .: (0.023421) test_Hit_bit_score: .: (0.023900) test_Hit_definition: .: (0.026796) test_Hit_evalue: .: (0.024046) test_Hit_hit_id: .: (0.024981) test_Hit_hsps: .: (0.026055) test_Hit_identity: .: (0.027348) test_Hit_lap_at: .: (0.025184) test_Hit_len: .: (0.024765) test_Hit_midline: .: (0.025389) test_Hit_num: .: (0.023290) test_Hit_overlap: .: (0.025262) test_Hit_query_def: .: (0.023141) test_Hit_query_end: .: (0.023635) test_Hit_query_id: .: (0.023284) test_Hit_query_len: .: (0.023854) test_Hit_query_seq: .: (0.024746) test_Hit_query_start: .: (0.023829) test_Hit_taeget_def: .: (0.025011) test_Hit_target_end: .: (0.024116) test_Hit_target_id: .: (0.026608) test_Hit_target_len: .: (0.024913) test_Hit_target_seq: .: (0.025990) test_Hit_target_start: .: (0.024400) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.001645) test_Hit_definition: .: (0.000592) test_Hit_evalue: .: (0.000575) test_Hit_hsps: .: (0.000540) test_Hit_identity: .: (0.000612) test_Hit_lap_at: .: (0.001380) test_Hit_len: .: (0.000671) test_Hit_midline: .: (0.000840) test_Hit_overlap: .: (0.000540) test_Hit_query_end: .: (0.000776) test_Hit_query_seq: .: (0.001216) test_Hit_query_start: .: (0.001163) test_Hit_taeget_def: .: (0.000642) test_Hit_target_end: .: (0.000763) test_Hit_target_id: .: (0.000809) test_Hit_target_len: .: (0.000549) test_Hit_target_seq: .: (0.000869) test_Hit_target_start: .: (0.001017) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.070915) test_Hit_bit_score: .: (0.073722) test_Hit_definition: .: (0.070732) test_Hit_evalue: .: (0.072786) test_Hit_hit_id: .: (0.074005) test_Hit_hsps: .: (0.070615) test_Hit_identity: .: (0.074738) test_Hit_lap_at: .: (0.094039) test_Hit_len: .: (0.155060) test_Hit_midline: .: (0.147679) test_Hit_num: .: (0.132374) test_Hit_overlap: .: (0.092863) test_Hit_query_def: .: (0.079398) test_Hit_query_end: .: (0.077119) test_Hit_query_id: .: (0.078028) test_Hit_query_len: .: (0.074179) test_Hit_query_seq: .: (0.075796) test_Hit_query_start: .: (0.075926) test_Hit_taeget_def: .: (0.071582) test_Hit_target_end: .: (0.076288) test_Hit_target_id: .: (0.076487) test_Hit_target_len: .: (0.074412) test_Hit_target_seq: .: (0.077431) test_Hit_target_start: .: (0.077952) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.074872) test_Hit_bit_score: .: (0.073115) test_Hit_definition: .: (0.122281) test_Hit_evalue: .: (0.081113) test_Hit_hit_id: .: (0.073283) test_Hit_hsps: .: (0.076412) test_Hit_identity: .: (0.079544) test_Hit_lap_at: .: (0.069857) test_Hit_len: .: (0.074211) test_Hit_midline: .: (0.075756) test_Hit_num: .: (0.073344) test_Hit_overlap: .: (0.082831) test_Hit_query_def: .: (0.074239) test_Hit_query_end: .: (0.072851) test_Hit_query_id: .: (0.070735) test_Hit_query_len: .: (0.072507) test_Hit_query_seq: .: (0.074267) test_Hit_query_start: .: (0.071470) test_Hit_taeget_def: .: (0.070246) test_Hit_target_end: .: (0.074252) test_Hit_target_id: .: (0.071954) test_Hit_target_len: .: (0.073976) test_Hit_target_seq: .: (0.074109) test_Hit_target_start: .: (0.075134) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.024422) test_Hit_bit_score: .: (0.025772) test_Hit_definition: .: (0.024021) test_Hit_evalue: .: (0.026368) test_Hit_hit_id: .: (0.024096) test_Hit_hsps: .: (0.023958) test_Hit_identity: .: (0.023565) test_Hit_lap_at: .: (0.023954) test_Hit_len: .: (0.025791) test_Hit_midline: .: (0.023929) test_Hit_num: .: (0.024497) test_Hit_overlap: .: (0.024848) test_Hit_query_def: .: (0.027579) test_Hit_query_end: .: (0.025133) test_Hit_query_id: .: (0.024460) test_Hit_query_len: .: (0.023776) test_Hit_query_seq: .: (0.024063) test_Hit_query_start: .: (0.026071) test_Hit_taeget_def: .: (0.024132) test_Hit_target_end: .: (0.023920) test_Hit_target_id: .: (0.023355) test_Hit_target_len: .: (0.028505) test_Hit_target_seq: .: (0.023297) test_Hit_target_start: .: (0.022634) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000585) test_Hit_bit_score: .: (0.000227) test_Hit_definition: .: (0.000166) test_Hit_evalue: .: (0.000165) test_Hit_hit_id: .: (0.000176) test_Hit_hsps: .: (0.000164) test_Hit_identity: .: (0.000345) test_Hit_lap_at: .: (0.000239) test_Hit_len: .: (0.000187) test_Hit_midline: .: (0.000466) test_Hit_num: .: (0.000211) test_Hit_overlap: .: (0.000186) test_Hit_query_def: .: (0.000198) test_Hit_query_end: .: (0.000190) test_Hit_query_id: .: (0.000185) test_Hit_query_len: .: (0.000162) test_Hit_query_seq: .: (0.000165) test_Hit_query_start: .: (0.000171) test_Hit_taeget_def: .: (0.000168) test_Hit_target_end: .: (0.000175) test_Hit_target_id: .: (0.000173) test_Hit_target_len: .: (0.000308) test_Hit_target_seq: .: (0.000268) test_Hit_target_start: .: (0.000161) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.022812) test_Hsp_bit_score: .: (0.025802) test_Hsp_density: .: (0.023900) test_Hsp_evalue: .: (0.023490) test_Hsp_gaps: .: (0.023213) test_Hsp_hit_frame: .: (0.024804) test_Hsp_hit_from: .: (0.025900) test_Hsp_hit_to: .: (0.023909) test_Hsp_hseq: .: (0.023170) test_Hsp_identity: .: (0.024265) test_Hsp_midline: .: (0.026562) test_Hsp_mismatch_count: .: (0.024697) test_Hsp_num: .: (0.023924) test_Hsp_pattern_from: .: (0.026222) test_Hsp_pattern_to: .: (0.024757) test_Hsp_percent_identity: .: (0.026611) test_Hsp_positive: .: (0.025201) test_Hsp_qseq: .: (0.023953) test_Hsp_query_frame: .: (0.022498) test_Hsp_query_from: .: (0.024571) test_Hsp_query_to: .: (0.023191) test_Hsp_score: .: (0.023806) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.001493) test_Hsp_bit_score: .: (0.000676) test_Hsp_evalue: .: (0.000598) test_Hsp_gaps: .: (0.000567) test_Hsp_hit_frame: .: (0.000699) test_Hsp_hit_from: .: (0.001157) test_Hsp_hit_to: .: (0.000984) test_Hsp_hseq: .: (0.000872) test_Hsp_identity: .: (0.000583) test_Hsp_midline: .: (0.001059) test_Hsp_percent_identity: .: (0.000728) test_Hsp_positive: .: (0.000663) test_Hsp_qseq: .: (0.000881) test_Hsp_query_frame: .: (0.000624) test_Hsp_query_from: .: (0.001143) test_Hsp_query_to: .: (0.000753) test_Hsp_score: .: (0.000548) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.077244) test_Hsp_bit_score: .: (0.147032) test_Hsp_density: .: (0.074929) test_Hsp_evalue: .: (0.072657) test_Hsp_gaps: .: (0.070366) test_Hsp_hit_frame: .: (0.075783) test_Hsp_hit_from: .: (0.073402) test_Hsp_hit_to: .: (0.071213) test_Hsp_hseq: .: (0.073984) test_Hsp_identity: .: (0.073425) test_Hsp_midline: .: (0.065685) test_Hsp_mismatch_count: .: (0.076635) test_Hsp_num: .: (0.132946) test_Hsp_pattern_from: .: (0.068681) test_Hsp_pattern_to: .: (0.072380) test_Hsp_percent_identity: .: (0.073848) test_Hsp_positive: .: (0.069752) test_Hsp_qseq: .: (0.073390) test_Hsp_query_frame: .: (0.072578) test_Hsp_query_from: .: (0.071747) test_Hsp_query_to: .: (0.075301) test_Hsp_score: .: (0.071743) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.087053) test_Hsp_bit_score: .: (0.151876) test_Hsp_density: .: (0.150952) test_Hsp_evalue: .: (0.145286) test_Hsp_gaps: .: (0.146746) test_Hsp_hit_frame: .: (0.156008) test_Hsp_hit_from: .: (0.134612) test_Hsp_hit_to: .: (0.073864) test_Hsp_hseq: .: (0.069269) test_Hsp_identity: .: (0.069810) test_Hsp_midline: .: (0.071290) test_Hsp_mismatch_count: .: (0.073355) test_Hsp_num: .: (0.072386) test_Hsp_pattern_from: .: (0.074519) test_Hsp_pattern_to: .: (0.071209) test_Hsp_percent_identity: .: (0.070876) test_Hsp_positive: .: (0.073996) test_Hsp_qseq: .: (0.072346) test_Hsp_query_frame: .: (0.069564) test_Hsp_query_from: .: (0.153114) test_Hsp_query_to: .: (0.151803) test_Hsp_score: .: (0.137089) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.024954) test_Hsp_bit_score: .: (0.028525) test_Hsp_density: .: (0.028028) test_Hsp_evalue: .: (0.024532) test_Hsp_gaps: .: (0.024398) test_Hsp_hit_frame: .: (0.023734) test_Hsp_hit_from: .: (0.025642) test_Hsp_hit_to: .: (0.024169) test_Hsp_hseq: .: (0.024621) test_Hsp_identity: .: (0.025174) test_Hsp_midline: .: (0.025188) test_Hsp_mismatch_count: .: (0.026782) test_Hsp_num: .: (0.025442) test_Hsp_pattern_from: .: (0.022925) test_Hsp_pattern_to: .: (0.024264) test_Hsp_percent_identity: .: (0.025047) test_Hsp_positive: .: (0.026341) test_Hsp_qseq: .: (0.024074) test_Hsp_query_frame: .: (0.022041) test_Hsp_query_from: .: (0.022856) test_Hsp_query_to: .: (0.025364) test_Hsp_score: .: (0.024672) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000609) test_Hsp_bit_score: .: (0.000188) test_Hsp_density: .: (0.000483) test_Hsp_evalue: .: (0.000192) test_Hsp_gaps: .: (0.000177) test_Hsp_hit_frame: .: (0.000175) test_Hsp_hit_from: .: (0.000174) test_Hsp_hit_to: .: (0.000172) test_Hsp_hseq: .: (0.000171) test_Hsp_identity: .: (0.000171) test_Hsp_midline: .: (0.000441) test_Hsp_mismatch_count: .: (0.000221) test_Hsp_num: .: (0.000188) test_Hsp_pattern_from: .: (0.000177) test_Hsp_pattern_to: .: (0.000181) test_Hsp_percent_identity: .: (0.000179) test_Hsp_positive: .: (0.000185) test_Hsp_qseq: .: (0.000597) test_Hsp_query_frame: .: (0.000212) test_Hsp_query_from: .: (0.000200) test_Hsp_query_to: .: (0.000188) test_Hsp_score: .: (0.000188) Bio::TestBlastReportIteration: test_hits: .: (0.024531) test_message: .: (0.024580) test_num: .: (0.024798) test_statistics: .: (0.026087) Bio::TestBlastReportIterationDefault: test_hits: .: (0.001011) test_message: .: (0.000523) test_num: .: (0.001071) Bio::TestBlastReportIterationMulti: test_each: .: (0.069032) test_hits: .: (0.073085) test_message: .: (0.081726) test_num: .: (0.072369) test_query_def: .: (0.072952) test_query_id: .: (0.073867) test_query_len: .: (0.071887) test_statistics: .: (0.075894) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.075976) test_hits: .: (0.074483) test_message: .: (0.077228) test_num: .: (0.078041) test_query_def: .: (0.122304) test_query_id: .: (0.166989) test_query_len: .: (0.149396) test_statistics: .: (0.131197) Bio::TestBlastReportIterationREXML: test_hits: .: (0.049292) test_message: .: (0.052057) test_num: .: (0.047917) test_statistics: .: (0.047749) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000523) test_message: .: (0.000245) test_num: .: (0.000154) test_statistics: .: (0.000176) Bio::TestBlastReportMulti: test_db: .: (0.148558) test_db_len: .: (0.075130) test_db_num: .: (0.064848) test_each_hit: .: (0.066692) test_each_iteration: .: (0.067470) test_eff_space: .: (0.064576) test_entropy: .: (0.074970) test_expect: .: (0.143071) test_filter: .: (0.135727) test_gap_extend: .: (0.148946) test_gap_open: .: (0.159665) test_hits: .: (0.092090) test_hsp_len: .: (0.075623) test_iterations: .: (0.075537) test_kappa: .: (0.074457) test_lambda: .: (0.073539) test_matrix: .: (0.076733) test_message: .: (0.075490) test_parameters: .: (0.072387) test_pattern: .: (0.075840) test_program: .: (0.076762) test_query_def: .: (0.072715) test_query_id: .: (0.075409) test_query_len: .: (0.077081) test_reference: .: (0.075815) test_reports: .: (0.147528) test_statistics: .: (0.109073) test_version: .: (0.075676) Bio::TestBlastReportMultiREXML: test_db: .: (0.075941) test_db_len: .: (0.078549) test_db_num: .: (0.077171) test_each_hit: .: (0.077228) test_each_iteration: .: (0.076528) test_eff_space: .: (0.075732) test_entropy: .: (0.080166) test_expect: .: (0.073781) test_filter: .: (0.074127) test_gap_extend: .: (0.074900) test_gap_open: .: (0.067388) test_hits: .: (0.065605) test_hsp_len: .: (0.092595) test_iterations: .: (0.074092) test_kappa: .: (0.072554) test_lambda: .: (0.072310) test_matrix: .: (0.075148) test_message: .: (0.074732) test_parameters: .: (0.073256) test_pattern: .: (0.076322) test_program: .: (0.078502) test_query_def: .: (0.077684) test_query_id: .: (0.074376) test_query_len: .: (0.077691) test_reference: .: (0.077564) test_reports: .: (0.076792) test_statistics: .: (0.071344) test_version: .: (0.072674) Bio::TestBlastReportREXML: test_db: .: (0.024573) test_db_len: .: (0.025849) test_db_num: .: (0.025074) test_each_hit: .: (0.025585) test_each_iteration: .: (0.025332) test_eff_space: .: (0.029601) test_entrez_query: .: (0.027232) test_entropy: .: (0.026583) test_expect: .: (0.025707) test_filter: .: (0.028093) test_gap_extend: .: (0.026626) test_gap_open: .: (0.025855) test_hits: .: (0.025069) test_hsp_len: .: (0.025411) test_inclusion: .: (0.027389) test_iterations: .: (0.025511) test_kappa: .: (0.024337) test_lambda: .: (0.024829) test_matrix: .: (0.025635) test_message: .: (0.024331) test_parameters: .: (0.024041) test_pattern: .: (0.023619) test_program: .: (0.033149) test_query_def: .: (0.058666) test_query_id: .: (0.053281) test_query_len: .: (0.056469) test_reference: .: (0.030393) test_sc_match: .: (0.026587) test_sc_mismatch: .: (0.041334) test_statistics: .: (0.048839) test_version: .: (0.050717) Bio::TestBlastReportTabular: test_db: .: (0.000527) test_db_len: .: (0.000486) test_db_num: .: (0.000214) test_each_hit: .: (0.000180) test_each_iteration: .: (0.000167) test_eff_space: .: (0.000176) test_entrez_query: .: (0.000187) test_entropy: .: (0.008541) test_expect: .: (0.000331) test_filter: .: (0.000202) test_gap_extend: .: (0.000198) test_gap_open: .: (0.000177) test_hits: .: (0.000201) test_hsp_len: .: (0.000190) test_inclusion: .: (0.000191) test_iterations: .: (0.000544) test_kappa: .: (0.000173) test_lambda: .: (0.000168) test_matrix: .: (0.000172) test_message: .: (0.000222) test_parameters: .: (0.000360) test_pattern: .: (0.000222) test_program: .: (0.000215) test_query_def: .: (0.000238) test_query_id: .: (0.000229) test_query_len: .: (0.000218) test_reference: .: (0.000211) test_sc_match: .: (0.000208) test_sc_mismatch: .: (0.000519) test_statistics: .: (0.000268) test_version: .: (0.000184) Bio::TestChain: test_aaseq: .: (0.009023) test_addLigand: .: (0.000235) test_addResidue: .: (0.000183) test_atom_seq: .: (0.000192) test_comp: .: (0.000192) test_each: .: (0.000164) test_each_heterogen: .: (0.000172) test_each_residue: .: (0.000175) test_get_heterogen_by_id: .: (0.000166) test_get_residue_by_id: .: (0.000165) test_inspect: .: (0.000215) test_rehash: .: (0.000176) test_rehash_heterogens: .: (0.000148) test_rehash_residues: .: (0.000453) test_square_brace: .: (0.000191) test_to_s: .: (0.000219) Bio::TestChainFinder: test_chains: .: (0.000458) test_each_chain: .: (0.000206) test_find_chain: .: (0.000175) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.015776) test_header: .: (0.001019) test_match_line: .: (0.001311) test_sequence0: .: (0.000869) test_sequence1: .: (0.000807) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.015091) test_header: .: (0.001378) test_match_line: .: (0.001781) test_sequence0: .: (0.001138) test_sequence1: .: (0.001083) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.018951) test_header: .: (0.001202) test_match_line: .: (0.001270) test_sequence0: .: (0.000991) test_sequence1: .: (0.001241) Bio::TestCodonTable: test_Tables: .: (0.000688) test_accessor: .: (0.000183) test_definition: .: (0.000115) test_each: .: (0.000133) test_revtrans: .: (0.000225) test_self_accessor: .: (0.000125) test_self_copy: .: (0.001076) test_set_accessor: .: (0.217817) test_start: .: (0.000194) test_start_codon?: .: (0.000160) test_stop: .: (0.000133) test_stop_codon?: .: (0.000152) test_table: .: (0.000127) Bio::TestCodonTableConstants: test_Definitions: .: (0.000335) test_Starts: .: (0.000336) test_Tables: .: (0.000123) test_stops: .: (0.000148) Bio::TestColorScheme: test_buried: .: (0.001960) Bio::TestCommand: test_command_constants: .: (0.000370) test_escape_shell: .: (0.000213) test_escape_shell_unix: .: (0.000170) test_escape_shell_windows: .: (0.000168) test_make_cgi_params_by_array_of_array: .: (0.000606) test_make_cgi_params_by_array_of_hash: .: (0.000396) test_make_cgi_params_by_array_of_string: .: (0.000535) test_make_cgi_params_by_hash_in_string: .: (0.000639) test_make_cgi_params_by_hash_in_symbol: .: (0.000977) test_make_cgi_params_by_string: .: (0.000268) test_make_command_line: .: (0.000183) test_make_command_line_unix: .: (0.000170) test_make_command_line_windows: .: (0.000185) test_safe_command_line_array: .: (0.000195) test_safe_command_line_array_passthrough: .: (0.000214) Bio::TestContingencyTable: test_lite_example: .: (0.241455) Bio::TestDB: test_entry_id: .: (0.000465) test_exists: .: (0.000125) test_fetch: .: (0.000226) test_get: .: (0.000136) test_open: .: (0.000140) test_tags: .: (0.000144) Bio::TestDataType: test_const_like_method: .: (0.001076) test_pdb_achar: .: (0.000475) test_pdb_atom: .: (0.000263) test_pdb_character: .: (0.000243) test_pdb_date: .: (0.000240) test_pdb_idcode: .: (0.000251) test_pdb_integer: .: (0.000131) test_pdb_list: .: (0.000152) test_pdb_lstring: .: (0.000250) test_pdb_real: .: (0.000230) test_pdb_resudue_name: .: (0.000303) test_pdb_slist: .: (0.000162) test_pdb_string: .: (0.000629) test_pdb_stringrj: .: (0.000150) test_pdb_symop: .: (0.000276) test_specification_list: .: (0.000409) Bio::TestEMBL: test_ac: .: (0.000777) test_accession: .: (0.000462) test_cc: .: (0.000435) test_de: .: (0.000749) test_division: .: (0.000747) test_dr: .: (0.000477) test_dt: .: (0.000497) test_dt_created: .: (0.000484) test_dt_iterator: .: (0.000450) test_dt_updated: .: (0.000442) test_each_cds: .: (0.001057) test_each_gene: .: (0.000789) test_entry: .: (0.000848) test_fh: .: (0.000552) test_ft: .: (0.001056) test_ft_accessor: .: (0.000721) test_ft_iterator: .: (0.000875) test_id_line: .: (0.000520) test_id_line_data_class: .: (0.000576) test_id_line_division: .: (0.000824) test_id_line_entry_name: .: (0.000767) test_id_line_iterator: .: (0.000559) test_id_line_molecule_type: .: (0.000527) test_id_line_sequence_length: .: (0.000497) test_kw: .: (0.000673) test_molecule: .: (0.000979) test_oc: .: (0.000610) test_og: .: (0.000500) test_os: .: (0.000547) test_ref: .: (0.000872) test_references: .: (0.001172) test_seq: .: (0.000922) test_sequence_length: .: (0.000576) test_sq: .: (0.000578) test_sq_get: .: (0.000549) test_sv: .: (0.000889) test_version: .: (0.000637) Bio::TestEMBL89: test_ac: .: (0.000765) test_accession: .: (0.000445) test_cc: .: (0.000403) test_de: .: (0.000667) test_division: .: (0.000584) test_dr: .: (0.000477) test_dt: .: (0.000483) test_dt_created: .: (0.000433) test_dt_iterator: .: (0.000590) test_dt_updated: .: (0.000431) test_each_cds: .: (0.001046) test_each_gene: .: (0.000757) test_entry: .: (0.000796) test_fh: .: (0.000514) test_ft: .: (0.000784) test_ft_accessor: .: (0.001159) test_ft_iterator: .: (0.000777) test_id_line: .: (0.000522) test_id_line_data_class: .: (0.000553) test_id_line_division: .: (0.000554) test_id_line_entry_name: .: (0.000894) test_id_line_iterator: .: (0.000513) test_id_line_molecule_type: .: (0.000467) test_id_line_sequence_length: .: (0.000467) test_id_line_sequence_version: .: (0.000666) test_kw: .: (0.000457) test_molecule: .: (0.000805) test_oc: .: (0.000601) test_og: .: (0.000774) test_os: .: (0.000527) test_ref: .: (0.000606) test_references: .: (0.001110) test_seq: .: (0.001121) test_sequence_length: .: (0.000593) test_sq: .: (0.000546) test_sq_get: .: (0.000507) test_sv: .: (0.000931) test_version: .: (0.000482) Bio::TestEMBLAPI: test_ac: .: (0.000431) test_accessions: .: (0.000203) Bio::TestEMBLCommon: test_ac: .: (0.000295) test_accession: .: (0.000122) test_accessions: .: (0.000396) test_de: .: (0.000119) test_definition: .: (0.000132) test_description: .: (0.000124) test_dr: .: (0.000233) test_keywords: .: (0.000163) test_kw: .: (0.000149) test_oc: .: (0.000141) test_og: .: (0.000139) test_os: .: (0.000151) test_ref: .: (0.000126) test_references: .: (0.000119) Bio::TestEMBLDB: test_fetch: .: (0.000414) test_p_entry2hash: .: (0.000106) Bio::TestEMBLToBioSequence: test_classification: .: (0.005667) test_date_created: .: (0.000958) test_date_modified: .: (0.000769) test_definition: .: (0.000593) test_division: .: (0.000606) test_entry_id: .: (0.001041) test_entry_version: .: (0.000536) test_features: .: (0.000761) test_keywords: .: (0.000542) test_molecule_type: .: (0.000724) test_primary_accession: .: (0.000840) test_references: .: (0.006098) test_release_created: .: (0.000652) test_release_modified: .: (0.000550) test_secondary_accessions: .: (0.001092) test_sequence_version: .: (0.000544) test_species: .: (0.000587) test_topology: .: (0.000542) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.005106) test_date_created: .: (0.004533) test_date_modified: .: (0.005289) test_definition: .: (0.005407) test_division: .: (0.005422) test_entry_id: .: (0.005466) test_entry_version: .: (0.004656) test_features: .: (0.005315) test_keywords: .: (0.005031) test_molecule_type: .: (0.005371) test_primary_accession: .: (0.005383) test_references: .: (0.005733) test_release_created: .: (0.004636) test_release_modified: .: (0.003801) test_secondary_accessions: .: (0.003643) test_sequence_version: .: (0.003482) test_species: .: (0.004688) test_topology: .: (0.009123) Bio::TestFasta: test_db: .: (0.000360) test_format: .: (0.000135) test_format_arg_integer: .: (0.000170) test_format_arg_str: .: (0.000150) test_ktup: .: (0.000153) test_matrix: .: (0.000159) test_option: .: (0.000211) test_options: .: (0.000475) test_output: .: (0.000126) test_program: .: (0.000147) test_server: .: (0.000162) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000707) test_accession: .: (0.000196) test_accessions: .: (0.000200) test_description: .: (0.000183) test_descriptions: .: (0.000181) test_entry_id: .: (0.000182) test_get_all_by_type: .: (0.000178) test_gi: .: (0.000170) test_id_strings: .: (0.000252) test_list_ids: .: (0.000167) test_locus: .: (0.000164) test_words: .: (0.000216) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000618) test_accession: .: (0.000155) test_accessions: .: (0.000169) test_description: .: (0.000160) test_descriptions: .: (0.000169) test_emb: .: (0.000216) test_entry_id: .: (0.000270) test_get_all_by_type: .: (0.000187) test_get_emb: .: (0.000169) test_gi: .: (0.000166) test_id_strings: .: (0.000526) test_list_ids: .: (0.000169) test_locus: .: (0.000136) test_words: .: (0.000201) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000336) test_accession: .: (0.000162) test_accessions: .: (0.000154) test_description: .: (0.000143) test_descriptions: .: (0.000148) test_entry_id: .: (0.000143) test_get_all_by_type: .: (0.000135) test_gi: .: (0.000162) test_id_strings: .: (0.000232) test_list_ids: .: (0.000448) test_locus: .: (0.000183) test_sp: .: (0.000198) test_words: .: (0.000231) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000711) test_accession: .: (0.000236) test_accessions: .: (0.000252) test_description: .: (0.000219) test_descriptions: .: (0.000220) test_entry_id: .: (0.000217) test_get_all_by_type: .: (0.000233) test_gi: .: (0.000482) test_id_strings: .: (0.000429) test_list_ids: .: (0.000248) test_locus: .: (0.000599) test_words: .: (0.000484) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000403) test_accession: .: (0.000203) test_accessions: .: (0.000169) test_description: .: (0.000179) test_descriptions: .: (0.000207) test_entry_id: .: (0.000178) test_get_all_by_type: .: (0.000184) test_gi: .: (0.000190) test_id_strings: .: (0.000315) test_list_ids: .: (0.000218) test_locus: .: (0.000230) test_words: .: (0.000364) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000385) test_accession: .: (0.000163) test_accessions: .: (0.000168) test_description: .: (0.000554) test_descriptions: .: (0.000170) test_entry_id: .: (0.000138) test_get_all_by_type: .: (0.000136) test_gi: .: (0.000143) test_id_strings: .: (0.000188) test_list_ids: .: (0.000160) test_locus: .: (0.000150) test_words: .: (0.000187) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000348) test_accession: .: (0.000249) test_accessions: .: (0.000151) test_description: .: (0.000161) test_descriptions: .: (0.000158) test_entry_id: .: (0.000148) test_get: .: (0.000179) test_get_all_by_type: .: (0.000187) test_id_strings: .: (0.000296) test_list_ids: .: (0.000449) test_locus: .: (0.000181) test_sp: .: (0.000189) test_words: .: (0.000277) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000355) test_accession: .: (0.000172) test_accessions: .: (0.000171) test_description: .: (0.000159) test_descriptions: .: (0.000155) test_entry_id: .: (0.000155) test_get: .: (0.000169) test_get_all_by_type: .: (0.000517) test_id_strings: .: (0.000637) test_list_ids: .: (0.000182) test_locus: .: (0.000174) test_tr: .: (0.000203) test_words: .: (0.000367) Bio::TestFastaFirstName: test_first_name1: .: (0.000344) test_first_name_multi_identifier: .: (0.000145) test_first_name_single_worded_defintion: .: (0.000126) test_no_definition: .: (0.000143) test_space_before_first_name: .: (0.000139) test_tabbed_defintion: .: (0.000140) Bio::TestFastaFormat: test_aalen: .: (0.001164) test_aaseq: .: (0.000296) test_acc_version: .: (0.000247) test_accession: .: (0.000210) test_accessions: .: (0.000242) test_data: .: (0.000165) test_definition: .: (0.000160) test_entry: .: (0.000170) test_entry_id: .: (0.000231) test_entry_overrun: .: (0.000173) test_first_name: .: (0.000184) test_gi: .: (0.000235) test_identifiers: .: (0.000247) test_length: .: (0.000779) test_query: .: (0.000269) test_seq: .: (0.000169) Bio::TestFastaFormatConst: test_delimiter: .: (0.000344) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000389) test_data: .: (0.000157) test_definition: .: (0.000147) test_entry: .: (0.000158) test_entry_id: .: (0.000228) test_first_name: .: (0.000193) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000676) test_naseq: .: (0.000196) test_naseq_class: .: (0.000186) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000474) Bio::TestFastaInitialize: test_new_1: .: (0.000768) test_option: .: (0.000140) test_option_backward_compatibility: .: (0.000182) Bio::TestFastaNumericFormat: test_arg: .: (0.000595) test_data: .: (0.000237) test_definition: .: (0.000170) test_each: .: (0.000226) test_entry: .: (0.000551) test_entry_id: .: (0.000188) test_length: .: (0.000202) test_to_biosequence: .: (0.001349) Bio::TestFastaQuery: test_query: .: (0.000562) test_self_local: .: (0.000098) test_self_parser: .: (0.000094) test_self_remote: .: (0.000096) Bio::TestFastacmd: test_database: .: (0.000280) test_fastacmd: .: (0.000130) test_methods: .: (0.000180) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.001345) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.001162) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000720) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000660) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000922) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.001092) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000723) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000664) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000703) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000796) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000870) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001059) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.001016) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.001989) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.002265) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.001020) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000894) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000769) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.010177) test_error_probabilities_as_sanger: .: (0.010300) test_error_probabilities_as_solexa: .: (0.015749) test_quality_scores_as_illumina: .: (0.000696) test_quality_scores_as_sanger: .: (0.000466) test_quality_scores_as_solexa: .: (0.000918) test_validate_format: .: (0.000899) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.002057) test_entry_id: .: (0.002105) test_error_probabilities: .: (0.332691) test_nalen: .: (0.002252) test_naseq: .: (0.001838) test_quality_scores: .: (0.003417) test_quality_string: .: (0.002153) test_roundtrip: .: (0.288905) test_seq: .: (0.001722) test_sequence_string: .: (0.002216) test_to_biosequence: .: (0.272656) test_to_biosequence_and_output: .: (0.008321) test_to_s: .: (0.002277) test_validate_format: .: (0.001784) test_validate_format_with_array: .: (0.002125) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.001051) test_mask_20_with_empty_string: .: (0.000809) test_mask_20_with_longer_string: .: (0.000848) test_mask_20_with_x: .: (0.000558) test_mask_60: .: (0.000635) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.014627) test_error_probabilities_as_sanger: .: (0.013816) test_error_probabilities_as_solexa: .: (0.014126) test_quality_scores_as_illumina: .: (0.000679) test_quality_scores_as_sanger: .: (0.000396) test_quality_scores_as_solexa: .: (0.000574) test_validate_format: .: (0.000818) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.012685) test_error_probabilities_as_sanger: .: (0.013167) test_error_probabilities_as_solexa: .: (0.010983) test_quality_scores_as_illumina: .: (0.000982) test_quality_scores_as_sanger: .: (0.000554) test_quality_scores_as_solexa: .: (0.000396) test_validate_format: .: (0.000893) Bio::TestFeature: test_append: .: (0.000721) test_append_nil: .: (0.000143) test_assoc: .: (0.000157) test_each: .: (0.000136) test_feature: .: (0.000128) test_locations: .: (0.000244) test_new: .: (0.000136) test_position: .: (0.000351) test_qualifiers: .: (0.000126) Bio::TestFeatures: test_append: .: (0.000389) test_arg: .: (0.000142) test_each: .: (0.000143) test_features: .: (0.000162) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.001870) test_aaindex2: .: (0.000324) test_blast: .: (0.000235) test_blastxml: .: (0.000726) test_embl: .: (0.000532) test_embl_oldrelease: .: (0.000611) test_fastaformat: .: (0.000492) test_fastanumericformat: .: (0.000189) test_fastq: .: (0.000263) test_genbank: .: (0.000387) test_genpept: .: (0.000379) test_hmmer: .: (0.000338) test_maxml_cluster: .: (0.005134) test_maxml_sequence: .: (0.000227) test_medline: .: (0.000258) test_prosite: .: (0.004039) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.004147) test_transfac: .: (0.003113) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000474) test_auto_1arg_filename: .: (0.000567) test_auto_1arg_io: .: (0.000494) test_auto_1arg_io_with_block: .: (0.001164) test_auto_1arg_with_block: .: (0.001228) test_auto_2arg_filename_mode: .: (0.000514) test_auto_2arg_filename_mode_with_block: .: (0.001003) test_auto_3arg: .: (0.000420) test_auto_3arg_with_block: .: (0.001415) test_foreach: .: (0.000733) test_new_2arg_class: .: (0.000228) test_new_2arg_nil: .: (0.000418) test_open_0arg: .: (0.000201) test_open_1arg_class: .: (0.000176) test_open_1arg_filename: .: (0.000446) test_open_1arg_io: .: (0.000678) test_open_1arg_io_with_block: .: (0.001381) test_open_1arg_nil: .: (0.000181) test_open_1arg_with_block: .: (0.000906) test_open_2arg_autodetect: .: (0.000432) test_open_2arg_autodetect_io: .: (0.000485) test_open_2arg_autodetect_io_with_block: .: (0.001580) test_open_2arg_autodetect_with_block: .: (0.000850) test_open_2arg_class: .: (0.000221) test_open_2arg_class_io: .: (0.000219) test_open_2arg_class_io_with_block: .: (0.000689) test_open_2arg_class_with_block: .: (0.001132) test_open_2arg_filename_mode: .: (0.000527) test_open_2arg_filename_mode_with_block: .: (0.001092) test_open_3arg: .: (0.000958) test_open_3arg_with_block: .: (0.002915) test_open_4arg: .: (0.002669) test_to_a: .: (0.000689) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000668) test_close: .: (0.000178) test_dbclass: .: (0.000171) test_dbclass_eq: .: (0.000255) test_dbclass_nil: .: (0.000309) test_each: .: (0.000950) test_each_entry: .: (0.000654) test_ended_pos: .: (0.000344) test_entry_pos_flag: .: (0.000209) test_entry_raw: .: (0.000409) test_eof?: .: (0.000362) test_next_entry: .: (0.000479) test_path: .: (0.000179) test_pos: .: (0.000807) test_raw: .: (0.000536) test_rewind: .: (0.000348) test_start_pos: .: (0.000355) test_start_pos_ended_pos_not_recorded: .: (0.000406) test_to_io: .: (0.000239) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000478) test_simpleformat2: .: (0.000273) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000550) test_eof_false_after_prefetch: .: (0.000471) test_eof_false_first: .: (0.000162) test_eof_true: .: (0.000221) test_getc: .: (0.000142) test_getc_after_prefetch: .: (0.000205) test_gets: .: (0.000146) test_gets_equal_prefetch_gets: .: (0.000155) test_gets_paragraph_mode: .: (0.000230) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000385) test_gets_paragraph_mode_within_buffer: .: (0.000483) test_gets_rs: .: (0.000203) test_gets_rs_equal_prefetch_gets: .: (0.000509) test_gets_rs_within_buffer: .: (0.000453) test_pos: .: (0.000157) test_pos=: .: (0.000376) test_prefetch_buffer: .: (0.000179) test_prefetch_gets: .: (0.000158) test_prefetch_gets_with_arg: .: (0.000187) test_rewind: .: (0.000137) test_skip_spaces: .: (0.000178) test_to_io: .: (0.000173) test_ungetc: .: (0.000169) test_ungetc_after_prefetch: .: (0.000182) test_ungets: .: (0.000208) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000725) test_self_open_file: .: (0.000197) test_self_open_file_with_block: .: (0.000238) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000348) test_parse_file_open_arg_int_perm: .: (0.000138) test_parse_file_open_arg_int_perm_opt: .: (0.000147) test_parse_file_open_arg_integer: .: (0.000131) test_parse_file_open_arg_nil: .: (0.000113) test_parse_file_open_arg_opt: .: (0.000200) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000145) test_parse_file_open_arg_str: .: (0.000136) test_parse_file_open_arg_str_opt: .: (0.000147) test_parse_file_open_arg_str_perm: .: (0.000136) test_parse_file_open_arg_str_perm_opt: .: (0.000224) test_parse_file_open_arg_str_with_enc: .: (0.000179) test_parse_file_open_arg_str_with_ext_enc: .: (0.000150) test_parse_file_open_mode_integer: .: (0.000125) test_parse_file_open_mode_nil: .: (0.000151) test_parse_file_open_mode_str: .: (0.000143) test_parse_file_open_mode_str_with_enc: .: (0.000147) test_parse_file_open_mode_str_with_ext_enc: .: (0.000149) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000380) test_entry: .: (0.000186) test_entry_ended_pos: .: (0.000397) test_entry_pos_flag: .: (0.000199) test_entry_start_pos: .: (0.000172) test_get_entry: .: (0.000282) test_rewind: .: (0.000469) test_skip_leader: .: (0.000177) test_stream: .: (0.000127) test_stream_pos: .: (0.000165) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000331) test_delimiter_overrun: .: (0.000124) test_entry: .: (0.000160) test_entry_ended_pos: .: (0.000129) test_entry_ended_pos_default_nil: .: (0.000151) test_entry_start_pos: .: (0.000154) test_entry_start_pos_default_nil: .: (0.000146) test_get_entry: .: (0.000517) test_get_parsed_entry: .: (0.000338) test_header: .: (0.000141) test_skip_leader: .: (0.000491) test_skip_leader_without_header: .: (0.000254) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000526) test_entry_ended_pos: .: (0.000447) test_entry_start_pos: .: (0.000321) test_flag_to_fetch_header: .: (0.000524) test_get_entry: .: (0.000463) test_get_parsed_entry: .: (0.000466) test_rewind: .: (0.000579) test_skip_leader: .: (0.000185) Bio::TestGCGMsf: test_alignment: .: (0.001827) test_checksum: .: (0.000335) test_compcheck: .: (0.000334) test_date: .: (0.000513) test_description: .: (0.000322) test_entry_id: .: (0.000320) test_gap_length_weight: .: (0.000522) test_gap_weight: .: (0.000326) test_heading: .: (0.000322) test_length: .: (0.000315) test_seq_type: .: (0.000366) test_symbol_comparison_table: .: (0.000372) test_validate_checksum: .: (0.002924) Bio::TestGFF: test_record_class: .: (0.000689) test_records: .: (0.000675) Bio::TestGFF2: test_const_version: .: (0.001163) test_gff_version: .: (0.000671) test_metadata: .: (0.000602) test_metadata_size: .: (0.000832) test_records_size: .: (0.000829) test_to_s: .: (0.001447) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000397) test_attributes_case2: .: (0.000244) test_attributes_incompatible_backslash_semicolon: .: (0.000301) Bio::TestGFF2MetaData: test_data: .: (0.000244) test_directive: .: (0.000357) test_parse: .: (0.000144) Bio::TestGFF2Record: test_attribute: .: (0.000680) test_attribute_nonexistent: .: (0.000476) test_attributes: .: (0.000380) test_attributes_to_hash: .: (0.000424) test_comment_only?: .: (0.000383) test_delete_attribute: .: (0.006090) test_delete_attribute_multiple: .: (0.000556) test_delete_attribute_multiple2: .: (0.000526) test_delete_attribute_multiple_nil: .: (0.000422) test_delete_attribute_nil: .: (0.000413) test_delete_attribute_nonexistent: .: (0.000690) test_delete_attributes: .: (0.000402) test_delete_attributes_multiple: .: (0.000465) test_delete_attributes_nonexistent: .: (0.000422) test_end: .: (0.000420) test_eqeq: .: (0.001586) test_eqeq_false: .: (0.000794) test_feature: .: (0.000329) test_frame: .: (0.000417) test_get_attribute: .: (0.000757) test_get_attribute_nonexistent: .: (0.000338) test_get_attributes: .: (0.000569) test_get_attributes_nonexistent: .: (0.000642) test_replace_attributes: .: (0.000452) test_replace_attributes_multiple_multiple_over: .: (0.000467) test_replace_attributes_multiple_multiple_same: .: (0.000658) test_replace_attributes_multiple_multiple_two: .: (0.000372) test_replace_attributes_multiple_single: .: (0.000372) test_replace_attributes_nonexistent: .: (0.000370) test_replace_attributes_nonexistent_multiple: .: (0.000560) test_replace_attributes_single_multiple: .: (0.000693) test_score: .: (0.000361) test_self_parse: .: (0.000981) test_seqname: .: (0.000376) test_set_attribute: .: (0.001016) test_set_attribute_multiple: .: (0.000481) test_set_attribute_nonexistent: .: (0.000354) test_sort_attributes_by_tag!: .: (0.000488) test_sort_attributes_by_tag_bang_test2: .: (0.000476) test_sort_attributes_by_tag_bang_with_block: .: (0.000530) test_source: .: (0.000702) test_start: .: (0.000354) test_strand: .: (0.000584) test_to_s: .: (0.000613) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000330) test_comment_eq: .: (0.000137) test_comment_only?: .: (0.000134) test_comment_only_false: .: (0.000134) test_to_s: .: (0.000473) test_to_s_not_empty: .: (0.000245) Bio::TestGFF3: test_const_version: .: (0.001432) test_gff_version: .: (0.001311) test_records: .: (0.000940) test_sequence_regions: .: (0.001262) test_sequences: .: (0.000966) test_to_s: .: (0.002151) Bio::TestGFF3MetaData: test_data: .: (0.000317) test_directive: .: (0.000112) test_parse: .: (0.000137) Bio::TestGFF3Record: test_attributes: .: (0.000535) test_end: .: (0.000605) test_feature: .: (0.000342) test_frame: .: (0.000332) test_id: .: (0.000349) test_score: .: (0.000431) test_seqname: .: (0.000422) test_source: .: (0.000586) test_start: .: (0.000313) test_strand: .: (0.000312) test_to_s: .: (0.000605) test_to_s_attr_order_changed: .: (0.001012) Bio::TestGFF3RecordEscape: test_escape: .: (0.000464) test_escape_attribute: .: (0.000224) test_escape_seqid: .: (0.000230) test_unescape: .: (0.000196) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000504) test_eqeq: .: (0.000312) test_new_from_sequences_na: .: (0.000582) test_new_from_sequences_na_aa: .: (0.000484) test_new_from_sequences_na_aa_boundary_gap: .: (0.000686) test_new_from_sequences_na_aa_example: .: (0.000592) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000590) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000435) test_process_sequences_na: .: (0.000874) test_process_sequences_na_aa: .: (0.000646) test_process_sequences_na_aa_reverse_frameshift: .: (0.000355) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000353) test_process_sequences_na_aa_tooshort: .: (0.000455) test_process_sequences_na_tooshort: .: (0.000362) test_to_s: .: (0.000320) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000819) test_attributes_one: .: (0.000176) test_attributes_with_escaping: .: (0.000518) test_id_multiple: .: (0.000446) test_id_multiple2: .: (0.000332) test_id_replace: .: (0.000208) test_id_set: .: (0.000257) test_initialize_9: .: (0.000126) test_phase: .: (0.000232) test_score: .: (0.000515) test_to_s_void: .: (0.000163) Bio::TestGFF3RecordTarget: test_end: .: (0.000365) test_parse: .: (0.000676) test_start: .: (0.000174) test_strand: .: (0.000167) test_target_id: .: (0.000174) test_to_s: .: (0.000312) Bio::TestGFF3SequenceRegion: test_end: .: (0.000360) test_parse: .: (0.000299) test_seqid: .: (0.000465) test_start: .: (0.000145) test_to_s: .: (0.000237) Bio::TestGFFRecord: test_attributes: .: (0.000574) test_comment: .: (0.000170) test_end: .: (0.000169) test_feature: .: (0.000165) test_frame: .: (0.000162) test_score: .: (0.000167) test_seqname: .: (0.000164) test_source: .: (0.000184) test_start: .: (0.000187) test_strand: .: (0.000191) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000708) Bio::TestGeneAssociation: test_aspect: .: (0.000351) test_assigned_by: .: (0.000500) test_date: .: (0.000182) test_db: .: (0.000141) test_db_object_id: .: (0.000141) test_db_object_name: .: (0.000153) test_db_object_symbol: .: (0.000153) test_db_object_synonym: .: (0.000153) test_db_object_type: .: (0.000151) test_db_reference: .: (0.000230) test_evidence: .: (0.000153) test_goid: .: (0.000476) test_parser: .: (0.000803) test_qualifier: .: (0.000224) test_taxon: .: (0.000490) test_to_str: .: (0.000205) test_with: .: (0.000185) Bio::TestGenscanReport: test_date_run: .: (0.001922) test_gccontent: .: (0.001320) test_genscan_version: .: (0.000982) test_isochore: .: (0.001481) test_length: .: (0.001389) test_matrix: .: (0.001544) test_predictions_size: .: (0.000989) test_query_name: .: (0.001827) test_time: .: (0.001079) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.001126) test_donor_score: .: (0.001569) test_exon_type: .: (0.001196) test_exon_type_long: .: (0.001259) test_first: .: (0.001217) test_initiation_score: .: (0.005884) test_last: .: (0.015705) test_number: .: (0.007781) test_p_value: .: (0.005333) test_phase: .: (0.020076) test_range: .: (0.006387) test_score: .: (0.028060) test_strand: .: (0.032499) test_t_score: .: (0.001600) test_termination_score: .: (0.001110) Bio::TestGenscanReportGene: test_aaseq: .: (0.002215) test_naseq: .: (0.001263) test_number: .: (0.001345) test_polyA: .: (0.001380) test_promoter: .: (0.001561) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.002920) test_reports_ary_contents: .: (0.001069) Bio::TestHMMERReportConstants: test_rs: .: (0.000371) Bio::TestHMMERReportHit: test_accession: .: (0.001675) test_append_hsp: .: (0.000996) test_bit_score: .: (0.000943) test_definition: .: (0.001596) test_description: .: (0.001132) test_each: .: (0.001155) test_each_hsp: .: (0.001260) test_entry_id: .: (0.001126) test_evalue: .: (0.001017) test_hit: .: (0.001392) test_hit_id: .: (0.001225) test_hsps: .: (0.000972) test_num: .: (0.001297) test_score: .: (0.001091) test_target_def: .: (0.001306) test_target_id: .: (0.001393) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.001288) test_each: .: (0.001346) test_each_hit: .: (0.001439) test_histogram: .: (0.000965) test_hits: .: (0.001014) test_hsps: .: (0.001857) test_parameter: .: (0.001120) test_program: .: (0.001032) test_query_info: .: (0.001672) test_statistical_detail: .: (0.001124) test_total_seq_searched: .: (0.000981) test_whole_seq_top_hits: .: (0.001231) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.001962) test_histogram: .: (0.001630) test_statistical_detail: .: (0.001233) test_total_seq_searched: .: (0.001356) test_whole_seq_top_hit: .: (0.001690) Bio::TestHMMERReportHsp: test_accession: .: (0.001237) test_bit_score: .: (0.001600) test_csline: .: (0.001106) test_domain: .: (0.001073) test_evalue: .: (0.001048) test_flatseq: .: (0.001479) test_hmm_f: .: (0.000982) test_hmm_t: .: (0.001053) test_hmmseq: .: (0.001334) test_hsp: .: (0.001469) test_midline: .: (0.000936) test_query_frame: .: (0.001383) test_query_from: .: (0.001486) test_query_seq: .: (0.001035) test_query_to: .: (0.001259) test_rfline: .: (0.001106) test_score: .: (0.001586) test_seq_f: .: (0.001390) test_seq_ft: .: (0.000968) test_seq_t: .: (0.001056) test_set_alignment: .: (0.001587) test_targat_to: .: (0.000992) test_target_frame: .: (0.000863) test_target_from: .: (0.000880) test_target_seq: .: (0.001545) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000825) test_find_hetatm: .: (0.000317) test_hetatms: .: (0.000415) Bio::TestHeterogen: test_addAtom: .: (0.000938) test_each: .: (0.000299) test_each_hetatm: .: (0.000299) test_get_residue_id_from_atom: .: (0.000282) test_het_atom: .: (0.000246) test_iCode: .: (0.000263) test_inspect: .: (0.000289) test_resSeq: .: (0.000254) test_sort: .: (0.000633) test_square_bracket: .: (0.000264) test_to_s: .: (0.000738) test_update_resudue_id: .: (0.000233) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000384) test_find_heterogen: .: (0.000172) test_heterogens: .: (0.000194) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000446) test_match_description: .: (0.000248) test_match_evalue: .: (0.000580) test_match_ipr_description: .: (0.000573) test_match_ipr_id: .: (0.000235) test_match_match_end: .: (0.000224) test_match_match_start: .: (0.000215) test_match_method: .: (0.000198) test_matches_size: .: (0.000192) test_query_id: .: (0.000197) test_query_length: .: (0.000195) Bio::TestIprscanRawReport: test_entry_id: .: (0.004458) test_match_accession: .: (0.004201) test_match_crc64: .: (0.004226) test_match_date: .: (0.007705) test_match_description: .: (0.004617) test_match_evalue: .: (0.004143) test_match_go_terms: .: (0.004281) test_match_ipr_description: .: (0.004261) test_match_ipr_id: .: (0.004003) test_match_match_end: .: (0.004400) test_match_match_start: .: (0.004228) test_match_method: .: (0.003829) test_match_query_id: .: (0.003926) test_match_query_length: .: (0.003671) test_match_status: .: (0.003716) test_obj: .: (0.003609) test_query_id: .: (0.005826) test_query_length: .: (0.004173) test_self_reports_in_raw: .: (0.007377) Bio::TestIprscanReport: test_output_raw: .: (0.001286) test_to_raw: .: (0.000729) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000896) test_match_accession: .: (0.001125) test_match_date: .: (0.001168) test_match_description: .: (0.000709) test_match_evalue: .: (0.000674) test_match_go_terms: .: (0.000936) test_match_ipr_description: .: (0.001193) test_match_ipr_id: .: (0.000764) test_match_match_end: .: (0.000737) test_match_match_start: .: (0.000861) test_match_method: .: (0.000673) test_match_status: .: (0.000717) test_matches_size: .: (0.000760) test_query_id: .: (0.001010) test_query_length: .: (0.000728) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.001316) test_to_hash_match?: .: (0.001443) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.002413) Bio::TestKeggCompound: test_comment: .: (0.000666) test_dblinks_as_hash: .: (0.000726) test_dblinks_as_strings: .: (0.000457) test_entry_id: .: (0.000740) test_enzymes: .: (0.000884) test_formula: .: (0.000386) test_kcf: .: (0.000329) test_mass: .: (0.000579) test_name: .: (0.000422) test_names: .: (0.000514) test_pathways_as_hash: .: (0.000775) test_pathways_as_strings: .: (0.000478) test_reactions: .: (0.001343) test_remark: .: (0.000441) test_rpairs: .: (0.000404) Bio::TestKeggEnzyme: test_all_reac: .: (0.001031) test_classes: .: (0.000621) test_cofactors: .: (0.000693) test_comment: .: (0.001336) test_dblinks_as_hash: .: (0.000871) test_dblinks_as_strings: .: (0.000750) test_diseases: .: (0.000619) test_entry: .: (0.000667) test_entry_id: .: (0.001019) test_genes: .: (0.027279) test_genes_as_hash: .: (0.023927) test_genes_as_strings: .: (0.009303) test_inhibitors: .: (0.000827) test_iubmb_reactions: .: (0.000674) test_kegg_reactions: .: (0.001610) test_motifs: .: (0.000688) test_name: .: (0.000891) test_names: .: (0.000853) test_obsolete?: .: (0.001184) test_orthologs_as_hash: .: (0.000695) test_orthologs_as_strings: .: (0.000583) test_pathways_as_hash: .: (0.001281) test_pathways_as_strings: .: (0.001120) test_products: .: (0.000793) test_reaction: .: (0.000622) test_structures: .: (0.000939) test_substrates: .: (0.001391) test_sysname: .: (0.000775) Bio::TestKeggGenesDblinks: test_data: .: (0.000550) test_dblinks_0: .: (0.000216) test_dblinks_1: .: (0.000201) test_dblinks_2: .: (0.000175) Bio::TestKeggGenesStructure: test_data: .: (0.000334) test_ids: .: (0.000238) test_ids_in_array: .: (0.000493) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.020874) test_graphics__size: .: (0.016525) test_id: .: (0.016631) test_link: .: (0.016034) test_name: .: (0.091109) test_reaction: .: (0.018467) test_type: .: (0.031939) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.032103) test_graphics__size: .: (0.027342) test_id: .: (0.032316) test_link: .: (0.031905) test_name: .: (0.032186) test_reaction: .: (0.033259) test_type: .: (0.036824) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.032939) test_category: .: (0.032366) test_entry_id: .: (0.031172) test_fgcolor=: .: (0.031341) test_height=: .: (0.032101) test_label=: .: (0.033555) test_shape=: .: (0.031474) test_width=: .: (0.031843) test_x=: .: (0.031292) test_y=: .: (0.031947) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.031433) test_graphics__size: .: (0.031132) test_id: .: (0.038003) test_link: .: (0.032776) test_name: .: (0.036569) test_reaction: .: (0.035598) test_type: .: (0.027465) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000492) test_graphics=: .: (0.000173) test_id=: .: (0.000190) test_link=: .: (0.000206) test_name=: .: (0.000222) test_reaction=: .: (0.000195) test_type=: .: (0.000200) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000470) test_category=: .: (0.000594) test_entry_id=: .: (0.004536) test_fgcolor=: .: (0.000318) test_height=: .: (0.000262) test_label=: .: (0.000287) test_pathway=: .: (0.000196) test_shape=: .: (0.000240) test_width=: .: (0.000226) test_x=: .: (0.000225) test_y=: .: (0.000222) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.032465) test_coords: .: (0.036432) test_fgcolor: .: (0.033982) test_height: .: (0.032488) test_name: .: (0.031551) test_type: .: (0.031672) test_width: .: (0.032532) test_x: .: (0.032096) test_y: .: (0.032241) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.037945) test_coords: .: (0.031185) test_fgcolor: .: (0.031733) test_height: .: (0.030893) test_name: .: (0.029846) test_type: .: (0.029988) test_width: .: (0.027149) test_x: .: (0.037810) test_y: .: (0.032737) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000467) test_coords=: .: (0.000187) test_fgcolor=: .: (0.000178) test_height=: .: (0.000183) test_name=: .: (0.000160) test_type=: .: (0.000166) test_width=: .: (0.000161) test_x=: .: (0.000160) test_y=: .: (0.000163) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.035769) test_entries__size: .: (0.026614) test_image: .: (0.030226) test_link: .: (0.030616) test_name: .: (0.031451) test_number: .: (0.030515) test_org: .: (0.035423) test_reactions=: .: (0.027014) test_reactions__size: .: (0.031270) test_relations=: .: (0.030458) test_relations__size: .: (0.032603) test_title: .: (0.027409) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.061420) test_name: .: (0.060818) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000420) test_initialize_0: .: (0.000142) test_initialize_1: .: (0.000156) test_initialize_2: .: (0.000332) test_name=: .: (0.000222) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.027655) test_name: .: (0.030812) test_products: .: (0.030218) test_substrates: .: (0.023437) test_type: .: (0.018563) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000473) test_name=: .: (0.000245) test_products=: .: (0.000225) test_substraces=: .: (0.000218) test_type=: .: (0.000227) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000727) test_entry_id=: .: (0.000233) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.023493) test_entry2: .: (0.018462) test_name: .: (0.015007) test_type: .: (0.014921) test_value: .: (0.014733) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000333) test_node1=: .: (0.000750) test_node2=: .: (0.000233) test_rel=: .: (0.000236) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000341) test_entry2=: .: (0.000254) test_name=: .: (0.000181) test_type=: .: (0.000228) test_value=: .: (0.000219) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.031252) test_name: .: (0.028258) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000448) test_initialize_0: .: (0.000151) test_initialize_1: .: (0.000150) test_initialize_2: .: (0.000688) test_name=: .: (0.000222) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000380) test_initialize_0: .: (0.000127) test_initialize_1: .: (0.000138) test_initialize_2: .: (0.000139) test_name=: .: (0.000194) Bio::TestKeggModule: test_compounds: .: (0.000659) test_compounds_as_hash: .: (0.000411) test_compounds_as_strings: .: (0.000658) test_definition: .: (0.000451) test_entry_id: .: (0.000313) test_keggclass: .: (0.000308) test_name: .: (0.000299) test_new: .: (0.000319) test_orthologs: .: (0.000461) test_orthologs_as_array: .: (0.000422) test_orthologs_as_hash: .: (0.000933) test_orthologs_as_strings: .: (0.000377) test_pathways: .: (0.000268) test_pathways_as_hash: .: (0.000270) test_pathways_as_strings: .: (0.000606) test_reactions: .: (0.000449) test_reactions_as_hash: .: (0.000440) test_reactions_as_strings: .: (0.000379) Bio::TestKeggOrthology: test_dblinks: .: (0.001254) test_dblinks_as_hash: .: (0.000561) test_dblinks_as_strings: .: (0.000504) test_definition: .: (0.000560) test_entry_id: .: (0.000577) test_genes_as_hash: .: (0.022193) test_genes_as_strings: .: (0.007203) test_keggclass: .: (0.000846) test_keggclasses: .: (0.000713) test_modules: .: (0.000543) test_modules_as_hash: .: (0.000979) test_modules_as_strings: .: (0.000578) test_name: .: (0.000589) test_names: .: (0.000752) test_pathways_as_strings: .: (0.000855) test_pathways_in_keggclass: .: (0.000800) test_references: .: (0.000880) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000596) test_compounds_as_strings: .: (0.000325) test_dblinks_as_hash: .: (0.000319) test_dblinks_as_strings: .: (0.000466) test_description: .: (0.000655) test_diseases_as_hash: .: (0.000288) test_diseases_as_strings: .: (0.000293) test_entry_id: .: (0.000328) test_enzymes_as_strings: .: (0.000374) test_genes_as_hash: .: (0.000304) test_genes_as_strings: .: (0.000314) test_keggclass: .: (0.000382) test_ko_pathway: .: (0.000353) test_modules_as_hash: .: (0.001051) test_modules_as_strings: .: (0.000304) test_name: .: (0.000306) test_organism: .: (0.000301) test_orthologs_as_hash: .: (0.000274) test_orthologs_as_strings: .: (0.000268) test_pathways_as_hash: .: (0.000286) test_pathways_as_strings: .: (0.000275) test_reactions_as_hash: .: (0.000262) test_reactions_as_strings: .: (0.000891) test_references: .: (0.000469) test_rel_pathways_as_hash: .: (0.000403) test_rel_pathways_as_strings: .: (0.000339) Bio::TestKeggReaction: test_definition: .: (0.000599) test_entry_id: .: (0.000329) test_enzymes: .: (0.000330) test_equation: .: (0.000318) test_name: .: (0.000992) test_orthologs_as_hash: .: (0.000499) test_orthologs_as_strings: .: (0.000371) test_pathways_as_hash: .: (0.000405) test_pathways_as_strings: .: (0.000345) test_rpairs_as_hash: .: (0.000436) test_rpairs_as_strings: .: (0.000352) test_rpairs_as_tokens: .: (0.000637) Bio::TestLasergene: test_methods: .: (0.011588) Bio::TestLocations: test_complement: .: (0.000489) test_hat: .: (0.000231) test_normal: .: (0.000219) test_replace_single_base: .: (0.000189) test_should_not_modify_argument: .: (0.000181) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.006535) test_locations_to_s: .: (0.002639) Bio::TestMEDLINE: test_authors: .: (0.001589) test_authors_with_last_name_all_caps: .: (0.000275) test_authors_with_suffix: .: (0.000176) Bio::TestMEDLINE_20146148: test_ab: .: (0.000808) test_ad: .: (0.000522) test_au: .: (0.000750) test_authors: .: (0.000993) test_doi: .: (0.000646) test_dp: .: (0.000570) test_ip: .: (0.000583) test_mh: .: (0.001365) test_pages: .: (0.000552) test_pg: .: (0.000536) test_pii: .: (0.000589) test_pmid: .: (0.001312) test_pt: .: (0.000667) test_reference: .: (0.000860) test_self_new: .: (0.000564) test_so: .: (0.000663) test_ta: .: (0.000843) test_ti: .: (0.000631) test_ui: .: (0.000585) test_vi: .: (0.000793) test_year: .: (0.000578) Bio::TestMapSimple: test_attributes: .: (0.000678) Bio::TestMapping: test_add_mapping_as_map: .: (0.000527) test_add_mapping_as_marker: .: (0.000262) test_contains_marker?: .: (0.000206) test_mapped_to?: .: (0.000261) test_mapping_location_comparison: .: (0.000571) test_mappings_as_map_each: .: (0.000188) test_mappings_as_marker_each: .: (0.000250) test_mappings_on: .: (0.000228) test_multiple_mappings_between_same_marker_and_map: .: (0.000811) test_positions_on: .: (0.000273) test_raise_error_kind_of: .: (0.000530) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000925) test_check_options_with_invalid_opts: .: (0.000297) test_check_options_with_valid_opts: .: (0.000264) test_command_to_be_run: .: (0.000298) test_config_defaults: .: (0.000233) test_minimal_config: .: (0.000273) test_more_config: .: (0.000206) test_run: .: (0.000144) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000698) test_report_has_motifs: .: (0.000341) Bio::TestModel: test_addChain: .: (0.000692) test_comp: .: (0.000184) test_each: .: (0.000177) test_each_chain: .: (0.000166) test_inspect: .: (0.000179) test_rehash: .: (0.000157) test_square_brace: .: (0.000167) test_to_s: .: (0.000172) Bio::TestModelFinder: test_find_model: .: (0.000394) Bio::TestMotif: test_creation_and_attributes: .: (0.000401) test_length: .: (0.000134) Bio::TestMyGraph: test_cliquishness: .: (0.001021) Bio::TestNA: test_accessor: .: (0.000295) test_na: .: (0.000153) test_name: .: (0.000141) test_names: .: (0.000137) test_to_re: .: (0.000369) test_weight: .: (0.000178) test_weight_rna: .: (0.000168) Bio::TestNAConstants: test_NAMES: .: (0.000295) test_NAMES_1_to_name: .: (0.000138) test_WEIGHT: .: (0.000160) Bio::TestNATranslate: test_translate: .: (0.000783) test_translate_1: .: (0.000229) test_translate_2: .: (0.000144) test_translate_3: .: (0.000144) test_translate_4: .: (0.000219) test_translate_5: .: (0.000148) test_translate_6: .: (0.000143) Bio::TestNCBIDB: test_fetch: .: (0.000462) test_p_entry2hash: .: (0.000128) test_p_subtag2array: .: (0.000121) test_p_toptag2array: .: (0.000126) Bio::TestNewick: test_reparse: .: (0.007909) test_reparse_before_lazy_parsing: .: (0.000665) test_string_tree: .: (0.001854) Bio::TestNewick2: test_string_tree: .: (0.001906) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000654) test_parse_newick_leaf: .: (0.000305) test_parse_newick_tokenize: .: (0.000537) Bio::TestNexus: test_nexus: .: (0.021789) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000772) test_uncapitalized_letter_Q32725_9POAL: .: (0.000214) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000353) test_load_parameters: .: (0.000193) test_parameters: .: (0.000145) test_set_default_parameters: .: (0.000248) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.001567) test_expected_parameters_set_in_control_file: .: (0.001354) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000408) test_new_with_parameters: .: (0.000205) test_new_with_two_argument: .: (0.000202) test_new_without_argument: .: (0.000180) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.003036) test_rates_hundred_and_fiftieth_position: .: (0.002809) test_rates_last_position: .: (0.002081) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.012218) test_tree: .: (0.011940) test_tree_length: .: (0.012113) test_tree_log_likelihood: .: (0.012489) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.001062) test_parameters_should_be_loaded_from_control: .: (0.000393) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.001619) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000430) test_dN_dS: .: (0.000244) test_kappa: .: (0.000247) test_lnL: .: (0.000339) test_m3_classes: .: (0.000376) test_m3_lnL: .: (0.000237) test_m3_to_s: .: (0.000263) test_m3_tree: .: (0.001249) test_omega: .: (0.000218) test_to_s: .: (0.000172) test_tree: .: (0.000641) test_tree_length: .: (0.000170) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000717) test_p: .: (0.000799) test_position: .: (0.000773) test_probability: .: (0.000562) test_w: .: (0.001038) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000781) test_graph_omega: .: (0.000612) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.001126) test_footer: .: (0.000217) test_header: .: (0.000204) test_initialize: .: (0.000306) test_models: .: (0.000255) test_nb_sites: .: (0.000878) test_num_codons: .: (0.000213) test_num_sequences: .: (0.000808) test_significant: .: (0.000306) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000425) test_nb_sites: .: (0.000358) test_significant: .: (0.000251) test_sites: .: (0.002574) Bio::TestPDB: test_accession: .: (0.002174) test_addModel: .: (0.001712) test_authors: .: (0.001199) test_bracket: .: (0.001379) test_classification: .: (0.001490) test_dbref: .: (0.001673) test_definition: .: (0.001530) test_each: .: (0.001756) test_each_model: .: (0.001336) test_entry_id: .: (0.001670) test_helix: .: (0.016485) test_inspect: .: (0.018510) test_jrnl: .: (0.017053) test_keywords: .: (0.015352) test_record: .: (0.021156) test_remark: .: (0.002098) test_seqres: .: (0.002144) test_sheet: .: (0.002030) test_ssbond: .: (0.001985) test_to_s: .: (0.002047) test_turn: .: (0.001751) test_version: .: (0.001641) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000488) test_U12: .: (0.000551) test_U13: .: (0.000197) test_U22: .: (0.000193) test_U23: .: (0.000194) test_U33: .: (0.000192) test_altLoc: .: (0.000195) test_chainID: .: (0.000194) test_charge: .: (0.000539) test_element: .: (0.000208) test_iCode: .: (0.000199) test_name: .: (0.000236) test_resName: .: (0.000233) test_resSeq: .: (0.000228) test_segID: .: (0.000231) test_serial: .: (0.000632) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000391) test_anisou: .: (0.000144) test_chainID: .: (0.000120) test_charge: .: (0.000124) test_comparable: .: (0.000475) test_do_parse: .: (0.000155) test_element: .: (0.000151) test_iCode: .: (0.000143) test_name: .: (0.000143) test_occupancy: .: (0.000245) test_original_data: .: (0.000159) test_record_name: .: (0.000148) test_resName: .: (0.000148) test_resSeq: .: (0.000432) test_residue: .: (0.000168) test_segID: .: (0.000168) test_serial: .: (0.000162) test_sigatm: .: (0.000163) test_tempFactor: .: (0.000233) test_ter: .: (0.000430) test_to_a: .: (0.000183) test_to_s: .: (0.000237) test_x: .: (0.000194) test_xyz: .: (0.000189) test_y: .: (0.000189) test_z: .: (0.000192) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000700) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000307) test_idcode: .: (0.000145) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000650) test_chainID2: .: (0.000213) test_icode1: .: (0.000207) test_icode2: .: (0.000199) test_measure: .: (0.000211) test_modNum: .: (0.000208) test_pep1: .: (0.000215) test_pep2: .: (0.000221) test_seqNum1: .: (0.000201) test_seqNum2: .: (0.000194) test_serNum: .: (0.000188) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000690) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000320) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000330) test_alpha: .: (0.000191) test_b: .: (0.000171) test_beta: .: (0.000163) test_c: .: (0.000176) test_gamma: .: (0.000178) test_sGroup: .: (0.000191) test_z: .: (0.000183) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000451) test_database: .: (0.000959) test_dbAccession: .: (0.000246) test_dbIdCode: .: (0.000218) test_dbseqBegin: .: (0.000212) test_dbseqEnd: .: (0.000211) test_idCode: .: (0.000215) test_idbnsBeg: .: (0.000223) test_insertBegin: .: (0.000217) test_insertEnd: .: (0.000222) test_seqBegin: .: (0.000224) test_seqEnd: .: (0.000260) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000691) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000734) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000331) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000276) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000311) test_depDate: .: (0.000156) test_idCode: .: (0.000155) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000338) test_hetID: .: (0.000171) test_iCode: .: (0.000423) test_numHetAtoms: .: (0.000176) test_seqNum: .: (0.000168) test_text: .: (0.000447) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000374) test_anisou: .: (0.000156) test_chainID: .: (0.000158) test_charge: .: (0.000161) test_comparable: .: (0.000206) test_do_parse: .: (0.000160) test_element: .: (0.000154) test_iCode: .: (0.000138) test_name: .: (0.000155) test_occupancy: .: (0.000223) test_original_data: .: (0.000150) test_record_name: .: (0.000142) test_resName: .: (0.000145) test_resSeq: .: (0.000427) test_residue: .: (0.000148) test_segID: .: (0.000141) test_serial: .: (0.000140) test_sigatm: .: (0.000137) test_tempFactor: .: (0.000200) test_ter: .: (0.000168) test_to_a: .: (0.000176) test_to_s: .: (0.000230) test_x: .: (0.000206) test_xyz: .: (0.000474) test_y: .: (0.000222) test_z: .: (0.000215) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000468) test_ChainH: .: (0.000521) test_ICode1: .: (0.000220) test_altLoc1: .: (0.000230) test_altLoc2: .: (0.000230) test_altLocH: .: (0.000216) test_chainID2: .: (0.000230) test_iCode2: .: (0.000586) test_iCodeH: .: (0.000266) test_name1: .: (0.000280) test_name2: .: (0.000272) test_nameH: .: (0.000275) test_resName1: .: (0.000561) test_resName2: .: (0.000292) test_resSeq1: .: (0.000265) test_resSeq2: .: (0.000278) test_resSeqH: .: (0.000232) test_sym1: .: (0.000245) test_sym2: .: (0.000506) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000354) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000342) test_altLoc2: .: (0.000193) test_chainID1: .: (0.000196) test_chainID2: .: (0.000544) test_iCode1: .: (0.000218) test_iCode2: .: (0.000199) test_name1: .: (0.000206) test_name2: .: (0.000189) test_resName1: .: (0.000197) test_resName2: .: (0.000529) test_resSeq1: .: (0.000215) test_resSeq2: .: (0.000192) test_sym1: .: (0.000192) test_sym2: .: (0.000200) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000456) test_numCoord: .: (0.000468) test_numHelix: .: (0.000162) test_numHet: .: (0.000153) test_numRemark: .: (0.000150) test_numSeq: .: (0.000156) test_numSheet: .: (0.000174) test_numSite: .: (0.000173) test_numTer: .: (0.000207) test_numTurn: .: (0.000181) test_numXform: .: (0.000184) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000376) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000396) test_comment: .: (0.000186) test_iCode: .: (0.000181) test_idCode: .: (0.000181) test_resName: .: (0.000458) test_seqNum: .: (0.000187) test_stdRes: .: (0.000181) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000377) test_Mn2: .: (0.000151) test_Mn3: .: (0.000180) test_Vn: .: (0.000178) test_iGiven: .: (0.000175) test_serial: .: (0.000173) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000360) test_Mn2: .: (0.000177) test_Mn3: .: (0.000171) test_Vn: .: (0.000164) test_iGiven: .: (0.000167) test_serial: .: (0.000172) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.001158) test_Mn2: .: (0.000154) test_Mn3: .: (0.000147) test_Vn: .: (0.000151) test_iGiven: .: (0.000144) test_serial: .: (0.000145) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000334) test_rIdCode: .: (0.000185) test_repDate: .: (0.000180) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000356) test_On2: .: (0.000164) test_On3: .: (0.000460) test_Tn: .: (0.000172) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000699) test_modId: .: (0.000173) test_modNum: .: (0.000161) test_modType: .: (0.000163) test_record: .: (0.000168) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000299) test_text: .: (0.000149) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000308) test_Sn2: .: (0.000147) test_Sn3: .: (0.000149) test_Un: .: (0.000179) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000357) test_Sn2: .: (0.000170) test_Sn3: .: (0.000164) test_Un: .: (0.000291) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000354) test_Sn2: .: (0.000144) test_Sn3: .: (0.000137) test_Un: .: (0.000141) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000361) test_conflict: .: (0.000466) test_database: .: (0.000206) test_dbIdCode: .: (0.000191) test_dbRes: .: (0.000190) test_dbSeq: .: (0.000184) test_iCode: .: (0.000192) test_idCode: .: (0.000192) test_resName: .: (0.000468) test_seqNum: .: (0.000211) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000413) test_numRes: .: (0.000212) test_resName: .: (0.000224) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000454) test_curChainId: .: (0.000245) test_curICode: .: (0.000243) test_curResName: .: (0.000248) test_curResSeq: .: (0.000486) test_endChainID: .: (0.000251) test_endICode: .: (0.000241) test_endResName: .: (0.000248) test_endSeqNum: .: (0.000259) test_initChainID: .: (0.000276) test_initICode: .: (0.000640) test_initResName: .: (0.000279) test_initSeqNum: .: (0.000274) test_numStrands: .: (0.000279) test_prevAtom: .: (0.000535) test_prevChainId: .: (0.000245) test_prevICode: .: (0.000244) test_prevResName: .: (0.000244) test_prevResSeq: .: (0.000245) test_sense: .: (0.000243) test_sheetID: .: (0.000233) test_strand: .: (0.000554) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000501) test_chainID: .: (0.000232) test_charge: .: (0.000535) test_element: .: (0.000232) test_iCode: .: (0.000228) test_name: .: (0.000223) test_resName: .: (0.000226) test_resSeq: .: (0.000231) test_segID: .: (0.000202) test_serial: .: (0.000489) test_sigOcc: .: (0.000188) test_sigTemp: .: (0.000199) test_sigX: .: (0.000196) test_sigY: .: (0.000210) test_sigZ: .: (0.000196) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000809) test_SigmaU12: .: (0.000215) test_SigmaU13: .: (0.000223) test_SigmaU22: .: (0.000219) test_SigmaU23: .: (0.000222) test_SigmaU33: .: (0.000594) test_altLoc: .: (0.000241) test_chainID: .: (0.000230) test_charge: .: (0.000233) test_element: .: (0.000208) test_iCode: .: (0.000207) test_name: .: (0.000210) test_resName: .: (0.000200) test_resSeq: .: (0.000529) test_segID: .: (0.000201) test_serial: .: (0.000200) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000823) test_chainID2: .: (0.000262) test_chainID3: .: (0.000258) test_chainID4: .: (0.000264) test_iCode1: .: (0.000255) test_iCode2: .: (0.000254) test_iCode3: .: (0.000256) test_iCode4: .: (0.000247) test_numRes: .: (0.000228) test_resName1: .: (0.000351) test_resName2: .: (0.000565) test_resName3: .: (0.000237) test_resName4: .: (0.000208) test_seq1: .: (0.000203) test_seq2: .: (0.000208) test_seq3: .: (0.000222) test_seq4: .: (0.007120) test_seqNum: .: (0.000271) test_siteID: .: (0.000245) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000514) test_altLoc2: .: (0.000166) test_atom1: .: (0.000175) test_atom2: .: (0.000176) test_chainID1: .: (0.000181) test_chainID2: .: (0.000179) test_iCode1: .: (0.000188) test_iCode2: .: (0.000185) test_resName1: .: (0.000473) test_resName2: .: (0.000214) test_resSeq1: .: (0.000578) test_resSeq2: .: (0.000204) test_sym1: .: (0.000217) test_sym2: .: (0.000204) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000413) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000367) test_sIdCode: .: (0.000182) test_sprsdeDate: .: (0.000166) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000642) test_iCode: .: (0.000154) test_resName: .: (0.000153) test_resSeq: .: (0.000165) test_serial: .: (0.000161) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000317) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000338) test_t1: .: (0.000189) test_t2: .: (0.000181) test_t3: .: (0.000182) test_text: .: (0.000185) Bio::TestPROSITE: test_ac: .: (0.002919) test_cc: .: (0.003001) test_de: .: (0.002861) test_division: .: (0.003104) test_dr: .: (0.024383) test_dt: .: (0.003209) test_false_neg: .: (0.002430) test_false_pos: .: (0.003024) test_false_positive_sequences: .: (0.002882) test_list_falsenegative: .: (0.103223) test_list_falsepositive: .: (0.026669) test_list_potentialhit: .: (0.026647) test_list_truepositive: .: (0.031453) test_list_unknown: .: (0.027581) test_list_xref: .: (0.027777) test_ma: .: (0.003014) test_max_repeat: .: (0.002420) test_name: .: (0.003126) test_nr: .: (0.003015) test_pa: .: (0.002993) test_pa2re: .: (0.002761) test_partial: .: (0.003173) test_pdb_xref: .: (0.003054) test_pdoc_xref: .: (0.003091) test_positive: .: (0.002917) test_positive_hits: .: (0.002942) test_positive_sequences: .: (0.003260) test_release: .: (0.002952) test_ru: .: (0.003150) test_self_pa2re: .: (0.002686) test_site: .: (0.003304) test_skip_flag: .: (0.003049) test_swissprot_release_number: .: (0.003234) test_swissprot_release_sequences: .: (0.003228) test_taxon_range: .: (0.002736) test_total: .: (0.003244) test_total_hits: .: (0.003085) test_total_sequences: .: (0.003281) test_unknown: .: (0.003043) test_unknown_hits: .: (0.002958) test_unknown_sequences: .: (0.003096) Bio::TestPROSITEConst: test_delimiter: .: (0.000440) test_tagsize: .: (0.000140) Bio::TestPTS1: test_function_set: .: (0.000654) test_function_set_number_1: .: (0.000167) test_function_set_number_2: .: (0.000208) test_function_set_number_3: .: (0.000145) test_function_show: .: (0.000140) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000337) Bio::TestPTS1New: test_fungi: .: (0.000281) test_general: .: (0.000192) test_metazoa: .: (0.000137) Bio::TestQualifier: test_qualifier: .: (0.000361) test_value: .: (0.000144) Bio::TestREBASE: test_methods: .: (0.002048) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001412) test_bit_score: .: (0.001331) test_evalue: .: (0.001022) test_gaps: .: (0.000998) test_hit_from: .: (0.000911) test_hit_to: .: (0.001279) test_hseq: .: (0.001057) test_identity: .: (0.001048) test_midline: .: (0.001380) test_percent_identity: .: (0.000938) test_positive: .: (0.000874) test_qseq: .: (0.001037) test_query_from: .: (0.001447) test_query_to: .: (0.000989) test_score: .: (0.000922) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.001091) test_hits_size: .: (0.002245) test_iterations_size: .: (0.002256) test_program: .: (0.000830) test_query_def: .: (0.002503) test_query_len: .: (0.001992) test_version: .: (0.001114) test_version_date: .: (0.000901) test_version_number: .: (0.000857) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.001615) test_definition: .: (0.001016) test_evalue: .: (0.000984) test_hsps_size: .: (0.000955) test_identity: .: (0.001489) test_lap_at: .: (0.001087) test_len: .: (0.001265) test_midline: .: (0.001256) test_overlap: .: (0.001112) test_query_end: .: (0.001040) test_query_seq: .: (0.001286) test_query_start: .: (0.001164) test_target_def: .: (0.007045) test_target_end: .: (0.001391) test_target_len: .: (0.000966) test_target_seq: .: (0.001570) test_target_start: .: (0.001193) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001245) test_get_entry: .: (0.000785) test_rewind: .: (0.000169) test_skip_leader: .: (0.000339) Bio::TestReference: test_abstract: .: (0.000361) test_affiliations: .: (0.000173) test_authors: .: (0.000169) test_format_bibitem: .: (0.000277) test_format_bibtex: .: (0.001111) test_format_bibtex_with_arguments: .: (0.000293) test_format_cell: .: (0.000160) test_format_current: .: (0.000152) test_format_endnote: .: (0.000219) test_format_general: .: (0.000207) test_format_genome_biol: .: (0.000187) test_format_genome_res: .: (0.000184) test_format_nar: .: (0.000188) test_format_nature: .: (0.000215) test_format_rd: .: (0.000784) test_format_science: .: (0.000647) test_format_trends: .: (0.000177) test_issue: .: (0.000154) test_journal: .: (0.000147) test_mesh: .: (0.000162) test_pages: .: (0.000143) test_pubmed: .: (0.000150) test_pubmed_url: .: (0.000158) test_url: .: (0.000129) test_volume: .: (0.000136) test_year: .: (0.000136) Bio::TestReference_noURL: test_format_endnote: .: (0.001321) test_url: .: (0.000154) Bio::TestReferences: test_append: .: (0.000405) test_each: .: (0.000176) Bio::TestRelation: test_comparison_operator: .: (0.000374) test_uniq: .: (0.000207) Bio::TestResidue: test_addAtom: .: (0.000543) test_each: .: (0.000304) test_each_atom: .: (0.001440) test_get_residue_id_from_atom: .: (0.000269) test_het_atom: .: (0.000219) test_iCode: .: (0.000234) test_inspect: .: (0.000497) test_resSeq: .: (0.000231) test_sort: .: (0.000320) test_square_bracket: .: (0.000292) test_to_s: .: (0.001599) test_update_resudue_id: .: (0.000257) Bio::TestResidueFinder: test_each_residue: .: (0.000381) test_find_residue: .: (0.000156) test_residues: .: (0.000184) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.224990) test_cut_from_bio_sequence_na: .: (0.063339) test_cut_without_permutations: .: (0.044975) test_view_ranges: .: (0.041227) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.002441) test_cuts_after_remove_incomplete_cuts: .: (0.001452) test_strands_for_display: .: (0.005408) test_strands_for_display_current: .: (0.001734) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000942) test_fragments_for_display_1: .: (0.001647) test_fragments_for_display_10: .: (0.002056) test_fragments_for_display_2: .: (0.001422) test_fragments_for_display_3: .: (0.002379) test_fragments_for_display_4: .: (0.002130) test_fragments_for_display_5: .: (0.001182) test_fragments_for_display_6: .: (0.001434) test_fragments_for_display_7: .: (0.001570) test_fragments_for_display_8: .: (0.001029) test_fragments_for_display_9: .: (0.004537) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000692) test_obj_3: .: (0.000465) test_obj_7: .: (0.000424) test_obj_z: .: (0.000470) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000999) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000515) test_bracket_eq: .: (0.000622) test_concat: .: (0.000208) test_delete: .: (0.000193) test_dup: .: (0.000274) test_each: .: (0.000281) test_eqeq: .: (0.000179) test_eqeq_false: .: (0.000161) test_eqeq_other: .: (0.000154) test_eqeq_self: .: (0.000169) test_include?: .: (0.000201) test_internal_data: .: (0.000185) test_internal_data_eq: .: (0.000206) test_length: .: (0.000169) test_ltlt: .: (0.000489) test_ltlt_larger: .: (0.000218) test_ltlt_middle: .: (0.000214) test_plus: .: (0.000219) test_plus_error: .: (0.000259) test_push: .: (0.000192) test_reverse_each: .: (0.000288) test_self_bracket: .: (0.000154) test_self_new: .: (0.000188) test_size: .: (0.000153) test_sort!: .: (0.000150) test_to_a: .: (0.000339) test_uniq!: .: (0.000169) test_unshift: .: (0.000251) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.008453) test_complement: .: (0.007887) test_complement_with_cut_symbols: .: (0.007746) test_cut_locations: .: (0.007426) test_cut_locations_in_enzyme_notation: .: (0.007411) test_primary: .: (0.007161) test_primary_with_cut_symbols: .: (0.007636) test_to_re: .: (0.007048) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.001679) test_align_with_cuts: .: (0.001784) test_argument_error: .: (0.001681) test_ds: .: (0.001851) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000829) test_complement: .: (0.000373) test_contents: .: (0.000350) test_primary: .: (0.000517) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000624) test_complement: .: (0.000312) test_contents: .: (0.000303) test_primary: .: (0.000306) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000436) test_contents: .: (0.000275) test_primary: .: (0.000263) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.001012) test_complement_to_array_index: .: (0.000436) test_complement_to_array_index_class: .: (0.000341) test_contents: .: (0.000269) test_primary: .: (0.000250) test_primary_to_array_index: .: (0.000378) test_primary_to_array_index_class: .: (0.000329) test_to_array_index: .: (0.000722) test_to_array_index_class: .: (0.001029) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000928) test_rebase: .: (0.000243) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.001786) test_creation_with_no_cuts: .: (0.001055) test_cut_locations: .: (0.000778) test_cut_locations_in_enzyme_notation: .: (0.000752) test_orientation: .: (0.001024) test_pattern: .: (0.000926) test_pattern_palindromic?: .: (0.000854) test_stripped: .: (0.000708) test_to_re: .: (0.001227) test_with_cut_symbols: .: (0.000827) test_with_spaces: .: (0.000867) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.001876) test_creation_with_no_cuts: .: (0.000847) test_cut_locations: .: (0.000762) test_cut_locations_in_enzyme_notation: .: (0.000764) test_orientation: .: (0.000573) test_pattern: .: (0.000893) test_pattern_palindromic?: .: (0.000810) test_stripped: .: (0.001004) test_to_re: .: (0.000652) test_with_cut_symbols: .: (0.001014) test_with_spaces: .: (0.001092) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000837) test_initialize_with_pattern: .: (0.000645) test_max: .: (0.000244) test_min: .: (0.000246) test_to_array_index: .: (0.000635) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000464) test_bracket_eq: .: (0.000210) test_concat: .: (0.000160) test_delete: .: (0.000156) test_dup: .: (0.000205) test_each: .: (0.000257) test_eqeq: .: (0.000152) test_eqeq_false: .: (0.000140) test_eqeq_other: .: (0.000126) test_eqeq_self: .: (0.000127) test_include?: .: (0.000146) test_internal_data_hash: .: (0.000134) test_internal_data_hash_eq: .: (0.000557) test_length: .: (0.000148) test_ltlt: .: (0.000176) test_ltlt_noeffect: .: (0.000172) test_plus: .: (0.000164) test_plus_error: .: (0.000234) test_private_push_element: .: (0.000168) test_private_push_element_intermediate: .: (0.000325) test_private_push_element_last: .: (0.000155) test_private_push_element_noeffect: .: (0.000139) test_private_sorted_keys: .: (0.000125) test_private_unshift_element: .: (0.000149) test_private_unshift_element_first: .: (0.000160) test_private_unshift_element_intermediate: .: (0.000158) test_private_unshift_element_noeffect: .: (0.000153) test_push: .: (0.000162) test_reverse_each: .: (0.000497) test_self_bracket: .: (0.000133) test_self_new: .: (0.000167) test_size: .: (0.000131) test_sort!: .: (0.000139) test_to_a: .: (0.000142) test_uniq!: .: (0.000135) test_unshift: .: (0.000162) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000556) test_left_padding: .: (0.000206) test_right_padding: .: (0.000220) test_strip_padding: .: (0.000227) Bio::TestSOFT: test_dataset: .: (0.018104) test_series: .: (0.013206) Bio::TestSOSUIReport: test_entry_id: .: (0.000462) test_prediction: .: (0.000651) test_tmh: .: (0.000221) test_tmhs: .: (0.000600) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000266) test_rs: .: (0.000114) Bio::TestSOSUITMH: test_grade: .: (0.000347) test_range: .: (0.000214) test_sequence: .: (0.000203) Bio::TestSampleGraph: test_bellman_ford: .: (0.001058) test_bfs_shortest_path: .: (0.000325) test_breadth_first_search: .: (0.000320) test_depth_first_search: .: (0.000742) test_dijkstra: .: (0.000379) test_dump_list: .: (0.000368) test_dump_matrix: .: (0.000506) test_extract_subgraph_by_label: .: (0.000313) test_extract_subgraph_by_list: .: (0.000618) test_extract_subgraph_retains_disconnected_nodes: .: (0.000491) test_small_world_aka_node_degree_histogram: .: (0.000248) test_to_matrix: .: (0.000569) test_to_matrix_fixed_index: .: (0.000499) test_undirected_cliquishness: .: (0.000554) Bio::TestScf_version_2: test_complement: .: (0.017132) test_seq: .: (0.016231) test_to_biosequence: .: (0.016482) Bio::TestScf_version_3: test_complement: .: (0.047961) test_seq: .: (0.046352) test_to_biosequence: .: (0.047104) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000674) test_AA_new_sequence_all_legal_symbols: .: (0.000151) test_AA_new_sequence_removes_whitespace: .: (0.000139) test_AA_new_sequence_upcases_symbols: .: (0.000137) test_DNA_new_blank_sequence: .: (0.000134) test_DNA_new_sequence_downcases_symbols: .: (0.000130) test_DNA_new_sequence_removes_whitespace: .: (0.000132) test_NA_randomize_with_counts: .: (0.001206) test_NA_randomize_with_counts_and_block: .: (0.002227) test_RNA_new_sequence: .: (0.000380) test_ambiguous_dna_sequence_complement: .: (0.000219) test_ambiguous_rna_sequence_complement: .: (0.000121) test_amino_acid_codes: .: (0.000178) test_amino_acid_molecular_weight: .: (0.000285) test_amino_acid_names: .: (0.000160) test_amino_acid_randomize_can_be_chained: .: (0.002318) test_amino_acid_randomize_has_same_composition: .: (0.001199) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000900) test_dna_composition: .: (0.000158) test_dna_gc_percent: .: (0.000459) test_dna_molecular_weight: .: (0.000525) test_dna_pikachu: .: (0.000150) test_dna_sequence_complement: .: (0.000137) test_dna_sequence_translate: .: (0.000717) test_dna_to_re: .: (0.000253) test_element_reference_operator_with_one_argument: .: (0.000153) test_element_reference_operator_with_two_arguments: .: (0.000151) test_invalid_nucleic_acid_illegal_bases: .: (0.000215) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000238) test_nucleic_acid_names: .: (0.000183) test_randomize_dna_can_be_chained: .: (0.001241) test_randomize_dna_retains_composition: .: (0.000408) test_randomize_dna_with_block: .: (0.000481) test_rna_composition: .: (0.000176) test_rna_gc_percent: .: (0.000208) test_rna_molecular_weight: .: (0.000283) test_rna_pikachu: .: (0.000170) test_rna_sequence_complement: .: (0.000155) test_rna_sequence_translate: .: (0.001201) test_rna_to_re: .: (0.000270) test_total: .: (0.000168) test_two_consecutive_dna_randomizations_not_equal: .: (0.000428) test_valid_dna_sequence_illegal_bases: .: (0.000137) Bio::TestSequenceAA: test_codes: .: (0.000342) test_molecular_weight: .: (0.000255) test_names: .: (0.000167) test_to_re: .: (0.000195) test_to_s: .: (0.000111) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000699) Bio::TestSequenceAANew: test_new: .: (0.000290) test_new_n: .: (0.000144) test_new_r: .: (0.000141) test_new_t: .: (0.000140) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000481) test_concat: .: (0.000152) test_push: .: (0.000117) test_seq: .: (0.000118) test_splicing: .: (0.000256) test_sum: .: (0.000129) test_to_s: .: (0.000125) test_to_str: .: (0.000119) test_total: .: (0.000360) test_window_search: .: (0.000755) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000333) test_normalize_A: .: (0.000146) test_normalize_a: .: (0.000150) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.002054) test_randomize_with_block: .: (0.007861) test_randomize_with_hash: .: (0.002642) test_randomize_with_hash_block: .: (0.078694) 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' =============================================================================== : (0.017475) 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' =============================================================================== : (0.001494) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000708) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000163) test_subseq_returns_subsequence: .: (0.000145) test_to_s_returns_self_as_string: .: (0.000177) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000347) test_window_search_with_width_3_step_two_with_residual: .: (0.000153) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000290) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000237) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000396) test_na_self_randomize: .: (0.000518) Bio::TestSequenceDBLink: test_database: .: (0.000287) test_id: .: (0.000130) test_secondary_ids: .: (0.000144) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000360) test_parse_uniprot_DR_line: .: (0.000211) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.001895) test_output_width_35: .: (0.000438) test_output_width_nil: .: (0.000413) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.001073) test_output_after_adding_sequence: .: (0.000487) test_output_after_truncating_sequence: .: (0.000622) test_output_from_error_probabilities: .: (0.005900) test_output_width45: .: (0.000456) test_output_with_converting_score_phred2solexa: .: (0.001508) test_output_with_converting_score_solexa2phred: .: (0.000562) test_output_with_default_score: .: (0.000350) Bio::TestSequenceMasker: test_mask: .: (0.000502) test_mask_with_enumerator: .: (0.000286) test_mask_with_enumerator_empty_mask_char: .: (0.000249) test_mask_with_enumerator_excess: .: (0.001162) test_mask_with_enumerator_longer_mask_char: .: (0.000265) test_mask_with_enumerator_shorter: .: (0.000295) test_mask_with_error_probability: .: (0.000463) test_mask_with_quality_score: .: (0.000214) Bio::TestSequenceNA: test_at_content: .: (0.000674) test_at_skew: .: (0.000431) test_codon_usage: .: (0.000210) test_complement: .: (0.000176) test_dna: .: (0.000164) test_dna!: .: (0.000443) test_forward_complement: .: (0.000256) test_gc_content: .: (0.000755) test_gc_percent: .: (0.000317) test_gc_skew: .: (0.000578) test_iliegal_bases: .: (0.000151) test_molecular_weight: .: (0.000231) test_names: .: (0.000211) test_reverse_complement: .: (0.000222) test_rna: .: (0.000140) test_rna!: .: (0.000142) test_splicing: .: (0.000231) test_to_re: .: (0.000388) test_to_s: .: (0.000127) Bio::TestSequenceNACommon: test_composition: .: (0.000396) test_concat: .: (0.000143) test_push: .: (0.000134) test_seq: .: (0.000130) test_splicing: .: (0.000222) test_sum: .: (0.000140) test_to_s: .: (0.000132) test_to_str: .: (0.000129) test_total: .: (0.000148) test_window_search: .: (0.000424) Bio::TestSequenceNANew: test_new: .: (0.000300) test_new_n: .: (0.000122) test_new_r: .: (0.000113) test_new_t: .: (0.000111) Bio::TestSequenceNATranslation: test_translate: .: (0.000527) test_translate_0: .: (0.001308) test_translate_1: .: (0.000353) test_translate_2: .: (0.000590) test_translate_3: .: (0.000492) test_translate_4: .: (0.000341) test_translate_5: .: (0.000306) test_translate_6: .: (0.000287) test_translate_7: .: (0.000747) test_translate_given_codon_table: .: (0.074664) test_translate_n1: .: (0.000808) test_translate_n2: .: (0.000662) test_translate_n3: .: (0.000735) test_translate_unknown_o: .: (0.000423) test_translate_unknown_x: .: (0.000386) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000352) test_convert_scores_from_phred_to_solexa: .: (0.000875) test_convert_scores_from_solexa_to_phred: .: (0.000253) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000251) test_convert_scores_from_phred: .: (0.000111) test_convert_scores_from_phred_to_solexa: .: (0.000929) test_convert_scores_from_solexa: .: (0.000297) test_convert_scores_from_solexa_to_phred: .: (0.000274) test_convert_scores_to_phred: .: (0.000129) test_convert_scores_to_solexa: .: (0.001130) test_p2q: .: (0.000260) test_phred_p2q: .: (0.000257) test_phred_q2p: .: (0.009504) test_q2p: .: (0.009305) test_quality_score_type: .: (0.000170) test_self_convert_scores_to_solexa: .: (0.000936) test_self_p2q: .: (0.000255) test_self_q2p: .: (0.009737) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000477) test_convert_scores_from_phred: .: (0.000822) test_convert_scores_from_phred_to_solexa: .: (0.001203) test_convert_scores_from_solexa: .: (0.000128) test_convert_scores_from_solexa_to_phred: .: (0.000269) test_convert_scores_to_phred: .: (0.000236) test_convert_scores_to_solexa: .: (0.000103) test_p2q: .: (0.000334) test_q2p: .: (0.014575) test_quality_score_type: .: (0.000150) test_self_convert_scores_to_phred: .: (0.000293) test_self_p2q: .: (0.000577) test_self_q2p: .: (0.010816) test_solexa_p2q: .: (0.000482) test_solexa_q2p: .: (0.010467) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000702) test_center: .: (0.000172) test_chomp: .: (0.000228) test_chop: .: (0.000212) test_delete: .: (0.000164) test_delete_prefix: .: (0.000156) test_delete_suffix: .: (0.000373) test_downcase: .: (0.000169) test_each_char: .: (0.000298) test_each_char_enum: .: (0.000256) test_each_grapheme_cluster: .: (0.000550) test_each_grapheme_cluster_enum: .: (0.000248) test_each_line: .: (0.000237) test_each_line_enum: .: (0.000188) test_gsub: .: (0.000182) test_gsub_with_block: .: (0.000766) test_ljust: .: (0.000151) test_lstrip: .: (0.000139) test_multiply: .: (0.000388) test_next: .: (0.000167) test_reverse: .: (0.000165) test_rjust: .: (0.000167) test_rstrip: .: (0.000161) test_slice: .: (0.000487) test_slice2: .: (0.000160) test_split: .: (0.000230) test_squeeze: .: (0.000167) test_strip: .: (0.000139) test_sub: .: (0.000159) test_sub_with_block: .: (0.000393) test_succ: .: (0.000156) test_swapcase: .: (0.000154) test_tr: .: (0.000310) test_tr_s: .: (0.000141) test_upcase: .: (0.000142) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000392) test_partition_nomatch: .: (0.000217) test_partition_sep_TSeq: .: (0.000242) test_partition_sep_regexp: .: (0.000234) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000396) test_rpartition_nomatch: .: (0.000205) test_rpartition_sep_TSeq: .: (0.000197) test_rpartition_sep_regexp: .: (0.000323) Bio::TestShRNA: test_blocK_it: .: (0.041253) test_blocK_it_: .: (0.045272) test_blocK_it_BLOCK_IT: .: (0.045938) test_blocK_it_BLOCK_iT: .: (0.072952) test_blocK_it_piGene: .: (0.090848) test_bottom_strand: .: (0.093837) test_bottom_strand_class: .: (0.087980) test_bottom_strand_nil: .: (0.095551) test_design: .: (0.081903) test_design_BLOCK_IT: .: (0.092082) test_report: .: (0.060874) test_report_before_design: .: (0.042700) test_top_strand: .: (0.042723) test_top_strand_class: .: (0.042780) test_top_strand_nil: .: (0.045756) Bio::TestShRNANew: test_new: .: (0.000642) Bio::TestSiRNA: test_antisense_size: .: (0.001347) test_design: .: (0.044249) test_design_reynolds: .: (0.052185) test_design_uitei: .: (0.044786) test_max_gc_percent: .: (0.000187) test_min_gc_percent: .: (0.000426) test_reynolds: .: (0.051002) test_reynolds?: .: (0.000203) test_uitei: .: (0.041829) test_uitei?: .: (0.000202) Bio::TestSiRNANew: test_new: .: (0.000592) Bio::TestSiRNAPair: test_antisense: .: (0.042892) test_gc_percent: .: (0.042166) test_report: .: (0.042410) test_rule: .: (0.041301) test_sense: .: (0.040919) test_start: .: (0.040479) test_stop: .: (0.039592) test_target: .: (0.044592) Bio::TestSiRNAPairNew: test_new: .: (0.001043) Bio::TestSim4Report: test_all_hits: .: (0.001122) test_each: .: (0.000315) test_each_hit: .: (0.000271) test_hits: .: (0.000272) test_num_hits: .: (0.000222) test_query_def: .: (0.000232) test_query_id: .: (0.000237) test_query_len: .: (0.000228) test_seq1: .: (0.000325) Bio::TestSim4Report2: test_all_hits: .: (0.008979) test_each: .: (0.000379) test_each_hit: .: (0.000304) test_hits: .: (0.000298) test_num_hits: .: (0.000254) test_query_def: .: (0.000257) test_query_id: .: (0.000266) test_query_len: .: (0.000271) test_seq1: .: (0.000374) Bio::TestSim4Report4: test_all_hits: .: (0.001349) test_each: .: (0.000288) test_each_hit: .: (0.000267) test_hits: .: (0.000276) test_num_hits: .: (0.000246) test_query_def: .: (0.000259) test_query_id: .: (0.000257) test_query_len: .: (0.000268) test_seq1: .: (0.000365) Bio::TestSim4ReportHit: test_align: .: (0.001303) test_complement?: .: (0.000248) test_definition: .: (0.000231) test_each: .: (0.000525) test_exons: .: (0.000482) test_hit_id: .: (0.000282) test_hsps: .: (0.000495) test_introns: .: (0.001266) test_len: .: (0.000411) test_query_def: .: (0.000233) test_query_id: .: (0.000226) test_query_len: .: (0.000320) test_segmentpairs: .: (0.000485) test_seq1: .: (0.000335) test_seq2: .: (0.000328) test_target_def: .: (0.000232) test_target_id: .: (0.000686) test_target_len: .: (0.000392) Bio::TestSim4ReportHit2: test_align: .: (0.000626) test_complement?: .: (0.000279) test_definition: .: (0.000259) test_each: .: (0.000503) test_exons: .: (0.000430) test_hit_id: .: (0.000510) test_hsps: .: (0.000692) test_introns: .: (0.000394) test_len: .: (0.000293) test_query_def: .: (0.000276) test_query_id: .: (0.000230) test_query_len: .: (0.000256) test_segmentpairs: .: (0.000490) test_seq1: .: (0.000337) test_seq2: .: (0.001001) test_target_def: .: (0.000297) test_target_id: .: (0.000231) test_target_len: .: (0.000217) Bio::TestSim4ReportHit4: test_align: .: (0.000716) test_complement?: .: (0.000271) test_definition: .: (0.000264) test_each: .: (0.000991) test_exons: .: (0.000943) test_hit_id: .: (0.000333) test_hsps: .: (0.000614) test_introns: .: (0.000568) test_len: .: (0.000244) test_query_def: .: (0.000251) test_query_id: .: (0.000324) test_query_len: .: (0.000262) test_segmentpairs: .: (0.000697) test_seq1: .: (0.000461) test_seq2: .: (0.000371) test_target_def: .: (0.000278) test_target_id: .: (0.000258) test_target_len: .: (0.000245) Bio::TestSim4ReportSegment: test_from: .: (0.000882) test_self_new: .: (0.000182) test_seq: .: (0.000121) test_to: .: (0.000118) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000607) test_direction: .: (0.000391) test_hit_from: .: (0.000421) test_hit_to: .: (0.000417) test_hseq: .: (0.000956) test_midline: .: (0.000462) test_percent_identity: .: (0.000350) test_qseq: .: (0.000337) test_query_from: .: (0.000332) test_query_to: .: (0.000365) test_seq1: .: (0.000635) test_seq2: .: (0.000446) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000653) test_direction: .: (0.000385) test_hit_from: .: (0.000363) test_hit_to: .: (0.000351) test_hseq: .: (0.000329) test_midline: .: (0.000498) test_percent_identity: .: (0.000354) test_qseq: .: (0.000561) test_query_from: .: (0.000350) test_query_to: .: (0.000364) test_seq1: .: (0.000445) test_seq2: .: (0.000633) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000712) test_direction: .: (0.000446) test_hit_from: .: (0.000686) test_hit_to: .: (0.000465) test_hseq: .: (0.000662) test_midline: .: (0.000502) test_percent_identity: .: (0.000471) test_qseq: .: (0.000460) test_query_from: .: (0.000460) test_query_to: .: (0.001047) test_seq1: .: (0.000516) test_seq2: .: (0.000481) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000609) test_direction: .: (0.000596) test_hit_from: .: (0.000782) test_hit_to: .: (0.000518) test_hseq: .: (0.000492) test_midline: .: (0.000695) test_percent_identity: .: (0.000501) test_qseq: .: (0.000437) test_query_from: .: (0.000440) test_query_to: .: (0.000762) test_seq1: .: (0.000522) test_seq2: .: (0.000606) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000691) test_direction: .: (0.000472) test_hit_from: .: (0.000445) test_hit_to: .: (0.000946) test_hseq: .: (0.000479) test_midline: .: (0.000430) test_percent_identity: .: (0.000451) test_qseq: .: (0.000467) test_query_from: .: (0.000773) test_query_to: .: (0.000885) test_seq1: .: (0.000620) test_seq2: .: (0.000512) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000747) test_direction: .: (0.000351) test_hit_from: .: (0.000326) test_hit_to: .: (0.000882) test_hseq: .: (0.000381) test_midline: .: (0.000386) test_percent_identity: .: (0.000382) test_qseq: .: (0.000649) test_query_from: .: (0.000415) test_query_to: .: (0.000327) test_seq1: .: (0.000841) test_seq2: .: (0.000433) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000514) test_direction: .: (0.000641) test_hit_from: .: (0.000474) test_hit_to: .: (0.000401) test_hseq: .: (0.000400) test_midline: .: (0.000672) test_percent_identity: .: (0.000296) test_qseq: .: (0.000332) test_query_from: .: (0.000549) test_query_to: .: (0.000372) test_seq1: .: (0.000379) test_seq2: .: (0.000377) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000349) test_entry_id: .: (0.000148) test_filename: .: (0.000164) test_len: .: (0.000153) test_self_new: .: (0.000179) test_self_parse: .: (0.000228) Bio::TestTMHMMReport: test_entry_id: .: (0.000857) test_exp_aas_in_tmhs: .: (0.000410) test_exp_first_60aa: .: (0.000419) test_helix: .: (0.000460) test_predicted_tmhs: .: (0.000642) test_query_len: .: (0.000648) test_tmhs: .: (0.000504) test_to_s: .: (0.000704) test_total_prob_of_N_in: .: (0.000468) Bio::TestTMHMMReport_reports: test_reports: .: (0.000351) Bio::TestTMHMMTMH: test_entry_id: .: (0.001030) test_pos: .: (0.000435) test_range: .: (0.000428) test_status: .: (0.000421) test_version: .: (0.000661) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000576) test_cutoff: .: (0.000634) test_entry_id: .: (0.000360) test_length: .: (0.000288) test_loc: .: (0.000276) test_name: .: (0.000277) test_networks: .: (0.000279) test_prediction: .: (0.000318) test_query_len: .: (0.000290) test_query_sequences: .: (0.000482) test_rc: .: (0.000324) test_version: .: (0.000704) Bio::TestTargetPReportConst: test_delimiter: .: (0.000317) test_rs: .: (0.000125) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000288) test_togows_access_wait: .: (2.006591) Bio::TestTogoWSREST: test_debug: .: (0.000786) test_debug_default: .: (0.000233) test_internal_http: .: (0.000262) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000481) test_entry: .: (0.000115) test_entry_database_list: .: (0.000108) test_new: .: (0.000262) test_new_with_uri_object: .: (0.000277) test_new_with_uri_string: .: (0.000535) test_retrieve: .: (0.000112) test_search: .: (0.000107) test_search_database_list: .: (0.000110) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000537) test_prepare_return_value: .: (0.000299) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000885) Bio::TestTree: test_get_edge_distance: .: (0.000381) test_get_edge_distance_string: .: (0.000208) test_get_node_name: .: (0.000149) test_initialize: .: (0.008473) test_options: .: (0.000161) test_root: .: (0.000127) test_root=: .: (0.000145) Bio::TestTree2: test_add_edge: .: (0.000598) test_add_node: .: (0.000352) test_adjacency_matrix: .: (0.000317) test_adjacency_matrix_with_block: .: (0.000483) test_adjacent_nodes: .: (0.000346) test_adjacent_nodes_nonexistent: .: (0.000204) test_ancestors: .: (0.000544) test_children: .: (0.000233) test_clear: .: (0.000294) test_clear_node: .: (0.000361) test_clear_node_nonexistent: .: (0.000363) test_collect_edge!: .: (0.000511) test_collect_node!: .: (0.000453) test_concat: .: (0.000611) test_descendents: .: (0.000248) test_distance_matrix: .: (0.001003) test_each_edge: .: (0.000347) test_each_node: .: (0.000315) test_each_out_edge: .: (0.000260) test_each_out_edge_chimpanzee: .: (0.000251) test_each_out_edge_human: .: (0.000245) test_each_out_edge_mammals: .: (0.000297) test_each_out_edge_nonexistent: .: (0.000403) test_each_out_edge_primates: .: (0.000644) test_each_out_edge_rat: .: (0.000298) test_each_out_edge_rodents: .: (0.000395) test_edges: .: (0.000275) test_get_edge: .: (0.000633) test_get_edge_indirect: .: (0.000234) test_get_edge_merged: .: (0.000463) test_get_edge_nonexistent: .: (0.000203) test_get_node_bootstrap: .: (0.000206) test_get_node_bootstrap_string=: .: (0.000208) test_get_node_by_name: .: (0.004858) test_get_node_by_name_noexistent: .: (0.000211) test_include?: .: (0.000283) test_include_nonexistent: .: (0.000211) test_insert_node: .: (0.000350) test_leaves: .: (0.000282) test_leaves_noargs: .: (0.000213) test_lowest_common_ancestor: .: (0.000273) test_nodes: .: (0.000252) test_number_of_edges: .: (0.000225) test_number_of_nodes: .: (0.008369) test_out_degree: .: (0.000451) test_out_degree_nonexistent: .: (0.000232) test_out_edges: .: (0.000329) test_out_edges_mammals: .: (0.000381) test_out_edges_nonexistent: .: (0.000246) test_out_edges_primates: .: (0.000433) test_out_edges_rodents: .: (0.000432) test_parent: .: (0.000315) test_path: .: (0.000571) test_remove_edge: .: (0.000279) test_remove_edge_if: .: (0.000283) test_remove_edge_if_nothing_removed: .: (0.000310) test_remove_edge_nonexistent: .: (0.000378) test_remove_node: .: (0.000390) test_remove_node_if: .: (0.000235) test_remove_node_if_false: .: (0.000300) test_remove_node_nonexistent: .: (0.000262) test_remove_nonsense_nodes: .: (0.000308) test_subtree: .: (0.009062) test_subtree_with_all_paths: .: (0.000566) test_total_distance: .: (0.000259) Bio::TestTreeEdge: test_distance: .: (0.000362) test_distance=: .: (0.000218) test_distance_string: .: (0.000130) test_distance_string=: .: (0.000191) test_initialize: .: (0.000184) test_inspect: .: (0.000132) test_to_s: .: (0.000125) Bio::TestTreeNode: test_bootstrap: .: (0.000575) test_bootstrap=: .: (0.000180) test_bootstrap_string: .: (0.000108) test_bootstrap_string=: .: (0.000343) test_initialize: .: (0.000175) test_inspect: .: (0.000176) test_name: .: (0.000140) test_to_s: .: (0.000125) Bio::TestUniProt: test_gene_name: .: (0.016391) Bio::TestUniProtKB: test_ac: .: (0.016019) test_accession: .: (0.019541) test_cc: .: (0.019208) test_cc_alternative_products: .: (0.026668) test_cc_database: .: (0.018378) test_cc_mass_spectrometry: .: (0.019463) test_de: .: (0.015120) test_dr: .: (0.018210) test_dr_with_key: .: (0.022217) test_dr_with_key_empty: .: (0.201110) test_dt: .: (0.015955) test_dt_annotation: .: (0.015740) test_dt_created: .: (0.015094) test_dt_sequence: .: (0.015948) test_entry: .: (0.016702) test_ft: .: (0.045072) test_gene_name: .: (0.015598) test_gene_names: .: (0.015246) test_gn: .: (0.016589) test_gn_old_parser: .: (0.015984) test_gn_uniprot_parser: .: (0.011528) test_id_line: .: (0.015647) test_id_line_data_class: .: (0.026655) test_id_line_entry_name: .: (0.015917) test_id_line_molecule_type: .: (0.011909) test_id_line_sequence_length: .: (0.015719) test_kw: .: (0.015639) test_molecule: .: (0.016107) test_oc: .: (0.022821) test_og_1: .: (0.011683) test_og_2: .: (0.014269) test_og_3: .: (0.015903) test_og_4: .: (0.015672) test_og_5: .: (0.015238) test_og_6: .: (0.015152) test_os: .: (0.016322) test_os_access: .: (0.015777) test_os_access2: .: (0.015688) test_ox: .: (0.015866) test_protein_name: .: (0.016408) test_ref: .: (0.038470) test_seq: .: (0.015903) test_sequence_length: .: (0.011498) test_sq: .: (0.015179) test_sq_crc64: .: (0.007545) test_sq_len: .: (0.007039) test_sq_mw: .: (0.007200) test_synonyms: .: (0.009076) Bio::TestUniProtKB_CC: test_allergen: .: (0.000439) test_alternative_products_access_as_hash: .: (0.000297) test_alternative_products_ai: .: (0.000793) test_alternative_products_apu: .: (0.001126) test_alternative_products_as: .: (0.000484) test_alternative_products_rf: .: (0.000145) test_biophysicochemical_properties: .: (0.000673) test_biotechnology: .: (0.000304) test_catalytic_activity: .: (0.000255) test_caution: .: (0.000321) test_cofactor: .: (0.000263) test_developmental_stage: .: (0.000614) test_disease: .: (0.000436) test_domain: .: (0.000498) test_enzyme_regulation: .: (0.000287) test_function: .: (0.000332) test_induction: .: (0.000265) test_interaction: .: (0.000613) test_mass_spectrometry: .: (0.000679) test_miscellaneous: .: (0.000236) test_pathway: .: (0.000290) test_pharmaceutical: .: (0.000300) test_polymorphism: .: (0.000471) test_ptm: .: (0.000255) test_rna_editing: .: (0.000343) test_similarity: .: (0.000243) test_subcellular_location: .: (0.000334) test_subunit: .: (0.000912) test_tissue_specificity: .: (0.000372) test_toxic_dose: .: (0.000247) test_web_resource: .: (0.000435) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000554) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000731) test_protein_name: .: (0.001038) test_synonyms: .: (0.000646) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000369) test_entry: .: (0.000172) test_entry_id: .: (0.000180) test_entry_name: .: (0.000175) test_id_line: .: (0.000185) test_molecule: .: (0.000171) test_sequence_length: .: (0.000166) Bio::TestUniProtKB_P28907: test_ac: .: (0.003482) test_accession: .: (0.003027) test_cc: .: (0.003954) test_cc_alternative_products: .: (0.003677) test_cc_database: .: (0.003717) test_cc_mass_spectrometry: .: (0.004101) test_de: .: (0.003034) test_dr: .: (0.007723) test_dr_with_key: .: (0.007402) test_dr_with_key_empty: .: (0.007627) test_dt: .: (0.002998) test_dt_annotation: .: (0.002943) test_dt_created: .: (0.002644) test_dt_sequence: .: (0.002495) test_entry: .: (0.003126) test_ft: .: (0.005016) test_gene_name: .: (0.002961) test_gene_names: .: (0.002732) test_gn: .: (0.002757) test_gn_old_parser: .: (0.002669) test_gn_uniprot_parser: .: (0.002907) test_id_line: .: (0.002726) test_id_line_data_class: .: (0.002308) test_id_line_entry_name: .: (0.002769) test_id_line_sequence_length: .: (0.002857) test_kw: .: (0.002609) test_oc: .: (0.002659) test_os: .: (0.002904) test_os_access: .: (0.006021) test_os_access2: .: (0.003569) test_ox: .: (0.002986) test_protein_name: .: (0.003256) test_protein_name_after_calling_de: .: (0.003076) test_ref: .: (0.005385) test_seq: .: (0.003311) test_sequence_length: .: (0.002992) test_sq: .: (0.003044) test_sq_crc64: .: (0.002681) test_sq_len: .: (0.003254) test_sq_mw: .: (0.003064) test_synonyms: .: (0.004149) test_synonyms_after_calling_de: .: (0.004698) Bio::TestUniProtKB_Ref: test_RA: .: (0.000710) test_RC: .: (0.001038) test_RG: .: (0.000433) test_RL: .: (0.000392) test_RN: .: (0.000396) test_RP: .: (0.000708) test_RT: .: (0.000351) test_RX: .: (0.000347) test_ref: .: (0.000799) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000463) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.001306) test_alternative_products_with_ft: .: (0.001420) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000553) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000776) test_RL_lines: .: (0.000201) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000886) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000360) test_RG_line: .: (0.000222) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.001237) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000419) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000280) test_RL_line: .: (0.000200) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.001444) test_RP_line: .: (0.000684) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000219) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000382) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000275) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000260) test_CC_interaction_isoform: .: (0.000256) test_CC_interaction_no_gene_name: .: (0.000527) test_CC_interaction_self_association: .: (0.000325) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000722) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000463) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000615) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000461) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000847) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000625) test_DT_line: .: (0.000237) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.006207) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.001322) test_CC_web_resource: .: (0.000131) test_FT_VER_SEQ: .: (0.000269) test_OH_line_exception: .: (0.000321) test_OH_lines: .: (0.000474) Bio::TestUtils: test_centreOfGravity: .: (0.001250) test_dihedral_angle: .: (0.000558) test_distance: .: (0.000483) test_geometricCentre: .: (0.000470) test_rad2deg: .: (0.000570) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000448) test_dijkstra_on_weighted_graph: .: (0.000472) Finished in 31.90071635 seconds. ------------------------------------------------------------------------------- 3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 120.91 tests/s, 673.53 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: user script /srv/workspace/pbuilder/3004191/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3004191/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3004191 and its subdirectories I: Current time: Sun May 26 03:44:57 +14 2024 I: pbuilder-time-stamp: 1716644697