I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 1 20:52:33 +14 2023 I: pbuilder-time-stamp: 1685602353 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/28272/tmp/hooks/D01_modify_environment starting debug: Running on virt64a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 1 20:52 /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/28272/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/28272/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=94c9113b5d134c9facd7b691652d2542 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=28272 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.9JVao602/pbuilderrc_vroP --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.9JVao602/b2 --logfile b2/build.log --extrapackages usrmerge ruby-bio_2.0.4-1.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 1 20:52 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/28272/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19324 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 46.1 MB of archives. After unpacking 153 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.8-1 [1373 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 36 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libassuan0 armhf 2.5.5-5 [42.0 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf gpgconf armhf 2.2.40-1.1 [547 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libksba8 armhf 1.6.3-2 [109 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libnpth0 armhf 1.6-3 [17.8 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf dirmngr armhf 2.2.40-1.1 [748 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf gnupg-utils armhf 2.2.40-1.1 [850 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf gpg armhf 2.2.40-1.1 [884 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf pinentry-curses armhf 1.2.1-1 [73.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf gpg-agent armhf 2.2.40-1.1 [652 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf gpg-wks-client armhf 2.2.40-1.1 [524 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf gpg-wks-server armhf 2.2.40-1.1 [517 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf gpgsm armhf 2.2.40-1.1 [637 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf gnupg all 2.2.40-1.1 [846 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libfile-dirlist-perl all 0.05-3 [7600 B] Get: 64 http://deb.debian.org/debian bookworm/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libfile-touch-perl all 0.12-2 [8816 B] Get: 67 http://deb.debian.org/debian bookworm/main armhf libio-pty-perl armhf 1:1.17-1 [34.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libipc-run-perl all 20220807.0-1 [104 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libclass-xsaccessor-perl armhf 1.19-4+b1 [35.5 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libb-hooks-op-check-perl armhf 0.22-2+b1 [10.3 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libdevel-callchecker-perl armhf 0.008-2 [15.7 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libparams-classify-perl armhf 0.015-2+b1 [21.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libimport-into-perl all 1.002005-2 [11.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libmoo-perl all 2.005005-1 [58.0 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libencode-locale-perl all 1.05-3 [12.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libhttp-date-perl all 6.05-2 [10.5 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libfile-listing-perl all 6.15-1 [12.6 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 86 http://deb.debian.org/debian bookworm/main armhf liburi-perl all 5.17-1 [90.4 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libhtml-parser-perl armhf 3.81-1 [97.4 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libhtml-tree-perl all 5.07-3 [211 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf libclone-perl armhf 0.46-1 [13.1 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf libio-html-perl all 1.004-3 [16.2 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libhttp-message-perl all 6.44-1 [81.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf perl-openssl-defaults armhf 7+b1 [7916 B] Get: 96 http://deb.debian.org/debian bookworm/main armhf libnet-ssleay-perl armhf 1.92-2+b1 [298 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf libnet-http-perl all 6.22-1 [25.3 kB] Get: 99 http://deb.debian.org/debian bookworm/main armhf liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 100 http://deb.debian.org/debian bookworm/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 101 http://deb.debian.org/debian bookworm/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 102 http://deb.debian.org/debian bookworm/main armhf libwww-perl all 6.68-1 [186 kB] Get: 103 http://deb.debian.org/debian bookworm/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 104 http://deb.debian.org/debian bookworm/main armhf wdiff armhf 1.2.2-5 [118 kB] Get: 105 http://deb.debian.org/debian bookworm/main armhf devscripts armhf 2.23.3 [1072 kB] Get: 106 http://deb.debian.org/debian bookworm/main armhf xml-core all 0.18+nmu1 [23.8 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf sgml-data all 2.0.11+nmu1 [179 kB] Get: 108 http://deb.debian.org/debian bookworm/main armhf docbook all 4.5-10 [131 kB] Get: 109 http://deb.debian.org/debian bookworm/main armhf libosp5 armhf 1.5.2-13+b2 [847 kB] Get: 110 http://deb.debian.org/debian bookworm/main armhf opensp armhf 1.5.2-13+b2 [405 kB] Get: 111 http://deb.debian.org/debian bookworm/main armhf docbook-to-man armhf 1:2.0.0-45 [73.1 kB] Get: 112 http://deb.debian.org/debian bookworm/main armhf rubygems-integration all 1.18 [6704 B] Get: 113 http://deb.debian.org/debian bookworm/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 116 http://deb.debian.org/debian bookworm/main armhf libruby armhf 1:3.1 [4968 B] Get: 117 http://deb.debian.org/debian bookworm/main armhf ruby-sdbm armhf 1.0.0-5+b1 [13.3 kB] Get: 118 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 119 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 120 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB] Get: 121 http://deb.debian.org/debian bookworm/main armhf libyaml-0-2 armhf 0.2.5-1 [46.8 kB] Get: 122 http://deb.debian.org/debian bookworm/main armhf libruby3.1 armhf 3.1.2-7 [5065 kB] Get: 123 http://deb.debian.org/debian bookworm/main armhf ruby3.1 armhf 3.1.2-7 [663 kB] Get: 124 http://deb.debian.org/debian bookworm/main armhf ruby-rubygems all 3.3.15-2 [293 kB] Get: 125 http://deb.debian.org/debian bookworm/main armhf ruby armhf 1:3.1 [5868 B] Get: 126 http://deb.debian.org/debian bookworm/main armhf rake all 13.0.6-3 [83.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main armhf gem2deb-test-runner armhf 2.1 [16.9 kB] Get: 128 http://deb.debian.org/debian bookworm/main armhf libgmpxx4ldbl armhf 2:6.2.1+dfsg1-1.1 [338 kB] Get: 129 http://deb.debian.org/debian bookworm/main armhf libgmp-dev armhf 2:6.2.1+dfsg1-1.1 [593 kB] Get: 130 http://deb.debian.org/debian bookworm/main armhf ruby3.1-dev armhf 3.1.2-7 [1002 kB] Get: 131 http://deb.debian.org/debian bookworm/main armhf ruby-all-dev armhf 1:3.1 [5976 B] Get: 132 http://deb.debian.org/debian bookworm/main armhf gem2deb armhf 2.1 [53.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian bookworm/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main armhf ruby-libxml armhf 3.2.4-2 [71.9 kB] Fetched 46.1 MB in 1s (35.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19324 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (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 ... 19640 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.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:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (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 ... 20074 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_armhf.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_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../007-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../010-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../013-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-3_armhf.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:armhf. Preparing to unpack .../027-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../029-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../030-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.21-12_armhf.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:armhf. Preparing to unpack .../035-libassuan0_2.5.5-5_armhf.deb ... Unpacking libassuan0:armhf (2.5.5-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../036-gpgconf_2.2.40-1.1_armhf.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package libksba8:armhf. Preparing to unpack .../037-libksba8_1.6.3-2_armhf.deb ... Unpacking libksba8:armhf (1.6.3-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../038-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../039-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../040-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnpth0:armhf. Preparing to unpack .../041-libnpth0_1.6-3_armhf.deb ... Unpacking libnpth0:armhf (1.6-3) ... Selecting previously unselected package dirmngr. Preparing to unpack .../042-dirmngr_2.2.40-1.1_armhf.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_armhf.deb ... Unpacking gnupg-utils (2.2.40-1.1) ... Selecting previously unselected package gpg. Preparing to unpack .../045-gpg_2.2.40-1.1_armhf.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package pinentry-curses. Preparing to unpack .../046-pinentry-curses_1.2.1-1_armhf.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_armhf.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_armhf.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_armhf.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_armhf.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_armhf.deb ... Unpacking libio-pty-perl (1:1.17-1) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../057-libipc-run-perl_20220807.0-1_all.deb ... Unpacking libipc-run-perl (20220807.0-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../058-libclass-method-modifiers-perl_2.14-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.14-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../059-libclass-xsaccessor-perl_1.19-4+b1_armhf.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libb-hooks-op-check-perl:armhf. Preparing to unpack .../060-libb-hooks-op-check-perl_0.22-2+b1_armhf.deb ... Unpacking libb-hooks-op-check-perl:armhf (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../061-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:armhf. Preparing to unpack .../062-libdevel-callchecker-perl_0.008-2_armhf.deb ... Unpacking libdevel-callchecker-perl:armhf (0.008-2) ... Selecting previously unselected package libparams-classify-perl:armhf. Preparing to unpack .../063-libparams-classify-perl_0.015-2+b1_armhf.deb ... Unpacking libparams-classify-perl:armhf (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../064-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../065-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../066-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../067-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../068-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../069-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../070-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../071-libhttp-date-perl_6.05-2_all.deb ... Unpacking libhttp-date-perl (6.05-2) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../072-libfile-listing-perl_6.15-1_all.deb ... Unpacking libfile-listing-perl (6.15-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../073-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../074-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../075-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:armhf. Preparing to unpack .../076-libhtml-parser-perl_3.81-1_armhf.deb ... Unpacking libhtml-parser-perl:armhf (3.81-1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../077-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libclone-perl:armhf. Preparing to unpack .../078-libclone-perl_0.46-1_armhf.deb ... Unpacking libclone-perl:armhf (0.46-1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../079-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../080-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../081-libhttp-message-perl_6.44-1_all.deb ... Unpacking libhttp-message-perl (6.44-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../082-libhttp-cookies-perl_6.10-1_all.deb ... Unpacking libhttp-cookies-perl (6.10-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../083-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:armhf. Preparing to unpack .../084-perl-openssl-defaults_7+b1_armhf.deb ... Unpacking perl-openssl-defaults:armhf (7+b1) ... Selecting previously unselected package libnet-ssleay-perl:armhf. Preparing to unpack .../085-libnet-ssleay-perl_1.92-2+b1_armhf.deb ... Unpacking libnet-ssleay-perl:armhf (1.92-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../086-libio-socket-ssl-perl_2.081-2_all.deb ... Unpacking libio-socket-ssl-perl (2.081-2) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../087-libnet-http-perl_6.22-1_all.deb ... Unpacking libnet-http-perl (6.22-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../088-liblwp-protocol-https-perl_6.10-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.10-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../089-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../090-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../091-libwww-perl_6.68-1_all.deb ... Unpacking libwww-perl (6.68-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../092-patchutils_0.4.2-1_armhf.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package wdiff. Preparing to unpack .../093-wdiff_1.2.2-5_armhf.deb ... Unpacking wdiff (1.2.2-5) ... Selecting previously unselected package devscripts. Preparing to unpack .../094-devscripts_2.23.3_armhf.deb ... Unpacking devscripts (2.23.3) ... Selecting previously unselected package xml-core. Preparing to unpack .../095-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package sgml-data. Preparing to unpack .../096-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook. Preparing to unpack .../097-docbook_4.5-10_all.deb ... Unpacking docbook (4.5-10) ... Selecting previously unselected package libosp5. Preparing to unpack .../098-libosp5_1.5.2-13+b2_armhf.deb ... Unpacking libosp5 (1.5.2-13+b2) ... Selecting previously unselected package opensp. Preparing to unpack .../099-opensp_1.5.2-13+b2_armhf.deb ... Unpacking opensp (1.5.2-13+b2) ... Selecting previously unselected package docbook-to-man. Preparing to unpack .../100-docbook-to-man_1%3a2.0.0-45_armhf.deb ... Unpacking docbook-to-man (1:2.0.0-45) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../101-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../102-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../103-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../104-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../105-libruby_1%3a3.1_armhf.deb ... Unpacking libruby:armhf (1:3.1) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../106-ruby-sdbm_1.0.0-5+b1_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b1) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../107-libbsd0_0.11.7-2_armhf.deb ... Unpacking libbsd0:armhf (0.11.7-2) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../108-libedit2_3.1-20221030-2_armhf.deb ... Unpacking libedit2:armhf (3.1-20221030-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../109-libncurses6_6.4-4_armhf.deb ... Unpacking libncurses6:armhf (6.4-4) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../110-libyaml-0-2_0.2.5-1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1) ... Selecting previously unselected package libruby3.1:armhf. Preparing to unpack .../111-libruby3.1_3.1.2-7_armhf.deb ... Unpacking libruby3.1:armhf (3.1.2-7) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../112-ruby3.1_3.1.2-7_armhf.deb ... Unpacking ruby3.1 (3.1.2-7) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../113-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../114-ruby_1%3a3.1_armhf.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package rake. Preparing to unpack .../115-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../116-gem2deb-test-runner_2.1_armhf.deb ... Unpacking gem2deb-test-runner (2.1) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../117-libgmpxx4ldbl_2%3a6.2.1+dfsg1-1.1_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.2.1+dfsg1-1.1) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../118-libgmp-dev_2%3a6.2.1+dfsg1-1.1_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.2.1+dfsg1-1.1) ... Selecting previously unselected package ruby3.1-dev:armhf. Preparing to unpack .../119-ruby3.1-dev_3.1.2-7_armhf.deb ... Unpacking ruby3.1-dev:armhf (3.1.2-7) ... Selecting previously unselected package ruby-all-dev:armhf. Preparing to unpack .../120-ruby-all-dev_1%3a3.1_armhf.deb ... Unpacking ruby-all-dev:armhf (1:3.1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../121-gem2deb_2.1_armhf.deb ... Unpacking gem2deb (2.1) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../122-ruby-rd_0.6.38-4.1_all.deb ... Unpacking ruby-rd (0.6.38-4.1) ... Selecting previously unselected package rdtool. Preparing to unpack .../123-rdtool_0.6.38-4.1_all.deb ... Unpacking rdtool (0.6.38-4.1) ... Selecting previously unselected package ruby-libxml:armhf. Preparing to unpack .../124-ruby-libxml_3.2.4-2_armhf.deb ... Unpacking ruby-libxml:armhf (3.2.4-2) ... Setting up libksba8:armhf (1.6.3-2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up wdiff (1.2.2-5) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libclone-perl:armhf (0.46-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (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:armhf (1:5.44-3) ... Setting up perl-openssl-defaults:armhf (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:armhf (1.6-3) ... Setting up file (1:5.44-3) ... Setting up libassuan0:armhf (2.5.5-5) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up libosp5 (1.5.2-13+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:armhf (2:6.2.1+dfsg1-1.1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libncurses6:armhf (6.4-4) ... 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:armhf (0.22-2+b1) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up libsasl2-2:armhf (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:armhf (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:armhf (0.11.7-2) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up liburi-perl (5.17-1) ... Setting up ruby-rd (0.6.38-4.1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libnet-ssleay-perl:armhf (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:armhf (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:armhf (3.1-20221030-2) ... Setting up libreadline8:armhf (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:armhf (0.008-2) ... Setting up libldap-2.5-0:armhf (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:armhf (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:armhf (3.11.2-6) ... Setting up libparams-classify-perl:armhf (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:armhf (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:armhf (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:armhf (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:armhf (3.1.2-7) ... Setting up gem2deb-test-runner (2.1) ... Setting up ruby3.1-dev:armhf (3.1.2-7) ... Setting up ruby-libxml:armhf (3.2.4-2) ... Setting up ruby-all-dev:armhf (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/28272/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/28272/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 armhf 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/arm-linux-gnueabihf/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/arm-linux-gnueabihf/rubygems-integration/3.1.0 ruby3.1 -S rake -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: .: (0.001254) test_dbs: .: (0.000625) test_go_ids: .: (0.000583) test_go_terms: .: (0.000991) test_parser: .: (0.001606) test_set_date: .: (0.000668) test_set_desc: .: (0.000598) test_to_str: .: (0.000923) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.002158) test_mktmpdir_without_block: .: (0.001876) test_remove_entry_secure: .: (0.001100) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.006208) test_call_command_fork: .: (0.000450) test_call_command_open3: .: (0.005479) test_call_command_popen: .: (0.004689) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.005233) test_call_command_fork: .: (0.000381) test_call_command_open3: .: (0.004752) test_call_command_popen: .: (0.005173) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.005494) test_call_command_fork: .: (0.000421) test_call_command_open3: .: (0.004969) test_call_command_popen: .: (0.004938) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.004214) test_call_command_fork_chdir: .: (0.000896) test_call_command_popen_chdir: .: (0.003276) test_query_command_chdir: .: (0.003276) test_query_command_fork_chdir: .: (0.000711) test_query_command_popen_chdir: .: (0.003842) Bio::FuncTestCommandQuery: test_query_command: .: (0.007495) test_query_command_fork: .: (0.003817) test_query_command_open3: .: (0.007372) test_query_command_popen: .: (0.006694) Bio::FuncTestCommandTmpdir: test_close!: .: (0.002316) test_initialize: .: (0.000895) test_path: .: (0.000628) test_path_after_close: .: (0.001180) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.057490) test_output_fasta: .: (0.023261) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000868) test_accession: .: (0.000534) test_accessions: .: (0.000532) test_comment: .: (0.000475) test_common_name: .: (0.000645) test_definition: .: (0.001084) test_features: .: (0.000982) test_gi: .: (0.000504) test_keywords: .: (0.000592) test_locus: .: (0.000382) test_nid: .: (0.000548) test_organism: .: (0.000629) test_origin: .: (0.000434) test_references: .: (0.001982) test_segment: .: (0.000517) test_source: .: (0.000844) test_taxonomy: .: (0.000535) test_version: .: (0.000494) test_versions: .: (0.000496) Bio::TestAA: test_13: .: (0.000621) test_1n: .: (0.000303) test_name2one: .: (0.000444) test_name2three: .: (0.000370) test_one2name: .: (0.000331) test_one2three: .: (0.000642) test_three2name: .: (0.000313) test_three2one: .: (0.000378) test_to_1_1: .: (0.000280) test_to_1_3: .: (0.000397) test_to_1_name: .: (0.000357) test_to_3_1: .: (0.000293) test_to_3_3: .: (0.000278) test_to_3_name: .: (0.000416) test_to_re: .: (0.000383) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000555) Bio::TestAAindex: test_api: .: (0.000449) test_auto_aax1: .: (0.000701) test_auto_aax2: .: (0.000693) Bio::TestAAindex1: test_author: .: (0.001013) test_comment: .: (0.000642) test_correlation_coefficient: .: (0.001121) test_dblinks: .: (0.000608) test_definition: .: (0.000617) test_entry_id: .: (0.000598) test_index: .: (0.000823) test_journal: .: (0.000720) test_title: .: (0.001229) Bio::TestAAindex2: test_access_A_R: .: (0.002190) test_access_R_A: .: (0.001708) test_author: .: (0.000752) test_cols: .: (0.000679) test_comment: .: (0.000634) test_dblinks: .: (0.000607) test_definition: .: (0.000646) test_entry_id: .: (0.000616) test_journal: .: (0.000749) test_matrix: .: (0.002358) test_matrix_1_2: .: (0.001913) test_matrix_2_2: .: (0.001753) test_matrix_A_R: .: (0.002345) test_matrix_R_A: .: (0.001870) test_matrix_determinant: .: (0.025480) test_matrix_rank: .: (0.015665) test_matrix_transpose: .: (0.003611) test_rows: .: (0.000669) test_title: .: (0.000646) Bio::TestAAindexConstant: test_delimiter: .: (0.000647) test_tagsize: .: (0.000307) Bio::TestAbif: test_complement: .: (0.021368) test_seq: .: (0.021282) test_to_biosequence: .: (0.021701) Bio::TestActsLikeMap: test_mixin: .: (0.000822) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000922) Bio::TestActsLikeMarker: test_mixin: .: (0.000651) Bio::TestAlignment: test_add_seq_no_key: .: (0.000779) test_add_seq_using_seq_with_aaseq_method: .: (0.000882) test_add_seq_using_seq_with_definition_method: .: (0.000372) test_add_seq_using_seq_with_entry_id_method: .: (0.000578) test_add_seq_using_seq_with_naseq_method: .: (0.000445) test_add_seq_using_seq_with_seq_method: .: (0.000416) test_consensus_iupac_gap_modes: .: (0.001199) test_consensus_iupac_missing_char: .: (0.000575) test_consensus_iupac_missing_char_option: .: (0.000712) test_consensus_iupac_no_gaps: .: (0.000782) test_consensus_iupac_of_ambiguous_bases: .: (0.001370) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.089169) test_consensus_opt_gap_mode: .: (0.002174) test_consensus_opt_missing_char: .: (0.000792) test_consensus_string_no_gaps: .: (0.000773) test_consensus_threshold_four_sequences: .: (0.001160) test_consensus_threshold_two_sequences: .: (0.001802) test_convert_match: .: (0.000749) test_convert_unmatch: .: (0.000608) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000539) test_convert_unmatch_different_match_char: .: (0.000478) test_convert_unmatch_multiple_sequences: .: (0.000674) test_default_gap_char: .: (0.000320) test_default_gap_regexp_matches_default_gap_char: .: (0.000350) test_default_missing_char: .: (0.000312) test_each_site_equal_length: .: (0.000790) test_each_site_unequal_length: .: (0.000528) test_equals: .: (0.000621) test_match_line_protein: .: (0.001338) test_normalizebang_extends_sequences_with_gaps: .: (0.000528) test_seq_length_is_max_seq_length: .: (0.000366) test_seq_length_when_one_sequence: .: (0.000333) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000332) test_seqclass_when_seqclass_set: .: (0.000374) test_seqclass_when_sequence_used: .: (0.000328) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000885) test_set_and_get_gap_char: .: (0.000334) test_store_cannot_override_key: .: (0.000350) test_store_with_default_keys_and_user_defined_keys: .: (0.000391) test_store_with_nil_key_uses_next_number_for_key: .: (0.000362) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000697) test_alignment_concat: .: (0.000451) test_alignment_length: .: (0.000319) test_alignment_lstrip!: .: (0.000515) test_alignment_lstrip_nil: .: (0.000394) test_alignment_normalize!: .: (0.000336) test_alignment_rstrip!: .: (0.000560) test_alignment_rstrip_nil: .: (0.000368) test_alignment_site: .: (0.000499) test_alignment_slice: .: (0.000283) test_alignment_strip!: .: (0.000584) test_alignment_strip_nil: .: (0.000330) test_alignment_subseq: .: (0.000348) test_alignment_window: .: (0.000269) test_collect_each_site: .: (0.000352) test_consensus_each_site_default: .: (0.000402) test_consensus_each_site_gap_mode_1: .: (0.000578) test_consensus_each_site_gap_mode_minus1: .: (0.000549) test_consensus_iupac: .: (0.001454) test_consensus_string_default: .: (0.000494) test_consensus_string_half: .: (0.000445) test_convert_match: .: (0.000417) test_convert_unmatch: .: (0.000285) test_each_seq: .: (0.000299) test_each_site: .: (0.000484) test_each_site_step: .: (0.000357) test_each_window: .: (0.000463) test_match_line: .: (0.002746) test_match_line_amino: .: (0.003959) test_match_line_nuc: .: (0.001124) test_private_alignment_site: .: (0.000392) test_remove_all_gaps!: .: (0.000495) test_seqclass: .: (0.000339) test_seqclass=: .: (0.000410) test_seqclass_default: .: (0.000278) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.009081) test_determine_seq_method: .: (0.005446) test_entries: .: (0.000977) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000795) test_avoid_same_name_numbering: .: (0.000545) test_clustal_have_same_name_true: .: (0.000897) test_have_same_name_false: .: (0.000372) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000609) test_gap_char_default: .: (0.000333) test_gap_char_never_nil: .: (0.000323) test_gap_regexp: .: (0.000388) test_gap_regexp=: .: (0.000360) test_gap_regexp_never_nil: .: (0.000332) test_get_all_property_default: .: (0.000334) test_get_all_property_nodefault: .: (0.000373) test_is_gap_default_false: .: (0.000329) test_is_gap_default_true: .: (0.000341) test_is_gap_nodefault_false: .: (0.000352) test_is_gap_nodefault_true: .: (0.000712) test_missing_char=: .: (0.000344) test_missing_char_default: .: (0.000323) test_missing_char_never_nil: .: (0.000305) test_seqclass=: .: (0.000345) test_seqclass_default: .: (0.000313) test_seqclass_never_nil: .: (0.000303) test_set_all_property: .: (0.000338) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.001737) test_consensus_string_50percent: .: (0.000395) test_consensus_string_50percent_nil: .: (0.000344) test_consensus_string_default: .: (0.000276) test_consensus_string_default_nil: .: (0.000392) test_has_gap_false: .: (0.000313) test_has_gap_true: .: (0.000273) test_match_line_amino_100percent: .: (0.000396) test_match_line_amino_missing: .: (0.000582) test_match_line_amino_strong: .: (0.000419) test_match_line_amino_weak: .: (0.000483) test_match_line_nuc_100percent: .: (0.000414) test_match_line_nuc_missing: .: (0.000358) test_remove_gaps!: .: (0.000267) test_remove_gaps_bang_not_removed: .: (0.000220) Bio::TestAtomFinder: test_atoms: .: (0.060454) test_each_atom: .: (0.000741) test_find_atom: .: (0.000647) Bio::TestBioFastaDefline: test_acc_version: .: (0.001345) test_accession: .: (0.001272) test_accessions: .: (0.001263) test_description: .: (0.001072) test_descriptions: .: (0.001034) test_entry_id: .: (0.001127) test_get: .: (0.001528) test_get_all_by_type: .: (0.000846) test_get_by_type: .: (0.000975) test_gi: .: (0.000821) test_id_strings: .: (0.002158) test_locus: .: (0.000876) test_method_missing: .: (0.001059) test_to_s: .: (0.000992) test_words: .: (0.002366) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.002240) test_goid2term: .: (0.001015) test_parse_goids: .: (0.001950) Bio::TestBioGenBank: test_basecount: .: (0.001011) test_circular: .: (0.000733) test_classification: .: (0.000859) test_date: .: (0.000722) test_date_modified: .: (0.001765) test_division: .: (0.000707) test_each_cds_feature: .: (0.003099) test_each_cds_qualifiers: .: (0.002227) test_each_gene: .: (0.002219) test_entry_id: .: (0.000921) test_length: .: (0.000723) test_locus_circular: .: (0.000841) test_locus_class: .: (0.000811) test_locus_date: .: (0.000804) test_locus_division: .: (0.000822) test_locus_entry_id: .: (0.000836) test_locus_length: .: (0.000792) test_locus_natype: .: (0.000831) test_locus_strand: .: (0.001401) test_natype: .: (0.000711) test_seq: .: (0.000888) test_seq_len: .: (0.000823) test_strand: .: (0.000720) test_strandedness: .: (0.000735) test_to_biosequence: .: (0.006071) Bio::TestBioGenPept: test_circular: .: (0.001044) test_date: .: (0.000617) test_dbsource: .: (0.001195) test_division: .: (0.000606) test_entry_id: .: (0.000623) test_length: .: (0.000643) test_locus: .: (0.000630) test_seq: .: (0.000671) test_seq_len: .: (0.000642) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.001188) test_aaseq: .: (0.000868) test_chromosome: .: (0.001623) test_codon_usage: .: (0.001115) test_cu_list: .: (0.000687) test_dblinks_as_hash: .: (0.000805) test_dblinks_as_strings: .: (0.000729) test_definition: .: (0.000763) test_division: .: (0.000699) test_eclinks: .: (0.000797) test_entry: .: (0.001538) test_entry_id: .: (0.000665) test_gbposition: .: (0.000753) test_gene: .: (0.000689) test_genes: .: (0.000706) test_keggclass: .: (0.000753) test_keggclasses: .: (0.000761) test_locations: .: (0.001004) test_motifs_as_hash: .: (0.000928) test_motifs_as_strings: .: (0.000648) test_name: .: (0.000652) test_names_as_array: .: (0.000800) test_new: .: (0.000734) test_ntlen: .: (0.000908) test_ntseq: .: (0.000994) test_organism: .: (0.000842) test_orthologs_as_hash: .: (0.000692) test_orthologs_as_strings: .: (0.000671) test_pathway: .: (0.000814) test_pathway_after_pathways_as_strings: .: (0.001155) test_pathway_before_pathways_as_strings: .: (0.001001) test_pathways_as_hash: .: (0.000994) test_pathways_as_strings: .: (0.000674) test_position: .: (0.000774) test_structure: .: (0.000758) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.003980) test_comment: .: (0.001361) test_data_source: .: (0.001246) test_definition: .: (0.001204) test_disease: .: (0.001106) test_entry_id: .: (0.001302) test_lineage: .: (0.001364) test_nalen: .: (0.001135) test_name: .: (0.001341) test_new: .: (0.001329) test_num_gene: .: (0.001219) test_num_rna: .: (0.001185) test_original_databases: .: (0.001149) test_original_db: .: (0.001236) test_plasmids: .: (0.001097) test_references: .: (0.007415) test_statistics: .: (0.001164) test_taxid: .: (0.001198) test_taxonomy: .: (0.001267) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001409) test_comment: .: (0.000827) test_data_source: .: (0.000701) test_definition: .: (0.000772) test_disease: .: (0.000735) test_entry_id: .: (0.000714) test_lineage: .: (0.000916) test_nalen: .: (0.000684) test_name: .: (0.000747) test_new: .: (0.000721) test_num_gene: .: (0.000754) test_num_rna: .: (0.000668) test_original_databases: .: (0.000734) test_original_db: .: (0.000734) test_plasmids: .: (0.001032) test_references: .: (0.001050) test_statistics: .: (0.000742) test_taxid: .: (0.000775) test_taxonomy: .: (0.000764) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.001088) test_compounds_as_strings: .: (0.000641) test_dblinks_as_hash: .: (0.000571) test_dblinks_as_strings: .: (0.000607) test_description: .: (0.000638) test_diseases_as_hash: .: (0.000566) test_diseases_as_strings: .: (0.000591) test_entry_id: .: (0.000687) test_enzymes_as_strings: .: (0.000614) test_genes_as_hash: .: (0.000599) test_genes_as_strings: .: (0.000550) test_keggclass: .: (0.000704) test_ko_pathway: .: (0.000631) test_modules_as_hash: .: (0.000614) test_modules_as_strings: .: (0.000819) test_name: .: (0.000678) test_new: .: (0.000687) test_organism: .: (0.000697) test_orthologs_as_hash: .: (0.000669) test_orthologs_as_strings: .: (0.000638) test_pathways_as_hash: .: (0.000620) test_pathways_as_strings: .: (0.000575) test_reactions_as_hash: .: (0.000673) test_reactions_as_strings: .: (0.000559) test_references: .: (0.000569) test_rel_pathways_as_hash: .: (0.000650) test_rel_pathways_as_strings: .: (0.000661) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.001592) test_compounds_as_strings: .: (0.000995) test_dblinks_as_hash: .: (0.000676) test_dblinks_as_strings: .: (0.000710) test_description: .: (0.000667) test_diseases_as_hash: .: (0.000748) test_diseases_as_strings: .: (0.000729) test_entry_id: .: (0.000667) test_enzymes_as_strings: .: (0.000686) test_genes_as_hash: .: (0.001069) test_genes_as_strings: .: (0.000949) test_keggclass: .: (0.000810) test_ko_pathway: .: (0.000929) test_modules_as_hash: .: (0.000722) test_modules_as_strings: .: (0.000772) test_name: .: (0.000726) test_new: .: (0.000713) test_organism: .: (0.000699) test_orthologs_as_hash: .: (0.000693) test_orthologs_as_strings: .: (0.000690) test_pathways_as_hash: .: (0.000669) test_pathways_as_strings: .: (0.000722) test_reactions_as_hash: .: (0.000642) test_reactions_as_strings: .: (0.000744) test_references: .: (0.000613) test_rel_pathways_as_hash: .: (0.000729) test_rel_pathways_as_strings: .: (0.000795) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.001081) test_compounds_as_strings: .: (0.000608) test_dblinks_as_hash: .: (0.000669) test_dblinks_as_strings: .: (0.000601) test_description: .: (0.000581) test_diseases_as_hash: .: (0.000530) test_diseases_as_strings: .: (0.000595) test_entry_id: .: (0.000609) test_enzymes_as_strings: .: (0.000532) test_genes_as_hash: .: (0.000560) test_genes_as_strings: .: (0.000538) test_keggclass: .: (0.000670) test_ko_pathway: .: (0.000590) test_modules_as_hash: .: (0.000528) test_modules_as_strings: .: (0.000642) test_name: .: (0.000618) test_new: .: (0.000672) test_organism: .: (0.000635) test_orthologs_as_hash: .: (0.000827) test_orthologs_as_strings: .: (0.000689) test_pathways_as_hash: .: (0.000620) test_pathways_as_strings: .: (0.000650) test_reactions_as_hash: .: (0.000611) test_reactions_as_strings: .: (0.000517) test_references: .: (0.000590) test_rel_pathways_as_hash: .: (0.000582) test_rel_pathways_as_strings: .: (0.000606) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000980) test_compounds_as_strings: .: (0.000713) test_dblinks_as_hash: .: (0.000772) test_dblinks_as_strings: .: (0.000743) test_description: .: (0.001038) test_diseases_as_hash: .: (0.000710) test_diseases_as_strings: .: (0.000603) test_entry_id: .: (0.000730) test_enzymes_as_strings: .: (0.000798) test_genes_as_hash: .: (0.000687) test_genes_as_strings: .: (0.000716) test_keggclass: .: (0.000732) test_ko_pathway: .: (0.000795) test_modules_as_hash: .: (0.000923) test_modules_as_strings: .: (0.000834) test_name: .: (0.000726) test_new: .: (0.000640) test_organism: .: (0.000718) test_orthologs_as_hash: .: (0.000707) test_orthologs_as_strings: .: (0.000651) test_pathways_as_hash: .: (0.000728) test_pathways_as_strings: .: (0.000784) test_reactions_as_hash: .: (0.000607) test_reactions_as_strings: .: (0.000630) test_references: .: (0.002251) test_rel_pathways_as_hash: .: (0.000864) test_rel_pathways_as_strings: .: (0.000671) Bio::TestBioKeggDRUG: test_activity: .: (0.001147) test_comment: .: (0.000793) test_dblinks_as_hash: .: (0.000961) test_dblinks_as_strings: .: (0.000916) test_entry_id: .: (0.000752) test_formula: .: (0.000771) test_kcf: .: (0.000714) test_mass: .: (0.000775) test_name: .: (0.000810) test_names: .: (0.000829) test_pathways_as_hash: .: (0.000883) test_pathways_as_strings: .: (0.000621) test_products: .: (0.000838) test_remark: .: (0.000799) Bio::TestBioKeggGLYCAN: test_comment: .: (0.001187) test_composition: .: (0.000925) test_compounds: .: (0.000803) test_dblinks_as_hash: .: (0.001361) test_dblinks_as_strings: .: (0.000824) test_entry_id: .: (0.000792) test_enzymes: .: (0.000915) test_kcf: .: (0.000638) test_keggclass: .: (0.000695) test_mass: .: (0.000820) test_name: .: (0.000751) test_orthologs_as_hash: .: (0.000970) test_orthologs_as_strings: .: (0.000861) test_pathways_as_hash: .: (0.000762) test_pathways_as_strings: .: (0.000770) test_reactions: .: (0.000988) test_references: .: (0.001109) test_remark: .: (0.000881) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.001177) test_composition: .: (0.000764) test_compounds: .: (0.000700) test_dblinks_as_hash: .: (0.000839) test_dblinks_as_strings: .: (0.000617) test_entry_id: .: (0.000641) test_enzymes: .: (0.000642) test_kcf: .: (0.000558) test_keggclass: .: (0.000648) test_mass: .: (0.000631) test_name: .: (0.000643) test_orthologs_as_hash: .: (0.000598) test_orthologs_as_strings: .: (0.000566) test_pathways_as_hash: .: (0.000592) test_pathways_as_strings: .: (0.000585) test_reactions: .: (0.000654) test_references: .: (0.000571) test_remark: .: (0.000652) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.001651) test_compounds_as_strings: .: (0.000953) test_dblinks_as_hash: .: (0.000710) test_dblinks_as_strings: .: (0.000667) test_description: .: (0.000774) test_diseases_as_hash: .: (0.000795) test_diseases_as_strings: .: (0.000765) test_entry_id: .: (0.000746) test_enzymes_as_strings: .: (0.000763) test_genes_as_hash: .: (0.000659) test_genes_as_strings: .: (0.000681) test_keggclass: .: (0.000806) test_ko_pathway: .: (0.000902) test_modules_as_hash: .: (0.000967) test_modules_as_strings: .: (0.000908) test_name: .: (0.000722) test_new: .: (0.000796) test_organism: .: (0.000724) test_orthologs_as_hash: .: (0.000658) test_orthologs_as_strings: .: (0.000701) test_pathways_as_hash: .: (0.000750) test_pathways_as_strings: .: (0.000853) test_reactions_as_hash: .: (0.001602) test_reactions_as_strings: .: (0.001126) test_references: .: (0.001664) test_rel_pathways_as_hash: .: (0.001261) test_rel_pathways_as_strings: .: (0.001001) Bio::TestBioLITDB: test_author: .: (0.001053) test_entry_id: .: (0.000653) test_field: .: (0.000615) test_journal: .: (0.000651) test_keyword: .: (0.000783) test_reference: .: (0.001093) test_title: .: (0.000668) test_volume: .: (0.000700) Bio::TestBioNBRF: test_aalen: .: (0.000854) test_aaseq: .: (0.000500) test_entry: .: (0.000459) test_length: .: (0.014180) test_nalen: .: (0.000775) test_naseq: .: (0.000607) test_seq: .: (0.000512) test_seq_class: .: (0.000497) test_to_nbrf: .: (0.000567) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000953) test_to_newick_format_leaf: .: (0.000877) test_to_newick_format_leaf_NHX: .: (0.000641) Bio::TestBl2seqReport: test_db_len: .: (0.002760) test_db_num: .: (0.001437) test_new: .: (0.000862) test_undefed_methods: .: (0.002973) test_undefed_methods_for_iteration: .: (0.002829) Bio::TestBl2seqReportConstants: test_rs: .: (0.001094) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.001179) test_hits: .: (0.000907) Bio::TestBlast: test_blast_reports_format0: .: (0.015107) test_blast_reports_format0_with_block: .: (0.002738) test_blast_reports_format7: .: (0.042954) test_blast_reports_format7_with_block: .: (0.040763) test_blast_reports_format7_with_parser: .: (0.038449) test_blast_reports_format7_with_parser_with_block: .: (0.039724) test_blast_reports_format8: .: (0.002576) test_blast_reports_format8_with_block: .: (0.001341) test_blast_reports_format8_with_parser: .: (0.000809) test_blast_reports_format8_with_parser_with_block: .: (0.000708) test_blast_reports_xml: .: (0.038165) test_blast_reports_xml_with_block: .: (0.048837) test_blastll: .: (0.000623) test_db: .: (0.000483) test_exec_genomenet: .: (0.000424) test_exec_local: .: (0.000418) test_exec_ncbi: .: (0.000452) test_filter: .: (0.000459) test_format: .: (0.000532) test_make_command_line: .: (0.001632) test_make_command_line_2: .: (0.001458) test_matrix: .: (0.000477) test_new: .: (0.000776) test_new_opt_string: .: (0.000758) test_option: .: (0.000563) test_option_set: .: (0.000764) test_option_set_m0: .: (0.000733) test_options: .: (0.000749) test_output: .: (0.000475) test_parse_result: .: (0.039489) test_parser: .: (0.000575) test_program: .: (0.000496) test_query: .: (0.000437) test_self_local: .: (0.000905) test_self_remote: .: (0.005063) test_server: .: (0.000585) Bio::TestBlastNCBIOptions: test_add_options: .: (0.001091) test_delete: .: (0.001134) test_equal_equal: .: (0.001140) test_get: .: (0.001374) test_make_command_line_options: .: (0.000950) test_normalize!: .: (0.000663) test_parse: .: (0.000689) test_set: .: (0.001522) Bio::TestBlastReport: test_db: .: (0.041970) test_db_len: .: (0.042421) test_db_num: .: (0.043400) test_each_hit: .: (0.049901) test_each_iteration: .: (0.044603) test_eff_space: .: (0.043246) test_entrez_query: .: (0.042087) test_entropy: .: (0.037390) test_expect: .: (0.037960) test_filter: .: (0.040765) test_gap_extend: .: (0.040564) test_gap_open: .: (0.042979) test_hits: .: (0.039446) test_hsp_len: .: (0.037600) test_inclusion: .: (0.040951) test_iterations: .: (0.039787) test_kappa: .: (0.039993) test_lambda: .: (0.038799) test_matrix: .: (0.042085) test_message: .: (0.042599) test_parameters: .: (0.042678) test_pattern: .: (0.037651) test_program: .: (0.040711) test_query_def: .: (0.043127) test_query_id: .: (0.040330) test_query_len: .: (0.037306) test_reference: .: (0.042406) test_sc_match: .: (0.040012) test_sc_mismatch: .: (0.041558) test_statistics: .: (0.043565) test_version: .: (0.041294) Bio::TestBlastReportDefault: test_db: .: (0.001945) test_db_len: .: (0.005923) test_db_num: .: (0.001226) test_each_hit: .: (0.001130) test_each_iteration: .: (0.001003) test_eff_space: .: (0.001316) test_entropy: .: (0.008054) test_expect: .: (0.001331) test_gap_extend: .: (0.001281) test_gap_open: .: (0.001295) test_gapped_entropy: .: (0.008002) test_gapped_kappa: .: (0.001127) test_gapped_lambda: .: (0.001291) test_hits: .: (0.001152) test_iterations: .: (0.001032) test_kappa: .: (0.007913) test_lambda: .: (0.001156) test_matrix: .: (0.001318) test_message: .: (0.000983) test_pattern: .: (0.001039) test_program: .: (0.008238) test_query_def: .: (0.001152) test_query_len: .: (0.001030) test_reference: .: (0.001130) test_sc_match: .: (0.001257) test_sc_mismatch: .: (0.005426) test_version: .: (0.001045) Bio::TestBlastReportHit: test_Hit_accession: .: (0.112391) test_Hit_bit_score: .: (0.043830) test_Hit_definition: .: (0.043415) test_Hit_evalue: .: (0.043197) test_Hit_hit_id: .: (0.045751) test_Hit_hsps: .: (0.041081) test_Hit_identity: .: (0.039438) test_Hit_lap_at: .: (0.047195) test_Hit_len: .: (0.042755) test_Hit_midline: .: (0.038344) test_Hit_num: .: (0.041436) test_Hit_overlap: .: (0.044886) test_Hit_query_def: .: (0.048831) test_Hit_query_end: .: (0.048379) test_Hit_query_id: .: (0.045679) test_Hit_query_len: .: (0.046348) test_Hit_query_seq: .: (0.044480) test_Hit_query_start: .: (0.045702) test_Hit_taeget_def: .: (0.044696) test_Hit_target_end: .: (0.044439) test_Hit_target_id: .: (0.048889) test_Hit_target_len: .: (0.044085) test_Hit_target_seq: .: (0.046288) test_Hit_target_start: .: (0.046636) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.002370) test_Hit_definition: .: (0.001217) test_Hit_evalue: .: (0.001180) test_Hit_hsps: .: (0.001181) test_Hit_identity: .: (0.001289) test_Hit_lap_at: .: (0.001910) test_Hit_len: .: (0.001279) test_Hit_midline: .: (0.002200) test_Hit_overlap: .: (0.001221) test_Hit_query_end: .: (0.001868) test_Hit_query_seq: .: (0.001777) test_Hit_query_start: .: (0.001716) test_Hit_taeget_def: .: (0.001349) test_Hit_target_end: .: (0.001944) test_Hit_target_id: .: (0.001299) test_Hit_target_len: .: (0.001083) test_Hit_target_seq: .: (0.001540) test_Hit_target_start: .: (0.001605) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.116963) test_Hit_bit_score: .: (0.114778) test_Hit_definition: .: (0.116185) test_Hit_evalue: .: (0.140934) test_Hit_hit_id: .: (0.137634) test_Hit_hsps: .: (0.136675) test_Hit_identity: .: (0.136905) test_Hit_lap_at: .: (0.139139) test_Hit_len: .: (0.133435) test_Hit_midline: .: (0.139480) test_Hit_num: .: (0.136026) test_Hit_overlap: .: (0.139672) test_Hit_query_def: .: (0.133913) test_Hit_query_end: .: (0.142321) test_Hit_query_id: .: (0.123263) test_Hit_query_len: .: (0.119398) test_Hit_query_seq: .: (0.120357) test_Hit_query_start: .: (0.120052) test_Hit_taeget_def: .: (0.125859) test_Hit_target_end: .: (0.131688) test_Hit_target_id: .: (0.126472) test_Hit_target_len: .: (0.122712) test_Hit_target_seq: .: (0.117006) test_Hit_target_start: .: (0.123633) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.121847) test_Hit_bit_score: .: (0.130272) test_Hit_definition: .: (0.127093) test_Hit_evalue: .: (0.142346) test_Hit_hit_id: .: (0.138222) test_Hit_hsps: .: (0.141681) test_Hit_identity: .: (0.143944) test_Hit_lap_at: .: (0.131074) test_Hit_len: .: (0.145597) test_Hit_midline: .: (0.124272) test_Hit_num: .: (0.124597) test_Hit_overlap: .: (0.130075) test_Hit_query_def: .: (0.144195) test_Hit_query_end: .: (0.135163) test_Hit_query_id: .: (0.135928) test_Hit_query_len: .: (0.138643) test_Hit_query_seq: .: (0.143590) test_Hit_query_start: .: (0.127969) test_Hit_taeget_def: .: (0.128293) test_Hit_target_end: .: (0.124625) test_Hit_target_id: .: (0.138309) test_Hit_target_len: .: (0.134236) test_Hit_target_seq: .: (0.139671) test_Hit_target_start: .: (0.134118) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.045249) test_Hit_bit_score: .: (0.047172) test_Hit_definition: .: (0.045455) test_Hit_evalue: .: (0.046578) test_Hit_hit_id: .: (0.046155) test_Hit_hsps: .: (0.044782) test_Hit_identity: .: (0.045527) test_Hit_lap_at: .: (0.047501) test_Hit_len: .: (0.049366) test_Hit_midline: .: (0.040617) test_Hit_num: .: (0.040799) test_Hit_overlap: .: (0.038629) test_Hit_query_def: .: (0.040062) test_Hit_query_end: .: (0.041340) test_Hit_query_id: .: (0.045025) test_Hit_query_len: .: (0.043321) test_Hit_query_seq: .: (0.039893) test_Hit_query_start: .: (0.042911) test_Hit_taeget_def: .: (0.041600) test_Hit_target_end: .: (0.042928) test_Hit_target_id: .: (0.046447) test_Hit_target_len: .: (0.050230) test_Hit_target_seq: .: (0.045070) test_Hit_target_start: .: (0.040281) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.001075) test_Hit_bit_score: .: (0.000843) test_Hit_definition: .: (0.000571) test_Hit_evalue: .: (0.000464) test_Hit_hit_id: .: (0.000540) test_Hit_hsps: .: (0.000487) test_Hit_identity: .: (0.000485) test_Hit_lap_at: .: (0.000502) test_Hit_len: .: (0.000474) test_Hit_midline: .: (0.000501) test_Hit_num: .: (0.000548) test_Hit_overlap: .: (0.000507) test_Hit_query_def: .: (0.000610) test_Hit_query_end: .: (0.000547) test_Hit_query_id: .: (0.000535) test_Hit_query_len: .: (0.000839) test_Hit_query_seq: .: (0.000598) test_Hit_query_start: .: (0.000556) test_Hit_taeget_def: .: (0.000513) test_Hit_target_end: .: (0.000482) test_Hit_target_id: .: (0.000475) test_Hit_target_len: .: (0.000510) test_Hit_target_seq: .: (0.000467) test_Hit_target_start: .: (0.000473) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.043110) test_Hsp_bit_score: .: (0.041031) test_Hsp_density: .: (0.040748) test_Hsp_evalue: .: (0.046033) test_Hsp_gaps: .: (0.047341) test_Hsp_hit_frame: .: (0.047713) test_Hsp_hit_from: .: (0.045411) test_Hsp_hit_to: .: (0.038620) test_Hsp_hseq: .: (0.039982) test_Hsp_identity: .: (0.040707) test_Hsp_midline: .: (0.042466) test_Hsp_mismatch_count: .: (0.042247) test_Hsp_num: .: (0.038903) test_Hsp_pattern_from: .: (0.041108) test_Hsp_pattern_to: .: (0.039115) test_Hsp_percent_identity: .: (0.046637) test_Hsp_positive: .: (0.049384) test_Hsp_qseq: .: (0.046535) test_Hsp_query_frame: .: (0.047265) test_Hsp_query_from: .: (0.038269) test_Hsp_query_to: .: (0.039598) test_Hsp_score: .: (0.039839) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.002122) test_Hsp_bit_score: .: (0.001203) test_Hsp_evalue: .: (0.001081) test_Hsp_gaps: .: (0.001489) test_Hsp_hit_frame: .: (0.001253) test_Hsp_hit_from: .: (0.002187) test_Hsp_hit_to: .: (0.001612) test_Hsp_hseq: .: (0.001864) test_Hsp_identity: .: (0.001150) test_Hsp_midline: .: (0.001679) test_Hsp_percent_identity: .: (0.001185) test_Hsp_positive: .: (0.001369) test_Hsp_qseq: .: (0.001631) test_Hsp_query_frame: .: (0.001074) test_Hsp_query_from: .: (0.001493) test_Hsp_query_to: .: (0.001569) test_Hsp_score: .: (0.001131) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.124194) test_Hsp_bit_score: .: (0.134646) test_Hsp_density: .: (0.138257) test_Hsp_evalue: .: (0.123469) test_Hsp_gaps: .: (0.134969) test_Hsp_hit_frame: .: (0.122271) test_Hsp_hit_from: .: (0.124255) test_Hsp_hit_to: .: (0.122081) test_Hsp_hseq: .: (0.122971) test_Hsp_identity: .: (0.123301) test_Hsp_midline: .: (0.128542) test_Hsp_mismatch_count: .: (0.120502) test_Hsp_num: .: (0.120981) test_Hsp_pattern_from: .: (0.114740) test_Hsp_pattern_to: .: (0.118279) test_Hsp_percent_identity: .: (0.121783) test_Hsp_positive: .: (0.124625) test_Hsp_qseq: .: (0.113086) test_Hsp_query_frame: .: (0.118841) test_Hsp_query_from: .: (0.113040) test_Hsp_query_to: .: (0.121118) test_Hsp_score: .: (0.119004) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.120081) test_Hsp_bit_score: .: (0.115741) test_Hsp_density: .: (0.120617) test_Hsp_evalue: .: (0.126563) test_Hsp_gaps: .: (0.123011) test_Hsp_hit_frame: .: (0.117474) test_Hsp_hit_from: .: (0.125951) test_Hsp_hit_to: .: (0.134128) test_Hsp_hseq: .: (0.125874) test_Hsp_identity: .: (0.115805) test_Hsp_midline: .: (0.131988) test_Hsp_mismatch_count: .: (0.121735) test_Hsp_num: .: (0.127206) test_Hsp_pattern_from: .: (0.115454) test_Hsp_pattern_to: .: (0.133131) test_Hsp_percent_identity: .: (0.123690) test_Hsp_positive: .: (0.142925) test_Hsp_qseq: .: (0.127529) test_Hsp_query_frame: .: (0.120991) test_Hsp_query_from: .: (0.120892) test_Hsp_query_to: .: (0.126358) test_Hsp_score: .: (0.128333) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.044668) test_Hsp_bit_score: .: (0.046872) test_Hsp_density: .: (0.042304) test_Hsp_evalue: .: (0.040831) test_Hsp_gaps: .: (0.037917) test_Hsp_hit_frame: .: (0.037887) test_Hsp_hit_from: .: (0.042124) test_Hsp_hit_to: .: (0.047562) test_Hsp_hseq: .: (0.044411) test_Hsp_identity: .: (0.042791) test_Hsp_midline: .: (0.044905) test_Hsp_mismatch_count: .: (0.043736) test_Hsp_num: .: (0.043470) test_Hsp_pattern_from: .: (0.046476) test_Hsp_pattern_to: .: (0.043475) test_Hsp_percent_identity: .: (0.044217) test_Hsp_positive: .: (0.042900) test_Hsp_qseq: .: (0.044076) test_Hsp_query_frame: .: (0.044324) test_Hsp_query_from: .: (0.045630) test_Hsp_query_to: .: (0.045331) test_Hsp_score: .: (0.043250) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.001137) test_Hsp_bit_score: .: (0.000524) test_Hsp_density: .: (0.000500) test_Hsp_evalue: .: (0.000520) test_Hsp_gaps: .: (0.000488) test_Hsp_hit_frame: .: (0.000498) test_Hsp_hit_from: .: (0.000557) test_Hsp_hit_to: .: (0.000495) test_Hsp_hseq: .: (0.000477) test_Hsp_identity: .: (0.000479) test_Hsp_midline: .: (0.000494) test_Hsp_mismatch_count: .: (0.000607) test_Hsp_num: .: (0.000481) test_Hsp_pattern_from: .: (0.000480) test_Hsp_pattern_to: .: (0.000491) test_Hsp_percent_identity: .: (0.000518) test_Hsp_positive: .: (0.000470) test_Hsp_qseq: .: (0.000445) test_Hsp_query_frame: .: (0.000471) test_Hsp_query_from: .: (0.000443) test_Hsp_query_to: .: (0.000446) test_Hsp_score: .: (0.000479) Bio::TestBlastReportIteration: test_hits: .: (0.038794) test_message: .: (0.039788) test_num: .: (0.042091) test_statistics: .: (0.042901) Bio::TestBlastReportIterationDefault: test_hits: .: (0.001745) test_message: .: (0.001067) test_num: .: (0.001067) Bio::TestBlastReportIterationMulti: test_each: .: (0.126880) test_hits: .: (0.184365) test_message: .: (0.160004) test_num: .: (0.121151) test_query_def: .: (0.120457) test_query_id: .: (0.123387) test_query_len: .: (0.123531) test_statistics: .: (0.116638) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.123747) test_hits: .: (0.128081) test_message: .: (0.119901) test_num: .: (0.122068) test_query_def: .: (0.119782) test_query_id: .: (0.121680) test_query_len: .: (0.125766) test_statistics: .: (0.123400) Bio::TestBlastReportIterationREXML: test_hits: .: (0.042589) test_message: .: (0.039749) test_num: .: (0.044494) test_statistics: .: (0.044855) Bio::TestBlastReportIterationTabular: test_hits: .: (0.001285) test_message: .: (0.000582) test_num: .: (0.000555) test_statistics: .: (0.001138) Bio::TestBlastReportMulti: test_db: .: (0.116877) test_db_len: .: (0.121001) test_db_num: .: (0.121531) test_each_hit: .: (0.127469) test_each_iteration: .: (0.126345) test_eff_space: .: (0.134644) test_entropy: .: (0.121006) test_expect: .: (0.125503) test_filter: .: (0.120427) test_gap_extend: .: (0.137036) test_gap_open: .: (0.121955) test_hits: .: (0.123156) test_hsp_len: .: (0.121144) test_iterations: .: (0.125954) test_kappa: .: (0.117862) test_lambda: .: (0.122677) test_matrix: .: (0.113879) test_message: .: (0.117006) test_parameters: .: (0.113859) test_pattern: .: (0.120880) test_program: .: (0.115426) test_query_def: .: (0.115972) test_query_id: .: (0.119642) test_query_len: .: (0.136221) test_reference: .: (0.132591) test_reports: .: (0.130371) test_statistics: .: (0.129346) test_version: .: (0.135245) Bio::TestBlastReportMultiREXML: test_db: .: (0.119658) test_db_len: .: (0.127017) test_db_num: .: (0.126419) test_each_hit: .: (0.118560) test_each_iteration: .: (0.114341) test_eff_space: .: (0.121321) test_entropy: .: (0.116159) test_expect: .: (0.122597) test_filter: .: (0.117904) test_gap_extend: .: (0.123089) test_gap_open: .: (0.116899) test_hits: .: (0.121814) test_hsp_len: .: (0.113739) test_iterations: .: (0.123256) test_kappa: .: (0.117350) test_lambda: .: (0.123727) test_matrix: .: (0.124336) test_message: .: (0.117003) test_parameters: .: (0.114574) test_pattern: .: (0.130290) test_program: .: (0.138867) test_query_def: .: (0.136766) test_query_id: .: (0.112462) test_query_len: .: (0.119966) test_reference: .: (0.121100) test_reports: .: (0.136449) test_statistics: .: (0.112038) test_version: .: (0.116180) Bio::TestBlastReportREXML: test_db: .: (0.039728) test_db_len: .: (0.037074) test_db_num: .: (0.041449) test_each_hit: .: (0.046832) test_each_iteration: .: (0.043280) test_eff_space: .: (0.041856) test_entrez_query: .: (0.042913) test_entropy: .: (0.043351) test_expect: .: (0.044846) test_filter: .: (0.047997) test_gap_extend: .: (0.044661) test_gap_open: .: (0.039720) test_hits: .: (0.039004) test_hsp_len: .: (0.038662) test_inclusion: .: (0.038011) test_iterations: .: (0.041273) test_kappa: .: (0.038290) test_lambda: .: (0.038414) test_matrix: .: (0.037554) test_message: .: (0.038624) test_parameters: .: (0.038247) test_pattern: .: (0.040597) test_program: .: (0.038912) test_query_def: .: (0.037965) test_query_id: .: (0.038834) test_query_len: .: (0.037321) test_reference: .: (0.038422) test_sc_match: .: (0.040061) test_sc_mismatch: .: (0.039327) test_statistics: .: (0.037588) test_version: .: (0.038919) Bio::TestBlastReportTabular: test_db: .: (0.001157) test_db_len: .: (0.000477) test_db_num: .: (0.000468) test_each_hit: .: (0.000510) test_each_iteration: .: (0.000474) test_eff_space: .: (0.000464) test_entrez_query: .: (0.000470) test_entropy: .: (0.000449) test_expect: .: (0.000439) test_filter: .: (0.000473) test_gap_extend: .: (0.000440) test_gap_open: .: (0.001004) test_hits: .: (0.000652) test_hsp_len: .: (0.000471) test_inclusion: .: (0.000491) test_iterations: .: (0.000464) test_kappa: .: (0.000461) test_lambda: .: (0.000510) test_matrix: .: (0.000448) test_message: .: (0.000458) test_parameters: .: (0.000458) test_pattern: .: (0.000474) test_program: .: (0.000467) test_query_def: .: (0.000470) test_query_id: .: (0.000465) test_query_len: .: (0.000440) test_reference: .: (0.000780) test_sc_match: .: (0.000560) test_sc_mismatch: .: (0.000469) test_statistics: .: (0.000517) test_version: .: (0.000477) Bio::TestChain: test_aaseq: .: (0.000940) test_addLigand: .: (0.000405) test_addResidue: .: (0.000397) test_atom_seq: .: (0.000398) test_comp: .: (0.000459) test_each: .: (0.000406) test_each_heterogen: .: (0.000375) test_each_residue: .: (0.000396) test_get_heterogen_by_id: .: (0.000368) test_get_residue_by_id: .: (0.000376) test_inspect: .: (0.000698) test_rehash: .: (0.000390) test_rehash_heterogens: .: (0.000356) test_rehash_residues: .: (0.000364) test_square_brace: .: (0.000451) test_to_s: .: (0.000424) Bio::TestChainFinder: test_chains: .: (0.000775) test_each_chain: .: (0.000425) test_find_chain: .: (0.000408) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.027580) test_header: .: (0.002380) test_match_line: .: (0.001754) test_sequence0: .: (0.001669) test_sequence1: .: (0.001538) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.026485) test_header: .: (0.003169) test_match_line: .: (0.002251) test_sequence0: .: (0.002198) test_sequence1: .: (0.002369) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.037995) test_header: .: (0.002338) test_match_line: .: (0.001850) test_sequence0: .: (0.001722) test_sequence1: .: (0.001570) Bio::TestCodonTable: test_Tables: .: (0.000657) test_accessor: .: (0.000428) test_definition: .: (0.000331) test_each: .: (0.000349) test_revtrans: .: (0.000512) test_self_accessor: .: (0.000342) test_self_copy: .: (0.002101) test_set_accessor: .: (0.272681) test_start: .: (0.000371) test_start_codon?: .: (0.000375) test_stop: .: (0.000315) test_stop_codon?: .: (0.000348) test_table: .: (0.000327) Bio::TestCodonTableConstants: test_Definitions: .: (0.000630) test_Starts: .: (0.000362) test_Tables: .: (0.000320) test_stops: .: (0.000338) Bio::TestColorScheme: test_buried: .: (0.002919) Bio::TestCommand: test_command_constants: .: (0.000642) test_escape_shell: .: (0.000480) test_escape_shell_unix: .: (0.000413) test_escape_shell_windows: .: (0.000418) test_make_cgi_params_by_array_of_array: .: (0.000928) test_make_cgi_params_by_array_of_hash: .: (0.001201) test_make_cgi_params_by_array_of_string: .: (0.000598) test_make_cgi_params_by_hash_in_string: .: (0.001282) test_make_cgi_params_by_hash_in_symbol: .: (0.001289) test_make_cgi_params_by_string: .: (0.000556) test_make_command_line: .: (0.000436) test_make_command_line_unix: .: (0.000392) test_make_command_line_windows: .: (0.000403) test_safe_command_line_array: .: (0.000905) test_safe_command_line_array_passthrough: .: (0.000406) Bio::TestContingencyTable: test_lite_example: .: (0.496170) Bio::TestDB: test_entry_id: .: (0.000738) test_exists: .: (0.000254) test_fetch: .: (0.000408) test_get: .: (0.000261) test_open: .: (0.000239) test_tags: .: (0.000224) Bio::TestDataType: test_const_like_method: .: (0.001550) test_pdb_achar: .: (0.000810) test_pdb_atom: .: (0.000576) test_pdb_character: .: (0.000585) test_pdb_date: .: (0.000612) test_pdb_idcode: .: (0.000564) test_pdb_integer: .: (0.000289) test_pdb_list: .: (0.000366) test_pdb_lstring: .: (0.000628) test_pdb_real: .: (0.000521) test_pdb_resudue_name: .: (0.000668) test_pdb_slist: .: (0.000363) test_pdb_string: .: (0.000611) test_pdb_stringrj: .: (0.000320) test_pdb_symop: .: (0.000579) test_specification_list: .: (0.000404) Bio::TestEMBL: test_ac: .: (0.001787) test_accession: .: (0.001044) test_cc: .: (0.000987) test_de: .: (0.000994) test_division: .: (0.001010) test_dr: .: (0.001034) test_dt: .: (0.001139) test_dt_created: .: (0.000937) test_dt_iterator: .: (0.000962) test_dt_updated: .: (0.000954) test_each_cds: .: (0.001535) test_each_gene: .: (0.001362) test_entry: .: (0.001157) test_fh: .: (0.000946) test_ft: .: (0.001379) test_ft_accessor: .: (0.001359) test_ft_iterator: .: (0.001419) test_id_line: .: (0.001027) test_id_line_data_class: .: (0.001171) test_id_line_division: .: (0.000998) test_id_line_entry_name: .: (0.001022) test_id_line_iterator: .: (0.001057) test_id_line_molecule_type: .: (0.001241) test_id_line_sequence_length: .: (0.001080) test_kw: .: (0.001109) test_molecule: .: (0.001049) test_oc: .: (0.001260) test_og: .: (0.001005) test_os: .: (0.001030) test_ref: .: (0.001303) test_references: .: (0.001841) test_seq: .: (0.001591) test_sequence_length: .: (0.001061) test_sq: .: (0.001035) test_sq_get: .: (0.001121) test_sv: .: (0.000970) test_version: .: (0.000990) Bio::TestEMBL89: test_ac: .: (0.001276) test_accession: .: (0.001041) test_cc: .: (0.001123) test_de: .: (0.001043) test_division: .: (0.001128) test_dr: .: (0.000950) test_dt: .: (0.000928) test_dt_created: .: (0.001115) test_dt_iterator: .: (0.000901) test_dt_updated: .: (0.000981) test_each_cds: .: (0.001420) test_each_gene: .: (0.001502) test_entry: .: (0.001133) test_fh: .: (0.000983) test_ft: .: (0.001536) test_ft_accessor: .: (0.001315) test_ft_iterator: .: (0.001431) test_id_line: .: (0.001154) test_id_line_data_class: .: (0.001222) test_id_line_division: .: (0.001145) test_id_line_entry_name: .: (0.001205) test_id_line_iterator: .: (0.001253) test_id_line_molecule_type: .: (0.001226) test_id_line_sequence_length: .: (0.001131) test_id_line_sequence_version: .: (0.001009) test_kw: .: (0.001035) test_molecule: .: (0.001295) test_oc: .: (0.001145) test_og: .: (0.000961) test_os: .: (0.001073) test_ref: .: (0.001426) test_references: .: (0.001650) test_seq: .: (0.001790) test_sequence_length: .: (0.001099) test_sq: .: (0.001265) test_sq_get: .: (0.000969) test_sv: .: (0.001131) test_version: .: (0.001090) Bio::TestEMBLAPI: test_ac: .: (0.000877) test_accessions: .: (0.000505) Bio::TestEMBLCommon: test_ac: .: (0.000739) test_accession: .: (0.000330) test_accessions: .: (0.000327) test_de: .: (0.000308) test_definition: .: (0.000318) test_description: .: (0.000320) test_dr: .: (0.000300) test_keywords: .: (0.000319) test_kw: .: (0.000290) test_oc: .: (0.000288) test_og: .: (0.000300) test_os: .: (0.000357) test_ref: .: (0.000303) test_references: .: (0.000297) Bio::TestEMBLDB: test_fetch: .: (0.000924) test_p_entry2hash: .: (0.000305) Bio::TestEMBLToBioSequence: test_classification: .: (0.010623) test_date_created: .: (0.001624) test_date_modified: .: (0.001374) test_definition: .: (0.001382) test_division: .: (0.001317) test_entry_id: .: (0.001252) test_entry_version: .: (0.001334) test_features: .: (0.001975) test_keywords: .: (0.001297) test_molecule_type: .: (0.001323) test_primary_accession: .: (0.001217) test_references: .: (0.002304) test_release_created: .: (0.001187) test_release_modified: .: (0.001226) test_secondary_accessions: .: (0.001392) test_sequence_version: .: (0.001345) test_species: .: (0.001321) test_topology: .: (0.001246) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.017023) test_date_created: .: (0.007783) test_date_modified: .: (0.007637) test_definition: .: (0.007887) test_division: .: (0.007749) test_entry_id: .: (0.008190) test_entry_version: .: (0.009015) test_features: .: (0.010208) test_keywords: .: (0.009981) test_molecule_type: .: (0.009827) test_primary_accession: .: (0.009588) test_references: .: (0.009271) test_release_created: .: (0.008304) test_release_modified: .: (0.008314) test_secondary_accessions: .: (0.009332) test_sequence_version: .: (0.008823) test_species: .: (0.008690) test_topology: .: (0.008109) Bio::TestFasta: test_db: .: (0.000655) test_format: .: (0.000310) test_format_arg_integer: .: (0.000364) test_format_arg_str: .: (0.000403) test_ktup: .: (0.000338) test_matrix: .: (0.000317) test_option: .: (0.000427) test_options: .: (0.000331) test_output: .: (0.000272) test_program: .: (0.000307) test_server: .: (0.000304) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.006817) test_accession: .: (0.000429) test_accessions: .: (0.000425) test_description: .: (0.000363) test_descriptions: .: (0.000370) test_entry_id: .: (0.000350) test_get_all_by_type: .: (0.000370) test_gi: .: (0.008329) test_id_strings: .: (0.000545) test_list_ids: .: (0.000352) test_locus: .: (0.000383) test_words: .: (0.000459) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000733) test_accession: .: (0.000393) test_accessions: .: (0.000395) test_description: .: (0.000456) test_descriptions: .: (0.000413) test_emb: .: (0.000505) test_entry_id: .: (0.000428) test_get_all_by_type: .: (0.000505) test_get_emb: .: (0.000469) test_gi: .: (0.000398) test_id_strings: .: (0.010204) test_list_ids: .: (0.000489) test_locus: .: (0.000434) test_words: .: (0.000502) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000726) test_accession: .: (0.000426) test_accessions: .: (0.000459) test_description: .: (0.000502) test_descriptions: .: (0.000440) test_entry_id: .: (0.000379) test_get_all_by_type: .: (0.000383) test_gi: .: (0.000405) test_id_strings: .: (0.000464) test_list_ids: .: (0.000335) test_locus: .: (0.000427) test_sp: .: (0.000416) test_words: .: (0.000438) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000766) test_accession: .: (0.000485) test_accessions: .: (0.007474) test_description: .: (0.000484) test_descriptions: .: (0.000505) test_entry_id: .: (0.000480) test_get_all_by_type: .: (0.000452) test_gi: .: (0.000437) test_id_strings: .: (0.005979) test_list_ids: .: (0.000543) test_locus: .: (0.000472) test_words: .: (0.000759) Bio::TestFastaDeflineSce: test_acc_version: .: (0.006923) test_accession: .: (0.000472) test_accessions: .: (0.000429) test_description: .: (0.000395) test_descriptions: .: (0.000393) test_entry_id: .: (0.000405) test_get_all_by_type: .: (0.000429) test_gi: .: (0.000377) test_id_strings: .: (0.000745) test_list_ids: .: (0.000472) test_locus: .: (0.000481) test_words: .: (0.000754) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000767) test_accession: .: (0.000415) test_accessions: .: (0.000405) test_description: .: (0.000347) test_descriptions: .: (0.000344) test_entry_id: .: (0.000316) test_get_all_by_type: .: (0.006179) test_gi: .: (0.000368) test_id_strings: .: (0.000401) test_list_ids: .: (0.000313) test_locus: .: (0.000309) test_words: .: (0.000423) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.005660) test_accession: .: (0.000393) test_accessions: .: (0.000364) test_description: .: (0.019005) test_descriptions: .: (0.000352) test_entry_id: .: (0.000339) test_get: .: (0.000395) test_get_all_by_type: .: (0.000336) test_id_strings: .: (0.000588) test_list_ids: .: (0.000376) test_locus: .: (0.000357) test_sp: .: (0.000369) test_words: .: (0.000529) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000667) test_accession: .: (0.000447) test_accessions: .: (0.001003) test_description: .: (0.000369) test_descriptions: .: (0.000332) test_entry_id: .: (0.000337) test_get: .: (0.000390) test_get_all_by_type: .: (0.000367) test_id_strings: .: (0.000628) test_list_ids: .: (0.000399) test_locus: .: (0.000356) test_tr: .: (0.000385) test_words: .: (0.000610) Bio::TestFastaFirstName: test_first_name1: .: (0.000636) test_first_name_multi_identifier: .: (0.000872) test_first_name_single_worded_defintion: .: (0.000321) test_no_definition: .: (0.000304) test_space_before_first_name: .: (0.000314) test_tabbed_defintion: .: (0.000330) Bio::TestFastaFormat: test_aalen: .: (0.000684) test_aaseq: .: (0.000369) test_acc_version: .: (0.000501) test_accession: .: (0.000501) test_accessions: .: (0.000461) test_data: .: (0.000329) test_definition: .: (0.000306) test_entry: .: (0.000368) test_entry_id: .: (0.000418) test_entry_overrun: .: (0.000378) test_first_name: .: (0.000344) test_gi: .: (0.000441) test_identifiers: .: (0.000484) test_length: .: (0.000349) test_query: .: (0.000453) test_seq: .: (0.000423) Bio::TestFastaFormatConst: test_delimiter: .: (0.000577) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000733) test_data: .: (0.000360) test_definition: .: (0.000320) test_entry: .: (0.000393) test_entry_id: .: (0.001196) test_first_name: .: (0.000370) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000712) test_naseq: .: (0.000353) test_naseq_class: .: (0.000375) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000682) Bio::TestFastaInitialize: test_new_1: .: (0.001492) test_option: .: (0.000345) test_option_backward_compatibility: .: (0.001145) Bio::TestFastaNumericFormat: test_arg: .: (0.000742) test_data: .: (0.000443) test_definition: .: (0.000321) test_each: .: (0.000448) test_entry: .: (0.000364) test_entry_id: .: (0.000345) test_length: .: (0.000427) test_to_biosequence: .: (0.002353) Bio::TestFastaQuery: test_query: .: (0.000560) test_self_local: .: (0.000260) test_self_parser: .: (0.000259) test_self_remote: .: (0.000212) Bio::TestFastacmd: test_database: .: (0.000762) test_fastacmd: .: (0.000301) test_methods: .: (0.000382) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.001707) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.001512) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.001419) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.001576) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.001655) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.001460) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.002139) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.001339) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001400) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001335) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.002066) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.001441) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.001448) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.003810) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.004306) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.001571) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.001326) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.001921) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.018886) test_error_probabilities_as_sanger: .: (0.018176) test_error_probabilities_as_solexa: .: (0.019620) test_quality_scores_as_illumina: .: (0.001532) test_quality_scores_as_sanger: .: (0.000939) test_quality_scores_as_solexa: .: (0.001837) test_validate_format: .: (0.001848) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.003889) test_entry_id: .: (0.003361) test_error_probabilities: .: (0.473756) test_nalen: .: (0.003166) test_naseq: .: (0.003232) test_quality_scores: .: (0.005387) test_quality_string: .: (0.002943) test_roundtrip: .: (0.479791) test_seq: .: (0.003604) test_sequence_string: .: (0.002883) test_to_biosequence: .: (0.461511) test_to_biosequence_and_output: .: (0.015601) test_to_s: .: (0.002927) test_validate_format: .: (0.003361) test_validate_format_with_array: .: (0.003547) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.001486) test_mask_20_with_empty_string: .: (0.001144) test_mask_20_with_longer_string: .: (0.001154) test_mask_20_with_x: .: (0.001069) test_mask_60: .: (0.001347) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.023612) test_error_probabilities_as_sanger: .: (0.023483) test_error_probabilities_as_solexa: .: (0.026935) test_quality_scores_as_illumina: .: (0.001182) test_quality_scores_as_sanger: .: (0.000929) test_quality_scores_as_solexa: .: (0.001696) test_validate_format: .: (0.001913) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.018109) test_error_probabilities_as_sanger: .: (0.017735) test_error_probabilities_as_solexa: .: (0.018104) test_quality_scores_as_illumina: .: (0.002060) test_quality_scores_as_sanger: .: (0.001168) test_quality_scores_as_solexa: .: (0.000914) test_validate_format: .: (0.001770) Bio::TestFeature: test_append: .: (0.001221) test_append_nil: .: (0.000360) test_assoc: .: (0.000353) test_each: .: (0.000300) test_feature: .: (0.000279) test_locations: .: (0.000488) test_new: .: (0.000294) test_position: .: (0.000278) test_qualifiers: .: (0.000323) Bio::TestFeatures: test_append: .: (0.000751) test_arg: .: (0.000354) test_each: .: (0.000359) test_features: .: (0.000354) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.002958) test_aaindex2: .: (0.000662) test_blast: .: (0.000565) test_blastxml: .: (0.001370) test_embl: .: (0.000706) test_embl_oldrelease: .: (0.000666) test_fastaformat: .: (0.001069) test_fastanumericformat: .: (0.000476) test_fastq: .: (0.000573) test_genbank: .: (0.000617) test_genpept: .: (0.000622) test_hmmer: .: (0.000681) test_maxml_cluster: .: (0.008824) test_maxml_sequence: .: (0.000422) test_medline: .: (0.000510) test_prosite: .: (0.006457) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.005687) test_transfac: .: (0.004520) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000790) test_auto_1arg_filename: .: (0.001142) test_auto_1arg_io: .: (0.000982) test_auto_1arg_io_with_block: .: (0.002025) test_auto_1arg_with_block: .: (0.001789) test_auto_2arg_filename_mode: .: (0.000978) test_auto_2arg_filename_mode_with_block: .: (0.002220) test_auto_3arg: .: (0.001004) test_auto_3arg_with_block: .: (0.001816) test_foreach: .: (0.001551) test_new_2arg_class: .: (0.000556) test_new_2arg_nil: .: (0.001263) test_open_0arg: .: (0.000504) test_open_1arg_class: .: (0.000395) test_open_1arg_filename: .: (0.000969) test_open_1arg_io: .: (0.000923) test_open_1arg_io_with_block: .: (0.001954) test_open_1arg_nil: .: (0.000393) test_open_1arg_with_block: .: (0.001812) test_open_2arg_autodetect: .: (0.001351) test_open_2arg_autodetect_io: .: (0.000915) test_open_2arg_autodetect_io_with_block: .: (0.001840) test_open_2arg_autodetect_with_block: .: (0.001823) test_open_2arg_class: .: (0.000555) test_open_2arg_class_io: .: (0.000948) test_open_2arg_class_io_with_block: .: (0.001633) test_open_2arg_class_with_block: .: (0.001445) test_open_2arg_filename_mode: .: (0.000969) test_open_2arg_filename_mode_with_block: .: (0.001871) test_open_3arg: .: (0.002366) test_open_3arg_with_block: .: (0.004630) test_open_4arg: .: (0.004388) test_to_a: .: (0.001508) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.001283) test_close: .: (0.000482) test_dbclass: .: (0.000479) test_dbclass_eq: .: (0.000569) test_dbclass_nil: .: (0.001125) test_each: .: (0.000876) test_each_entry: .: (0.001276) test_ended_pos: .: (0.000792) test_entry_pos_flag: .: (0.000581) test_entry_raw: .: (0.000999) test_eof?: .: (0.000917) test_next_entry: .: (0.001648) test_path: .: (0.000474) test_pos: .: (0.000658) test_raw: .: (0.001012) test_rewind: .: (0.000689) test_start_pos: .: (0.000761) test_start_pos_ended_pos_not_recorded: .: (0.000826) test_to_io: .: (0.000533) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000860) test_simpleformat2: .: (0.000599) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000636) test_eof_false_after_prefetch: .: (0.000961) test_eof_false_first: .: (0.000370) test_eof_true: .: (0.000650) test_getc: .: (0.000381) test_getc_after_prefetch: .: (0.000363) test_gets: .: (0.000371) test_gets_equal_prefetch_gets: .: (0.000446) test_gets_paragraph_mode: .: (0.000507) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000766) test_gets_paragraph_mode_within_buffer: .: (0.000962) test_gets_rs: .: (0.000508) test_gets_rs_equal_prefetch_gets: .: (0.000560) test_gets_rs_within_buffer: .: (0.000919) test_pos: .: (0.000457) test_pos=: .: (0.000711) test_prefetch_buffer: .: (0.000440) test_prefetch_gets: .: (0.000439) test_prefetch_gets_with_arg: .: (0.000473) test_rewind: .: (0.000391) test_skip_spaces: .: (0.000419) test_to_io: .: (0.000392) test_ungetc: .: (0.000396) test_ungetc_after_prefetch: .: (0.000422) test_ungets: .: (0.000501) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000713) test_self_open_file: .: (0.000478) test_self_open_file_with_block: .: (0.000527) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000924) test_parse_file_open_arg_int_perm: .: (0.000314) test_parse_file_open_arg_int_perm_opt: .: (0.000319) test_parse_file_open_arg_integer: .: (0.000299) test_parse_file_open_arg_nil: .: (0.000295) test_parse_file_open_arg_opt: .: (0.000460) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000356) test_parse_file_open_arg_str: .: (0.000326) test_parse_file_open_arg_str_opt: .: (0.000359) test_parse_file_open_arg_str_perm: .: (0.000337) test_parse_file_open_arg_str_perm_opt: .: (0.000337) test_parse_file_open_arg_str_with_enc: .: (0.000350) test_parse_file_open_arg_str_with_ext_enc: .: (0.000373) test_parse_file_open_mode_integer: .: (0.000295) test_parse_file_open_mode_nil: .: (0.000324) test_parse_file_open_mode_str: .: (0.000325) test_parse_file_open_mode_str_with_enc: .: (0.000733) test_parse_file_open_mode_str_with_ext_enc: .: (0.000354) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000627) test_entry: .: (0.000363) test_entry_ended_pos: .: (0.000345) test_entry_pos_flag: .: (0.000384) test_entry_start_pos: .: (0.000335) test_get_entry: .: (0.000457) test_rewind: .: (0.000357) test_skip_leader: .: (0.000374) test_stream: .: (0.000328) test_stream_pos: .: (0.000379) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000649) test_delimiter_overrun: .: (0.000651) test_entry: .: (0.000447) test_entry_ended_pos: .: (0.000398) test_entry_ended_pos_default_nil: .: (0.000424) test_entry_start_pos: .: (0.000399) test_entry_start_pos_default_nil: .: (0.000367) test_get_entry: .: (0.000688) test_get_parsed_entry: .: (0.000729) test_header: .: (0.000325) test_skip_leader: .: (0.000489) test_skip_leader_without_header: .: (0.000465) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.001192) test_entry_ended_pos: .: (0.000717) test_entry_start_pos: .: (0.000744) test_flag_to_fetch_header: .: (0.000635) test_get_entry: .: (0.000912) test_get_parsed_entry: .: (0.000919) test_rewind: .: (0.000855) test_skip_leader: .: (0.000440) Bio::TestGCGMsf: test_alignment: .: (0.002860) test_checksum: .: (0.000712) test_compcheck: .: (0.000729) test_date: .: (0.000710) test_description: .: (0.001249) test_entry_id: .: (0.000673) test_gap_length_weight: .: (0.000723) test_gap_weight: .: (0.000692) test_heading: .: (0.000697) test_length: .: (0.000661) test_seq_type: .: (0.001140) test_symbol_comparison_table: .: (0.000717) test_validate_checksum: .: (0.004497) Bio::TestGFF: test_record_class: .: (0.001439) test_records: .: (0.001047) Bio::TestGFF2: test_const_version: .: (0.001576) test_gff_version: .: (0.001243) test_metadata: .: (0.001747) test_metadata_size: .: (0.001209) test_records_size: .: (0.001141) test_to_s: .: (0.002522) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000721) test_attributes_case2: .: (0.000537) test_attributes_incompatible_backslash_semicolon: .: (0.000627) Bio::TestGFF2MetaData: test_data: .: (0.000606) test_directive: .: (0.000302) test_parse: .: (0.000372) Bio::TestGFF2Record: test_attribute: .: (0.001344) test_attribute_nonexistent: .: (0.000791) test_attributes: .: (0.000802) test_attributes_to_hash: .: (0.000828) test_comment_only?: .: (0.000711) test_delete_attribute: .: (0.001253) test_delete_attribute_multiple: .: (0.000879) test_delete_attribute_multiple2: .: (0.000976) test_delete_attribute_multiple_nil: .: (0.000849) test_delete_attribute_nil: .: (0.000868) test_delete_attribute_nonexistent: .: (0.000852) test_delete_attributes: .: (0.001441) test_delete_attributes_multiple: .: (0.000869) test_delete_attributes_nonexistent: .: (0.000860) test_end: .: (0.000754) test_eqeq: .: (0.002270) test_eqeq_false: .: (0.001657) test_feature: .: (0.000722) test_frame: .: (0.000780) test_get_attribute: .: (0.000961) test_get_attribute_nonexistent: .: (0.000746) test_get_attributes: .: (0.001691) test_get_attributes_nonexistent: .: (0.000696) test_replace_attributes: .: (0.000849) test_replace_attributes_multiple_multiple_over: .: (0.000860) test_replace_attributes_multiple_multiple_same: .: (0.001042) test_replace_attributes_multiple_multiple_two: .: (0.000864) test_replace_attributes_multiple_single: .: (0.001388) test_replace_attributes_nonexistent: .: (0.000904) test_replace_attributes_nonexistent_multiple: .: (0.000830) test_replace_attributes_single_multiple: .: (0.000828) test_score: .: (0.000769) test_self_parse: .: (0.001717) test_seqname: .: (0.001237) test_set_attribute: .: (0.000825) test_set_attribute_multiple: .: (0.001084) test_set_attribute_nonexistent: .: (0.000815) test_sort_attributes_by_tag!: .: (0.001044) test_sort_attributes_by_tag_bang_test2: .: (0.000999) test_sort_attributes_by_tag_bang_with_block: .: (0.000954) test_source: .: (0.001204) test_start: .: (0.000711) test_strand: .: (0.000784) test_to_s: .: (0.001110) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000663) test_comment_eq: .: (0.000335) test_comment_only?: .: (0.000340) test_comment_only_false: .: (0.000363) test_to_s: .: (0.000345) test_to_s_not_empty: .: (0.000514) Bio::TestGFF3: test_const_version: .: (0.002568) test_gff_version: .: (0.001482) test_records: .: (0.002382) test_sequence_regions: .: (0.001969) test_sequences: .: (0.001972) test_to_s: .: (0.003360) Bio::TestGFF3MetaData: test_data: .: (0.000592) test_directive: .: (0.000300) test_parse: .: (0.000349) Bio::TestGFF3Record: test_attributes: .: (0.001047) test_end: .: (0.001521) test_feature: .: (0.000698) test_frame: .: (0.000664) test_id: .: (0.000774) test_score: .: (0.000702) test_seqname: .: (0.000688) test_source: .: (0.001286) test_start: .: (0.000727) test_strand: .: (0.000663) test_to_s: .: (0.001086) test_to_s_attr_order_changed: .: (0.001336) Bio::TestGFF3RecordEscape: test_escape: .: (0.000738) test_escape_attribute: .: (0.000492) test_escape_seqid: .: (0.000501) test_unescape: .: (0.000563) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.001010) test_eqeq: .: (0.000675) test_new_from_sequences_na: .: (0.000749) test_new_from_sequences_na_aa: .: (0.001041) test_new_from_sequences_na_aa_boundary_gap: .: (0.002058) test_new_from_sequences_na_aa_example: .: (0.001018) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000934) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000882) test_process_sequences_na: .: (0.000737) test_process_sequences_na_aa: .: (0.000610) test_process_sequences_na_aa_reverse_frameshift: .: (0.000598) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000627) test_process_sequences_na_aa_tooshort: .: (0.001738) test_process_sequences_na_tooshort: .: (0.000736) test_to_s: .: (0.000619) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000829) test_attributes_one: .: (0.000451) test_attributes_with_escaping: .: (0.000465) test_id_multiple: .: (0.000718) test_id_multiple2: .: (0.001262) test_id_replace: .: (0.000516) test_id_set: .: (0.000536) test_initialize_9: .: (0.000289) test_phase: .: (0.000458) test_score: .: (0.000465) test_to_s_void: .: (0.000363) Bio::TestGFF3RecordTarget: test_end: .: (0.000714) test_parse: .: (0.000553) test_start: .: (0.001087) test_strand: .: (0.000416) test_target_id: .: (0.000438) test_to_s: .: (0.000755) Bio::TestGFF3SequenceRegion: test_end: .: (0.000756) test_parse: .: (0.000713) test_seqid: .: (0.000396) test_start: .: (0.000391) test_to_s: .: (0.000608) Bio::TestGFFRecord: test_attributes: .: (0.000742) test_comment: .: (0.000442) test_end: .: (0.000405) test_feature: .: (0.001128) test_frame: .: (0.000400) test_score: .: (0.000395) test_seqname: .: (0.000417) test_source: .: (0.000400) test_start: .: (0.000419) test_strand: .: (0.000391) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000632) Bio::TestGeneAssociation: test_aspect: .: (0.000736) test_assigned_by: .: (0.000392) test_date: .: (0.000423) test_db: .: (0.000421) test_db_object_id: .: (0.000404) test_db_object_name: .: (0.000404) test_db_object_symbol: .: (0.000375) test_db_object_synonym: .: (0.000378) test_db_object_type: .: (0.000390) test_db_reference: .: (0.000451) test_evidence: .: (0.000365) test_goid: .: (0.000400) test_parser: .: (0.001453) test_qualifier: .: (0.000423) test_taxon: .: (0.000407) test_to_str: .: (0.000402) test_with: .: (0.000356) Bio::TestGenscanReport: test_date_run: .: (0.003127) test_gccontent: .: (0.002057) test_genscan_version: .: (0.002589) test_isochore: .: (0.002122) test_length: .: (0.002116) test_matrix: .: (0.002778) test_predictions_size: .: (0.002076) test_query_name: .: (0.008374) test_time: .: (0.010354) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.010192) test_donor_score: .: (0.010422) test_exon_type: .: (0.002024) test_exon_type_long: .: (0.008725) test_first: .: (0.007713) test_initiation_score: .: (0.008763) test_last: .: (0.002210) test_number: .: (0.009489) test_p_value: .: (0.002143) test_phase: .: (0.008494) test_range: .: (0.007161) test_score: .: (0.002154) test_strand: .: (0.008728) test_t_score: .: (0.009117) test_termination_score: .: (0.009536) Bio::TestGenscanReportGene: test_aaseq: .: (0.029904) test_naseq: .: (0.002085) test_number: .: (0.002687) test_polyA: .: (0.002246) test_promoter: .: (0.002770) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.002611) test_reports_ary_contents: .: (0.001947) Bio::TestHMMERReportConstants: test_rs: .: (0.001282) Bio::TestHMMERReportHit: test_accession: .: (0.002131) test_append_hsp: .: (0.001712) test_bit_score: .: (0.001784) test_definition: .: (0.002202) test_description: .: (0.001918) test_each: .: (0.001888) test_each_hsp: .: (0.001919) test_entry_id: .: (0.002085) test_evalue: .: (0.001844) test_hit: .: (0.001774) test_hit_id: .: (0.001784) test_hsps: .: (0.002191) test_num: .: (0.001769) test_score: .: (0.001727) test_target_def: .: (0.001794) test_target_id: .: (0.002113) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.002089) test_each: .: (0.001739) test_each_hit: .: (0.002155) test_histogram: .: (0.001743) test_hits: .: (0.001716) test_hsps: .: (0.001720) test_parameter: .: (0.002187) test_program: .: (0.001879) test_query_info: .: (0.001767) test_statistical_detail: .: (0.001741) test_total_seq_searched: .: (0.002139) test_whole_seq_top_hits: .: (0.001713) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.002424) test_histogram: .: (0.002316) test_statistical_detail: .: (0.002079) test_total_seq_searched: .: (0.001888) test_whole_seq_top_hit: .: (0.002280) Bio::TestHMMERReportHsp: test_accession: .: (0.002625) test_bit_score: .: (0.001830) test_csline: .: (0.001803) test_domain: .: (0.002220) test_evalue: .: (0.001910) test_flatseq: .: (0.001733) test_hmm_f: .: (0.001861) test_hmm_t: .: (0.002096) test_hmmseq: .: (0.001939) test_hsp: .: (0.001964) test_midline: .: (0.002160) test_query_frame: .: (0.001944) test_query_from: .: (0.002144) test_query_seq: .: (0.001837) test_query_to: .: (0.001877) test_rfline: .: (0.002217) test_score: .: (0.001892) test_seq_f: .: (0.001963) test_seq_ft: .: (0.001852) test_seq_t: .: (0.002279) test_set_alignment: .: (0.001875) test_targat_to: .: (0.001843) test_target_frame: .: (0.001872) test_target_from: .: (0.001965) test_target_seq: .: (0.002223) Bio::TestHetatmFinder: test_each_hetatm: .: (0.001557) test_find_hetatm: .: (0.000838) test_hetatms: .: (0.001521) Bio::TestHeterogen: test_addAtom: .: (0.001095) test_each: .: (0.000721) test_each_hetatm: .: (0.000677) test_get_residue_id_from_atom: .: (0.000719) test_het_atom: .: (0.000539) test_iCode: .: (0.000961) test_inspect: .: (0.000680) test_resSeq: .: (0.000606) test_sort: .: (0.000642) test_square_bracket: .: (0.000595) test_to_s: .: (0.000855) test_update_resudue_id: .: (0.000563) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000766) test_find_heterogen: .: (0.000798) test_heterogens: .: (0.000527) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000867) test_match_description: .: (0.000509) test_match_evalue: .: (0.000566) test_match_ipr_description: .: (0.000512) test_match_ipr_id: .: (0.000493) test_match_match_end: .: (0.000494) test_match_match_start: .: (0.000514) test_match_method: .: (0.000949) test_matches_size: .: (0.000496) test_query_id: .: (0.000509) test_query_length: .: (0.000498) Bio::TestIprscanRawReport: test_entry_id: .: (0.007319) test_match_accession: .: (0.006652) test_match_crc64: .: (0.006215) test_match_date: .: (0.006082) test_match_description: .: (0.006469) test_match_evalue: .: (0.006709) test_match_go_terms: .: (0.007464) test_match_ipr_description: .: (0.006481) test_match_ipr_id: .: (0.014376) test_match_match_end: .: (0.007291) test_match_match_start: .: (0.007192) test_match_method: .: (0.007692) test_match_query_id: .: (0.006996) test_match_query_length: .: (0.007012) test_match_status: .: (0.006805) test_obj: .: (0.006907) test_query_id: .: (0.006727) test_query_length: .: (0.006565) test_self_reports_in_raw: .: (0.013438) Bio::TestIprscanReport: test_output_raw: .: (0.001920) test_to_raw: .: (0.001531) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.002279) test_match_accession: .: (0.001493) test_match_date: .: (0.001436) test_match_description: .: (0.001477) test_match_evalue: .: (0.001404) test_match_go_terms: .: (0.001958) test_match_ipr_description: .: (0.001420) test_match_ipr_id: .: (0.001442) test_match_match_end: .: (0.001548) test_match_match_start: .: (0.001970) test_match_method: .: (0.001565) test_match_status: .: (0.001463) test_matches_size: .: (0.001455) test_query_id: .: (0.001389) test_query_length: .: (0.001865) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.001993) test_to_hash_match?: .: (0.001893) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.004105) Bio::TestKeggCompound: test_comment: .: (0.001286) test_dblinks_as_hash: .: (0.001193) test_dblinks_as_strings: .: (0.001319) test_entry_id: .: (0.000968) test_enzymes: .: (0.001718) test_formula: .: (0.000821) test_kcf: .: (0.000840) test_mass: .: (0.000891) test_name: .: (0.001279) test_names: .: (0.001123) test_pathways_as_hash: .: (0.001576) test_pathways_as_strings: .: (0.001019) test_reactions: .: (0.001643) test_remark: .: (0.001362) test_rpairs: .: (0.000939) Bio::TestKeggEnzyme: test_all_reac: .: (0.001731) test_classes: .: (0.001239) test_cofactors: .: (0.001197) test_comment: .: (0.001313) test_dblinks_as_hash: .: (0.001741) test_dblinks_as_strings: .: (0.001308) test_diseases: .: (0.001126) test_entry: .: (0.001180) test_entry_id: .: (0.001292) test_genes: .: (0.047693) test_genes_as_hash: .: (0.041116) test_genes_as_strings: .: (0.012659) test_inhibitors: .: (0.001598) test_iubmb_reactions: .: (0.001634) test_kegg_reactions: .: (0.001637) test_motifs: .: (0.001416) test_name: .: (0.001751) test_names: .: (0.001941) test_obsolete?: .: (0.001491) test_orthologs_as_hash: .: (0.001550) test_orthologs_as_strings: .: (0.001439) test_pathways_as_hash: .: (0.001700) test_pathways_as_strings: .: (0.002595) test_products: .: (0.001548) test_reaction: .: (0.001631) test_structures: .: (0.002027) test_substrates: .: (0.001598) test_sysname: .: (0.001462) Bio::TestKeggGenesDblinks: test_data: .: (0.001743) test_dblinks_0: .: (0.000500) test_dblinks_1: .: (0.000463) test_dblinks_2: .: (0.000480) Bio::TestKeggGenesStructure: test_data: .: (0.000761) test_ids: .: (0.000619) test_ids_in_array: .: (0.000524) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.040411) test_graphics__size: .: (0.034064) test_id: .: (0.031275) test_link: .: (0.032367) test_name: .: (0.031827) test_reaction: .: (0.027709) test_type: .: (0.025011) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.026899) test_graphics__size: .: (0.023873) test_id: .: (0.024071) test_link: .: (0.023297) test_name: .: (0.022896) test_reaction: .: (0.023074) test_type: .: (0.024746) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.023615) test_category: .: (0.023278) test_entry_id: .: (0.023385) test_fgcolor=: .: (0.024358) test_height=: .: (0.024340) test_label=: .: (0.024814) test_shape=: .: (0.027575) test_width=: .: (0.024026) test_x=: .: (0.024182) test_y=: .: (0.023624) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.023005) test_graphics__size: .: (0.023544) test_id: .: (0.026045) test_link: .: (0.023095) test_name: .: (0.023832) test_reaction: .: (0.022980) test_type: .: (0.025388) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000781) test_graphics=: .: (0.000465) test_id=: .: (0.000444) test_link=: .: (0.000385) test_name=: .: (0.000404) test_reaction=: .: (0.000403) test_type=: .: (0.000396) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.001482) test_category=: .: (0.000560) test_entry_id=: .: (0.000532) test_fgcolor=: .: (0.000504) test_height=: .: (0.000475) test_label=: .: (0.000568) test_pathway=: .: (0.000455) test_shape=: .: (0.000466) test_width=: .: (0.000412) test_x=: .: (0.000403) test_y=: .: (0.000447) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.023350) test_coords: .: (0.028038) test_fgcolor: .: (0.023869) test_height: .: (0.024307) test_name: .: (0.024299) test_type: .: (0.022834) test_width: .: (0.026124) test_x: .: (0.025341) test_y: .: (0.025075) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.024562) test_coords: .: (0.023266) test_fgcolor: .: (0.024919) test_height: .: (0.025449) test_name: .: (0.027611) test_type: .: (0.023756) test_width: .: (0.023999) test_x: .: (0.023543) test_y: .: (0.022744) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000737) test_coords=: .: (0.000439) test_fgcolor=: .: (0.000512) test_height=: .: (0.000391) test_name=: .: (0.000405) test_type=: .: (0.000441) test_width=: .: (0.000386) test_x=: .: (0.000386) test_y=: .: (0.000467) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.025674) test_entries__size: .: (0.027746) test_image: .: (0.025214) test_link: .: (0.023337) test_name: .: (0.023591) test_number: .: (0.024636) test_org: .: (0.022889) test_reactions=: .: (0.025496) test_reactions__size: .: (0.027703) test_relations=: .: (0.026553) test_relations__size: .: (0.023829) test_title: .: (0.022992) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.051131) test_name: .: (0.064768) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000753) test_initialize_0: .: (0.000282) test_initialize_1: .: (0.000306) test_initialize_2: .: (0.000339) test_name=: .: (0.000397) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.023755) test_name: .: (0.023494) test_products: .: (0.022941) test_substrates: .: (0.024043) test_type: .: (0.025733) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.001315) test_name=: .: (0.000447) test_products=: .: (0.000449) test_substraces=: .: (0.000425) test_type=: .: (0.000431) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000752) test_entry_id=: .: (0.000523) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.024526) test_entry2: .: (0.026010) test_name: .: (0.023987) test_type: .: (0.023790) test_value: .: (0.108909) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000806) test_node1=: .: (0.011153) test_node2=: .: (0.000562) test_rel=: .: (0.000548) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000781) test_entry2=: .: (0.000570) test_name=: .: (0.000452) test_type=: .: (0.005669) test_value=: .: (0.000582) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.049708) test_name: .: (0.049606) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000935) test_initialize_0: .: (0.000363) test_initialize_1: .: (0.000395) test_initialize_2: .: (0.000383) test_name=: .: (0.000431) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.001018) test_initialize_0: .: (0.000361) test_initialize_1: .: (0.000379) test_initialize_2: .: (0.000378) test_name=: .: (0.000547) Bio::TestKeggModule: test_compounds: .: (0.001472) test_compounds_as_hash: .: (0.000906) test_compounds_as_strings: .: (0.000703) test_definition: .: (0.000717) test_entry_id: .: (0.000667) test_keggclass: .: (0.000679) test_name: .: (0.001125) test_new: .: (0.000624) test_orthologs: .: (0.000860) test_orthologs_as_array: .: (0.000961) test_orthologs_as_hash: .: (0.000843) test_orthologs_as_strings: .: (0.000971) test_pathways: .: (0.000731) test_pathways_as_hash: .: (0.000618) test_pathways_as_strings: .: (0.000593) test_reactions: .: (0.001198) test_reactions_as_hash: .: (0.000966) test_reactions_as_strings: .: (0.000812) Bio::TestKeggOrthology: test_dblinks: .: (0.001547) test_dblinks_as_hash: .: (0.001129) test_dblinks_as_strings: .: (0.000994) test_definition: .: (0.001057) test_entry_id: .: (0.001029) test_genes_as_hash: .: (0.037136) test_genes_as_strings: .: (0.012423) test_keggclass: .: (0.001382) test_keggclasses: .: (0.001421) test_modules: .: (0.001021) test_modules_as_hash: .: (0.001063) test_modules_as_strings: .: (0.001013) test_name: .: (0.001567) test_names: .: (0.001031) test_pathways_as_strings: .: (0.001230) test_pathways_in_keggclass: .: (0.001471) test_references: .: (0.001616) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000952) test_compounds_as_strings: .: (0.000615) test_dblinks_as_hash: .: (0.000606) test_dblinks_as_strings: .: (0.000649) test_description: .: (0.000901) test_diseases_as_hash: .: (0.000598) test_diseases_as_strings: .: (0.000577) test_entry_id: .: (0.000700) test_enzymes_as_strings: .: (0.000630) test_genes_as_hash: .: (0.000586) test_genes_as_strings: .: (0.000582) test_keggclass: .: (0.000702) test_ko_pathway: .: (0.000684) test_modules_as_hash: .: (0.000875) test_modules_as_strings: .: (0.001337) test_name: .: (0.000691) test_organism: .: (0.000648) test_orthologs_as_hash: .: (0.000592) test_orthologs_as_strings: .: (0.000586) test_pathways_as_hash: .: (0.000678) test_pathways_as_strings: .: (0.000620) test_reactions_as_hash: .: (0.000607) test_reactions_as_strings: .: (0.000587) test_references: .: (0.000596) test_rel_pathways_as_hash: .: (0.001190) test_rel_pathways_as_strings: .: (0.000855) Bio::TestKeggReaction: test_definition: .: (0.001060) test_entry_id: .: (0.000707) test_enzymes: .: (0.000693) test_equation: .: (0.000736) test_name: .: (0.005921) test_orthologs_as_hash: .: (0.001026) test_orthologs_as_strings: .: (0.000762) test_pathways_as_hash: .: (0.000761) test_pathways_as_strings: .: (0.000673) test_rpairs_as_hash: .: (0.000860) test_rpairs_as_strings: .: (0.000729) test_rpairs_as_tokens: .: (0.000858) Bio::TestLasergene: test_methods: .: (0.018912) Bio::TestLocations: test_complement: .: (0.000834) test_hat: .: (0.000456) test_normal: .: (0.000421) test_replace_single_base: .: (0.000421) test_should_not_modify_argument: .: (0.000361) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.010765) test_locations_to_s: .: (0.005023) Bio::TestMEDLINE: test_authors: .: (0.002007) test_authors_with_last_name_all_caps: .: (0.000406) test_authors_with_suffix: .: (0.000878) Bio::TestMEDLINE_20146148: test_ab: .: (0.001594) test_ad: .: (0.001147) test_au: .: (0.001062) test_authors: .: (0.001600) test_doi: .: (0.001265) test_dp: .: (0.001098) test_ip: .: (0.001091) test_mh: .: (0.001451) test_pages: .: (0.001349) test_pg: .: (0.001167) test_pii: .: (0.001127) test_pmid: .: (0.001397) test_pt: .: (0.001269) test_reference: .: (0.001668) test_self_new: .: (0.001133) test_so: .: (0.001525) test_ta: .: (0.001200) test_ti: .: (0.001145) test_ui: .: (0.001081) test_vi: .: (0.001532) test_year: .: (0.001197) Bio::TestMapSimple: test_attributes: .: (0.000833) Bio::TestMapping: test_add_mapping_as_map: .: (0.000953) test_add_mapping_as_marker: .: (0.000576) test_contains_marker?: .: (0.000476) test_mapped_to?: .: (0.000420) test_mapping_location_comparison: .: (0.001282) test_mappings_as_map_each: .: (0.000430) test_mappings_as_marker_each: .: (0.000496) test_mappings_on: .: (0.000577) test_multiple_mappings_between_same_marker_and_map: .: (0.000976) test_positions_on: .: (0.000584) test_raise_error_kind_of: .: (0.000969) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000941) test_check_options_with_invalid_opts: .: (0.000569) test_check_options_with_valid_opts: .: (0.000496) test_command_to_be_run: .: (0.000852) test_config_defaults: .: (0.000478) test_minimal_config: .: (0.000494) test_more_config: .: (0.000443) test_run: .: (0.000323) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.001147) test_report_has_motifs: .: (0.000802) Bio::TestModel: test_addChain: .: (0.000629) test_comp: .: (0.000368) test_each: .: (0.000662) test_each_chain: .: (0.000392) test_inspect: .: (0.000316) test_rehash: .: (0.000324) test_square_brace: .: (0.000329) test_to_s: .: (0.000333) Bio::TestModelFinder: test_find_model: .: (0.000623) Bio::TestMotif: test_creation_and_attributes: .: (0.000718) test_length: .: (0.000281) Bio::TestMyGraph: test_cliquishness: .: (0.001932) Bio::TestNA: test_accessor: .: (0.000576) test_na: .: (0.000282) test_name: .: (0.000322) test_names: .: (0.000278) test_to_re: .: (0.000659) test_weight: .: (0.000334) test_weight_rna: .: (0.000310) Bio::TestNAConstants: test_NAMES: .: (0.000574) test_NAMES_1_to_name: .: (0.000281) test_WEIGHT: .: (0.000341) Bio::TestNATranslate: test_translate: .: (0.000908) test_translate_1: .: (0.001110) test_translate_2: .: (0.000370) test_translate_3: .: (0.000332) test_translate_4: .: (0.000548) test_translate_5: .: (0.000401) test_translate_6: .: (0.000340) Bio::TestNCBIDB: test_fetch: .: (0.000658) test_p_entry2hash: .: (0.000258) test_p_subtag2array: .: (0.000258) test_p_toptag2array: .: (0.000242) Bio::TestNewick: test_reparse: .: (0.004107) test_reparse_before_lazy_parsing: .: (0.001243) test_string_tree: .: (0.002304) Bio::TestNewick2: test_string_tree: .: (0.002990) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000687) test_parse_newick_leaf: .: (0.000575) test_parse_newick_tokenize: .: (0.000935) Bio::TestNexus: test_nexus: .: (0.033798) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000837) test_uncapitalized_letter_Q32725_9POAL: .: (0.000500) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.001336) test_load_parameters: .: (0.000377) test_parameters: .: (0.000305) test_set_default_parameters: .: (0.000363) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.007442) test_expected_parameters_set_in_control_file: .: (0.002355) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000651) test_new_with_parameters: .: (0.000392) test_new_with_two_argument: .: (0.001081) test_new_without_argument: .: (0.000351) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.004599) test_rates_hundred_and_fiftieth_position: .: (0.004737) test_rates_last_position: .: (0.004498) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.026354) test_tree: .: (0.025719) test_tree_length: .: (0.024688) test_tree_log_likelihood: .: (0.026711) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.001346) test_parameters_should_be_loaded_from_control: .: (0.001490) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.004042) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000852) test_dN_dS: .: (0.000499) test_kappa: .: (0.000489) test_lnL: .: (0.000475) test_m3_classes: .: (0.001412) test_m3_lnL: .: (0.000697) test_m3_to_s: .: (0.000471) test_m3_tree: .: (0.001780) test_omega: .: (0.000490) test_to_s: .: (0.000513) test_tree: .: (0.001611) test_tree_length: .: (0.000505) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.001446) test_p: .: (0.001760) test_position: .: (0.001020) test_probability: .: (0.001045) test_w: .: (0.001094) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.002192) test_graph_omega: .: (0.001284) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000763) test_footer: .: (0.000802) test_header: .: (0.000586) test_initialize: .: (0.000497) test_models: .: (0.000559) test_nb_sites: .: (0.012107) test_num_codons: .: (0.000594) test_num_sequences: .: (0.000560) test_significant: .: (0.000536) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000897) test_nb_sites: .: (0.000774) test_significant: .: (0.000569) test_sites: .: (0.005140) Bio::TestPDB: test_accession: .: (0.003324) test_addModel: .: (0.003085) test_authors: .: (0.002135) test_bracket: .: (0.002665) test_classification: .: (0.002233) test_dbref: .: (0.002879) test_definition: .: (0.002254) test_each: .: (0.002692) test_each_model: .: (0.002212) test_entry_id: .: (0.002909) test_helix: .: (0.002989) test_inspect: .: (0.002965) test_jrnl: .: (0.002174) test_keywords: .: (0.002837) test_record: .: (0.002229) test_remark: .: (0.002739) test_seqres: .: (0.003393) test_sheet: .: (0.004194) test_ssbond: .: (0.002413) test_to_s: .: (0.003692) test_turn: .: (0.002238) test_version: .: (0.002596) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000773) test_U12: .: (0.000472) test_U13: .: (0.000417) test_U22: .: (0.000413) test_U23: .: (0.000414) test_U33: .: (0.000497) test_altLoc: .: (0.000421) test_chainID: .: (0.000457) test_charge: .: (0.000461) test_element: .: (0.000844) test_iCode: .: (0.000421) test_name: .: (0.000445) test_resName: .: (0.000510) test_resSeq: .: (0.000444) test_segID: .: (0.000454) test_serial: .: (0.000446) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000627) test_anisou: .: (0.000356) test_chainID: .: (0.000328) test_charge: .: (0.000327) test_comparable: .: (0.000405) test_do_parse: .: (0.000356) test_element: .: (0.000757) test_iCode: .: (0.000328) test_name: .: (0.000343) test_occupancy: .: (0.000465) test_original_data: .: (0.000325) test_record_name: .: (0.000318) test_resName: .: (0.000369) test_resSeq: .: (0.000309) test_residue: .: (0.000310) test_segID: .: (0.000309) test_serial: .: (0.000300) test_sigatm: .: (0.000344) test_tempFactor: .: (0.000451) test_ter: .: (0.000352) test_to_a: .: (0.000352) test_to_s: .: (0.000403) test_x: .: (0.000814) test_xyz: .: (0.000644) test_y: .: (0.000414) test_z: .: (0.000423) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000741) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000615) test_idcode: .: (0.000324) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000726) test_chainID2: .: (0.000415) test_icode1: .: (0.000448) test_icode2: .: (0.000413) test_measure: .: (0.000420) test_modNum: .: (0.000424) test_pep1: .: (0.000394) test_pep2: .: (0.000399) test_seqNum1: .: (0.000442) test_seqNum2: .: (0.000379) test_serNum: .: (0.000374) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000715) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000647) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000665) test_alpha: .: (0.000357) test_b: .: (0.000345) test_beta: .: (0.000368) test_c: .: (0.000987) test_gamma: .: (0.000356) test_sGroup: .: (0.000358) test_z: .: (0.000339) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000755) test_database: .: (0.000453) test_dbAccession: .: (0.000462) test_dbIdCode: .: (0.000477) test_dbseqBegin: .: (0.000482) test_dbseqEnd: .: (0.000436) test_idCode: .: (0.000432) test_idbnsBeg: .: (0.000470) test_insertBegin: .: (0.001157) test_insertEnd: .: (0.000477) test_seqBegin: .: (0.000451) test_seqEnd: .: (0.000487) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000776) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000650) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000618) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000646) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000641) test_depDate: .: (0.000407) test_idCode: .: (0.000374) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000741) test_hetID: .: (0.000377) test_iCode: .: (0.000393) test_numHetAtoms: .: (0.000435) test_seqNum: .: (0.000420) test_text: .: (0.000383) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000619) test_anisou: .: (0.000336) test_chainID: .: (0.000321) test_charge: .: (0.000326) test_comparable: .: (0.000442) test_do_parse: .: (0.000351) test_element: .: (0.000343) test_iCode: .: (0.000308) test_name: .: (0.000985) test_occupancy: .: (0.000498) test_original_data: .: (0.000335) test_record_name: .: (0.000335) test_resName: .: (0.000319) test_resSeq: .: (0.000301) test_residue: .: (0.000310) test_segID: .: (0.000340) test_serial: .: (0.000317) test_sigatm: .: (0.000298) test_tempFactor: .: (0.000408) test_ter: .: (0.000351) test_to_a: .: (0.000325) test_to_s: .: (0.000860) test_x: .: (0.000419) test_xyz: .: (0.000390) test_y: .: (0.000433) test_z: .: (0.000422) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000815) test_ChainH: .: (0.000487) test_ICode1: .: (0.000493) test_altLoc1: .: (0.000493) test_altLoc2: .: (0.000512) test_altLocH: .: (0.000989) test_chainID2: .: (0.000516) test_iCode2: .: (0.000522) test_iCodeH: .: (0.000478) test_name1: .: (0.000486) test_name2: .: (0.000523) test_nameH: .: (0.000469) test_resName1: .: (0.000513) test_resName2: .: (0.000501) test_resSeq1: .: (0.000489) test_resSeq2: .: (0.000656) test_resSeqH: .: (0.000605) test_sym1: .: (0.001245) test_sym2: .: (0.000620) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000733) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000754) test_altLoc2: .: (0.000455) test_chainID1: .: (0.000488) test_chainID2: .: (0.000445) test_iCode1: .: (0.000485) test_iCode2: .: (0.000481) test_name1: .: (0.000443) test_name2: .: (0.000491) test_resName1: .: (0.001085) test_resName2: .: (0.000456) test_resSeq1: .: (0.000440) test_resSeq2: .: (0.000459) test_sym1: .: (0.000445) test_sym2: .: (0.000436) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000669) test_numCoord: .: (0.000352) test_numHelix: .: (0.000374) test_numHet: .: (0.000344) test_numRemark: .: (0.000348) test_numSeq: .: (0.000344) test_numSheet: .: (0.000344) test_numSite: .: (0.000361) test_numTer: .: (0.000322) test_numTurn: .: (0.000391) test_numXform: .: (0.000325) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000587) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000742) test_comment: .: (0.000398) test_iCode: .: (0.000386) test_idCode: .: (0.000356) test_resName: .: (0.000347) test_seqNum: .: (0.000364) test_stdRes: .: (0.000387) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000672) test_Mn2: .: (0.000362) test_Mn3: .: (0.000382) test_Vn: .: (0.000334) test_iGiven: .: (0.000708) test_serial: .: (0.000346) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000628) test_Mn2: .: (0.000343) test_Mn3: .: (0.000380) test_Vn: .: (0.000300) test_iGiven: .: (0.000328) test_serial: .: (0.000318) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000674) test_Mn2: .: (0.000340) test_Mn3: .: (0.000387) test_Vn: .: (0.000328) test_iGiven: .: (0.000348) test_serial: .: (0.000320) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.001180) test_rIdCode: .: (0.000360) test_repDate: .: (0.000359) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000668) test_On2: .: (0.000339) test_On3: .: (0.000319) test_Tn: .: (0.000315) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000685) test_modId: .: (0.000377) test_modNum: .: (0.000407) test_modType: .: (0.000356) test_record: .: (0.000352) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000722) test_text: .: (0.000325) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000710) test_Sn2: .: (0.000312) test_Sn3: .: (0.000344) test_Un: .: (0.000313) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000655) test_Sn2: .: (0.000375) test_Sn3: .: (0.000332) test_Un: .: (0.000354) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000658) test_Sn2: .: (0.000334) test_Sn3: .: (0.000647) test_Un: .: (0.000352) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000838) test_conflict: .: (0.000415) test_database: .: (0.000405) test_dbIdCode: .: (0.000413) test_dbRes: .: (0.000441) test_dbSeq: .: (0.000389) test_iCode: .: (0.000406) test_idCode: .: (0.000497) test_resName: .: (0.000528) test_seqNum: .: (0.000453) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000753) test_numRes: .: (0.000414) test_resName: .: (0.000424) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000808) test_curChainId: .: (0.000529) test_curICode: .: (0.000621) test_curResName: .: (0.000999) test_curResSeq: .: (0.000567) test_endChainID: .: (0.000506) test_endICode: .: (0.000497) test_endResName: .: (0.000538) test_endSeqNum: .: (0.000510) test_initChainID: .: (0.000542) test_initICode: .: (0.000510) test_initResName: .: (0.000539) test_initSeqNum: .: (0.000539) test_numStrands: .: (0.000986) test_prevAtom: .: (0.000530) test_prevChainId: .: (0.000556) test_prevICode: .: (0.000560) test_prevResName: .: (0.000508) test_prevResSeq: .: (0.000544) test_sense: .: (0.000503) test_sheetID: .: (0.000508) test_strand: .: (0.000508) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000866) test_chainID: .: (0.000912) test_charge: .: (0.000471) test_element: .: (0.000470) test_iCode: .: (0.000425) test_name: .: (0.000424) test_resName: .: (0.000414) test_resSeq: .: (0.000501) test_segID: .: (0.000429) test_serial: .: (0.000415) test_sigOcc: .: (0.000442) test_sigTemp: .: (0.000410) test_sigX: .: (0.000404) test_sigY: .: (0.000429) test_sigZ: .: (0.000939) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000825) test_SigmaU12: .: (0.000426) test_SigmaU13: .: (0.000420) test_SigmaU22: .: (0.000409) test_SigmaU23: .: (0.000427) test_SigmaU33: .: (0.000474) test_altLoc: .: (0.000430) test_chainID: .: (0.000421) test_charge: .: (0.000443) test_element: .: (0.000410) test_iCode: .: (0.000405) test_name: .: (0.000804) test_resName: .: (0.000437) test_resSeq: .: (0.000532) test_segID: .: (0.000419) test_serial: .: (0.000411) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000814) test_chainID2: .: (0.000518) test_chainID3: .: (0.000488) test_chainID4: .: (0.000448) test_iCode1: .: (0.000451) test_iCode2: .: (0.000438) test_iCode3: .: (0.000986) test_iCode4: .: (0.000556) test_numRes: .: (0.000453) test_resName1: .: (0.000645) test_resName2: .: (0.000635) test_resName3: .: (0.000460) test_resName4: .: (0.000468) test_seq1: .: (0.000480) test_seq2: .: (0.000465) test_seq3: .: (0.000521) test_seq4: .: (0.000432) test_seqNum: .: (0.000511) test_siteID: .: (0.000441) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000877) test_altLoc2: .: (0.000430) test_atom1: .: (0.000393) test_atom2: .: (0.000421) test_chainID1: .: (0.000385) test_chainID2: .: (0.000444) test_iCode1: .: (0.000448) test_iCode2: .: (0.000382) test_resName1: .: (0.000387) test_resName2: .: (0.000386) test_resSeq1: .: (0.000398) test_resSeq2: .: (0.000403) test_sym1: .: (0.000446) test_sym2: .: (0.000894) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000674) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000667) test_sIdCode: .: (0.000349) test_sprsdeDate: .: (0.000388) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000680) test_iCode: .: (0.000351) test_resName: .: (0.000348) test_resSeq: .: (0.000344) test_serial: .: (0.000355) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000611) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.001157) test_t1: .: (0.000387) test_t2: .: (0.000349) test_t3: .: (0.000359) test_text: .: (0.000352) Bio::TestPROSITE: test_ac: .: (0.004439) test_cc: .: (0.004368) test_de: .: (0.003831) test_division: .: (0.004404) test_dr: .: (0.041796) test_dt: .: (0.020528) test_false_neg: .: (0.040709) test_false_pos: .: (0.035228) test_false_positive_sequences: .: (0.034318) test_list_falsenegative: .: (0.041336) test_list_falsepositive: .: (0.041276) test_list_potentialhit: .: (0.043827) test_list_truepositive: .: (0.050278) test_list_unknown: .: (0.043758) test_list_xref: .: (0.045728) test_ma: .: (0.004157) test_max_repeat: .: (0.005569) test_name: .: (0.004560) test_nr: .: (0.004615) test_pa: .: (0.004938) test_pa2re: .: (0.005078) test_partial: .: (0.005517) test_pdb_xref: .: (0.004273) test_pdoc_xref: .: (0.005574) test_positive: .: (0.010629) test_positive_hits: .: (0.005155) test_positive_sequences: .: (0.004572) test_release: .: (0.004289) test_ru: .: (0.005434) test_self_pa2re: .: (0.005283) test_site: .: (0.005385) test_skip_flag: .: (0.004967) test_swissprot_release_number: .: (0.004680) test_swissprot_release_sequences: .: (0.005576) test_taxon_range: .: (0.005564) test_total: .: (0.005149) test_total_hits: .: (0.005629) test_total_sequences: .: (0.004390) test_unknown: .: (0.004695) test_unknown_hits: .: (0.004597) test_unknown_sequences: .: (0.004210) Bio::TestPROSITEConst: test_delimiter: .: (0.000635) test_tagsize: .: (0.000270) Bio::TestPTS1: test_function_set: .: (0.001131) test_function_set_number_1: .: (0.000342) test_function_set_number_2: .: (0.000305) test_function_set_number_3: .: (0.000356) test_function_show: .: (0.000278) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000528) Bio::TestPTS1New: test_fungi: .: (0.000579) test_general: .: (0.000309) test_metazoa: .: (0.000298) Bio::TestQualifier: test_qualifier: .: (0.000551) test_value: .: (0.000266) Bio::TestREBASE: test_methods: .: (0.002888) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.002127) test_bit_score: .: (0.001625) test_evalue: .: (0.001616) test_gaps: .: (0.001970) test_hit_from: .: (0.001571) test_hit_to: .: (0.001558) test_hseq: .: (0.001623) test_identity: .: (0.001533) test_midline: .: (0.002110) test_percent_identity: .: (0.001580) test_positive: .: (0.001533) test_qseq: .: (0.001784) test_query_from: .: (0.001635) test_query_to: .: (0.001723) test_score: .: (0.001616) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.001775) test_hits_size: .: (0.003418) test_iterations_size: .: (0.003706) test_program: .: (0.001311) test_query_def: .: (0.003172) test_query_len: .: (0.003668) test_version: .: (0.001309) test_version_date: .: (0.001294) test_version_number: .: (0.001318) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.002069) test_definition: .: (0.002189) test_evalue: .: (0.001698) test_hsps_size: .: (0.001497) test_identity: .: (0.001611) test_lap_at: .: (0.002143) test_len: .: (0.001740) test_midline: .: (0.001758) test_overlap: .: (0.001609) test_query_end: .: (0.001893) test_query_seq: .: (0.001738) test_query_start: .: (0.001809) test_target_def: .: (0.001667) test_target_end: .: (0.001845) test_target_len: .: (0.001648) test_target_seq: .: (0.001769) test_target_start: .: (0.002008) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.001494) test_get_entry: .: (0.001344) test_rewind: .: (0.000352) test_skip_leader: .: (0.000607) Bio::TestReference: test_abstract: .: (0.000607) test_affiliations: .: (0.000343) test_authors: .: (0.000294) test_format_bibitem: .: (0.000446) test_format_bibtex: .: (0.000734) test_format_bibtex_with_arguments: .: (0.000647) test_format_cell: .: (0.000404) test_format_current: .: (0.000496) test_format_endnote: .: (0.000428) test_format_general: .: (0.000420) test_format_genome_biol: .: (0.000433) test_format_genome_res: .: (0.000457) test_format_nar: .: (0.000376) test_format_nature: .: (0.000462) test_format_rd: .: (0.000378) test_format_science: .: (0.000610) test_format_trends: .: (0.000325) test_issue: .: (0.000292) test_journal: .: (0.000290) test_mesh: .: (0.000311) test_pages: .: (0.000355) test_pubmed: .: (0.000313) test_pubmed_url: .: (0.000283) test_url: .: (0.000264) test_volume: .: (0.000257) test_year: .: (0.000259) Bio::TestReference_noURL: test_format_endnote: .: (0.000686) test_url: .: (0.000286) Bio::TestReferences: test_append: .: (0.000801) test_each: .: (0.000410) Bio::TestRelation: test_comparison_operator: .: (0.000708) test_uniq: .: (0.000395) Bio::TestResidue: test_addAtom: .: (0.001023) test_each: .: (0.000730) test_each_atom: .: (0.000581) test_get_residue_id_from_atom: .: (0.000597) test_het_atom: .: (0.000467) test_iCode: .: (0.000487) test_inspect: .: (0.000572) test_resSeq: .: (0.000469) test_sort: .: (0.000551) test_square_bracket: .: (0.000612) test_to_s: .: (0.000709) test_update_resudue_id: .: (0.000526) Bio::TestResidueFinder: test_each_residue: .: (0.000754) test_find_residue: .: (0.000392) test_residues: .: (0.000437) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.328293) test_cut_from_bio_sequence_na: .: (0.095227) test_cut_without_permutations: .: (0.074760) test_view_ranges: .: (0.067494) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.004163) test_cuts_after_remove_incomplete_cuts: .: (0.002568) test_strands_for_display: .: (0.009149) test_strands_for_display_current: .: (0.002218) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.002123) test_fragments_for_display_1: .: (0.002745) test_fragments_for_display_10: .: (0.003542) test_fragments_for_display_2: .: (0.002717) test_fragments_for_display_3: .: (0.004304) test_fragments_for_display_4: .: (0.003203) test_fragments_for_display_5: .: (0.002069) test_fragments_for_display_6: .: (0.002444) test_fragments_for_display_7: .: (0.002238) test_fragments_for_display_8: .: (0.001876) test_fragments_for_display_9: .: (0.002291) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.001200) test_obj_3: .: (0.000944) test_obj_7: .: (0.000801) test_obj_z: .: (0.000802) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.001355) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000867) test_bracket_eq: .: (0.000514) test_concat: .: (0.000447) test_delete: .: (0.000440) test_dup: .: (0.000536) test_each: .: (0.000605) test_eqeq: .: (0.000411) test_eqeq_false: .: (0.000374) test_eqeq_other: .: (0.000336) test_eqeq_self: .: (0.000371) test_include?: .: (0.000375) test_internal_data: .: (0.000364) test_internal_data_eq: .: (0.000435) test_length: .: (0.000566) test_ltlt: .: (0.000393) test_ltlt_larger: .: (0.000389) test_ltlt_middle: .: (0.000420) test_plus: .: (0.000450) test_plus_error: .: (0.000476) test_push: .: (0.000443) test_reverse_each: .: (0.000532) test_self_bracket: .: (0.000341) test_self_new: .: (0.000383) test_size: .: (0.000342) test_sort!: .: (0.000325) test_to_a: .: (0.000352) test_uniq!: .: (0.000379) test_unshift: .: (0.000429) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.013289) test_complement: .: (0.011759) test_complement_with_cut_symbols: .: (0.018144) test_cut_locations: .: (0.012211) test_cut_locations_in_enzyme_notation: .: (0.011526) test_primary: .: (0.011864) test_primary_with_cut_symbols: .: (0.012234) test_to_re: .: (0.011689) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.003179) test_align_with_cuts: .: (0.002505) test_argument_error: .: (0.003013) test_ds: .: (0.002724) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.001371) test_complement: .: (0.000681) test_contents: .: (0.000603) test_primary: .: (0.000585) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.001168) test_complement: .: (0.000685) test_contents: .: (0.000728) test_primary: .: (0.000608) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000815) test_contents: .: (0.000977) test_primary: .: (0.000486) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000810) test_complement_to_array_index: .: (0.000714) test_complement_to_array_index_class: .: (0.000698) test_contents: .: (0.000518) test_primary: .: (0.000516) test_primary_to_array_index: .: (0.000719) test_primary_to_array_index_class: .: (0.000644) test_to_array_index: .: (0.001636) test_to_array_index_class: .: (0.001219) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.001384) test_rebase: .: (0.000436) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.002699) test_creation_with_no_cuts: .: (0.001362) test_cut_locations: .: (0.001481) test_cut_locations_in_enzyme_notation: .: (0.001719) test_orientation: .: (0.001277) test_pattern: .: (0.001639) test_pattern_palindromic?: .: (0.001626) test_stripped: .: (0.001573) test_to_re: .: (0.001241) test_with_cut_symbols: .: (0.001421) test_with_spaces: .: (0.002002) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.002331) test_creation_with_no_cuts: .: (0.001379) test_cut_locations: .: (0.001752) test_cut_locations_in_enzyme_notation: .: (0.001461) test_orientation: .: (0.001237) test_pattern: .: (0.001811) test_pattern_palindromic?: .: (0.001563) test_stripped: .: (0.001322) test_to_re: .: (0.001185) test_with_cut_symbols: .: (0.001665) test_with_spaces: .: (0.001512) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.001297) test_initialize_with_pattern: .: (0.001239) test_max: .: (0.000408) test_min: .: (0.000595) test_to_array_index: .: (0.000482) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000661) test_bracket_eq: .: (0.000370) test_concat: .: (0.000295) test_delete: .: (0.000255) test_dup: .: (0.000351) test_each: .: (0.000688) test_eqeq: .: (0.000565) test_eqeq_false: .: (0.000294) test_eqeq_other: .: (0.000269) test_eqeq_self: .: (0.000275) test_include?: .: (0.000290) test_internal_data_hash: .: (0.000304) test_internal_data_hash_eq: .: (0.000323) test_length: .: (0.000285) test_ltlt: .: (0.000310) test_ltlt_noeffect: .: (0.000300) test_plus: .: (0.000289) test_plus_error: .: (0.000399) test_private_push_element: .: (0.000318) test_private_push_element_intermediate: .: (0.000306) test_private_push_element_last: .: (0.000311) test_private_push_element_noeffect: .: (0.000619) test_private_sorted_keys: .: (0.000282) test_private_unshift_element: .: (0.000298) test_private_unshift_element_first: .: (0.000310) test_private_unshift_element_intermediate: .: (0.000311) test_private_unshift_element_noeffect: .: (0.000335) test_push: .: (0.000313) test_reverse_each: .: (0.000504) test_self_bracket: .: (0.000277) test_self_new: .: (0.000326) test_size: .: (0.000262) test_sort!: .: (0.000252) test_to_a: .: (0.000266) test_uniq!: .: (0.000254) test_unshift: .: (0.000340) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000707) test_left_padding: .: (0.000444) test_right_padding: .: (0.000378) test_strip_padding: .: (0.000392) Bio::TestSOFT: test_dataset: .: (0.020553) test_series: .: (0.020036) Bio::TestSOSUIReport: test_entry_id: .: (0.000799) test_prediction: .: (0.000463) test_tmh: .: (0.000430) test_tmhs: .: (0.000490) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000526) test_rs: .: (0.000250) Bio::TestSOSUITMH: test_grade: .: (0.000680) test_range: .: (0.000436) test_sequence: .: (0.000706) Bio::TestSampleGraph: test_bellman_ford: .: (0.001302) test_bfs_shortest_path: .: (0.000553) test_breadth_first_search: .: (0.000553) test_depth_first_search: .: (0.000856) test_dijkstra: .: (0.000742) test_dump_list: .: (0.000687) test_dump_matrix: .: (0.000979) test_extract_subgraph_by_label: .: (0.000853) test_extract_subgraph_by_list: .: (0.000650) test_extract_subgraph_retains_disconnected_nodes: .: (0.000495) test_small_world_aka_node_degree_histogram: .: (0.000494) test_to_matrix: .: (0.001101) test_to_matrix_fixed_index: .: (0.000751) test_undirected_cliquishness: .: (0.000953) Bio::TestScf_version_2: test_complement: .: (0.030595) test_seq: .: (0.029104) test_to_biosequence: .: (0.029119) Bio::TestScf_version_3: test_complement: .: (0.094506) test_seq: .: (0.094036) test_to_biosequence: .: (0.094547) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000730) test_AA_new_sequence_all_legal_symbols: .: (0.000510) test_AA_new_sequence_removes_whitespace: .: (0.000651) test_AA_new_sequence_upcases_symbols: .: (0.000553) test_DNA_new_blank_sequence: .: (0.000588) test_DNA_new_sequence_downcases_symbols: .: (0.000536) test_DNA_new_sequence_removes_whitespace: .: (0.000287) test_NA_randomize_with_counts: .: (0.002677) test_NA_randomize_with_counts_and_block: .: (0.003428) test_RNA_new_sequence: .: (0.000359) test_ambiguous_dna_sequence_complement: .: (0.000390) test_ambiguous_rna_sequence_complement: .: (0.000352) test_amino_acid_codes: .: (0.000494) test_amino_acid_molecular_weight: .: (0.000681) test_amino_acid_names: .: (0.000401) test_amino_acid_randomize_can_be_chained: .: (0.003827) test_amino_acid_randomize_has_same_composition: .: (0.002156) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.002231) test_dna_composition: .: (0.000480) test_dna_gc_percent: .: (0.000549) test_dna_molecular_weight: .: (0.000708) test_dna_pikachu: .: (0.000600) test_dna_sequence_complement: .: (0.000467) test_dna_sequence_translate: .: (0.001594) test_dna_to_re: .: (0.000512) test_element_reference_operator_with_one_argument: .: (0.000314) test_element_reference_operator_with_two_arguments: .: (0.000294) test_invalid_nucleic_acid_illegal_bases: .: (0.000715) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000469) test_nucleic_acid_names: .: (0.000479) test_randomize_dna_can_be_chained: .: (0.001285) test_randomize_dna_retains_composition: .: (0.000745) test_randomize_dna_with_block: .: (0.001004) test_rna_composition: .: (0.000730) test_rna_gc_percent: .: (0.000407) test_rna_molecular_weight: .: (0.000696) test_rna_pikachu: .: (0.000317) test_rna_sequence_complement: .: (0.000345) test_rna_sequence_translate: .: (0.000955) test_rna_to_re: .: (0.000473) test_total: .: (0.000341) test_two_consecutive_dna_randomizations_not_equal: .: (0.000850) test_valid_dna_sequence_illegal_bases: .: (0.000297) Bio::TestSequenceAA: test_codes: .: (0.001001) test_molecular_weight: .: (0.000491) test_names: .: (0.001201) test_to_re: .: (0.000642) test_to_s: .: (0.000809) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.001431) Bio::TestSequenceAANew: test_new: .: (0.001820) test_new_n: .: (0.000543) test_new_r: .: (0.000280) test_new_t: .: (0.000268) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.001477) test_concat: .: (0.000299) test_push: .: (0.000434) test_seq: .: (0.000274) test_splicing: .: (0.000544) test_sum: .: (0.000276) test_to_s: .: (0.000294) test_to_str: .: (0.000236) test_total: .: (0.000299) test_window_search: .: (0.001342) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000579) test_normalize_A: .: (0.000448) test_normalize_a: .: (0.000351) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.020424) test_randomize_with_block: .: (0.016979) test_randomize_with_hash: .: (0.004108) test_randomize_with_hash_block: .: (0.026360) 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' =============================================================================== : (0.005280) 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' =============================================================================== : (0.002520) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000937) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000366) test_subseq_returns_subsequence: .: (0.000294) test_to_s_returns_self_as_string: .: (0.000454) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000784) test_window_search_with_width_3_step_two_with_residual: .: (0.000338) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000659) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000526) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.001144) test_na_self_randomize: .: (0.000542) Bio::TestSequenceDBLink: test_database: .: (0.000574) test_id: .: (0.000256) test_secondary_ids: .: (0.000250) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000640) test_parse_uniprot_DR_line: .: (0.000392) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.002960) test_output_width_35: .: (0.000958) test_output_width_nil: .: (0.001318) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.001394) test_output_after_adding_sequence: .: (0.000911) test_output_after_truncating_sequence: .: (0.000665) test_output_from_error_probabilities: .: (0.010478) test_output_width45: .: (0.000839) test_output_with_converting_score_phred2solexa: .: (0.002656) test_output_with_converting_score_solexa2phred: .: (0.001116) test_output_with_default_score: .: (0.000724) Bio::TestSequenceMasker: test_mask: .: (0.001193) test_mask_with_enumerator: .: (0.000560) test_mask_with_enumerator_empty_mask_char: .: (0.000609) test_mask_with_enumerator_excess: .: (0.001678) test_mask_with_enumerator_longer_mask_char: .: (0.000520) test_mask_with_enumerator_shorter: .: (0.001030) test_mask_with_error_probability: .: (0.001228) test_mask_with_quality_score: .: (0.000651) Bio::TestSequenceNA: test_at_content: .: (0.001438) test_at_skew: .: (0.000779) test_codon_usage: .: (0.000577) test_complement: .: (0.000378) test_dna: .: (0.000396) test_dna!: .: (0.000408) test_forward_complement: .: (0.000441) test_gc_content: .: (0.001434) test_gc_percent: .: (0.000635) test_gc_skew: .: (0.001337) test_iliegal_bases: .: (0.000386) test_molecular_weight: .: (0.000854) test_names: .: (0.000973) test_reverse_complement: .: (0.000817) test_rna: .: (0.000392) test_rna!: .: (0.000303) test_splicing: .: (0.001008) test_to_re: .: (0.001070) test_to_s: .: (0.000289) Bio::TestSequenceNACommon: test_composition: .: (0.000726) test_concat: .: (0.000291) test_push: .: (0.000275) test_seq: .: (0.000562) test_splicing: .: (0.000686) test_sum: .: (0.000567) test_to_s: .: (0.000278) test_to_str: .: (0.000300) test_total: .: (0.000311) test_window_search: .: (0.002054) Bio::TestSequenceNANew: test_new: .: (0.000646) test_new_n: .: (0.000330) test_new_r: .: (0.000320) test_new_t: .: (0.000301) Bio::TestSequenceNATranslation: test_translate: .: (0.001282) test_translate_0: .: (0.006012) test_translate_1: .: (0.002297) test_translate_2: .: (0.000705) test_translate_3: .: (0.001226) test_translate_4: .: (0.000869) test_translate_5: .: (0.001570) test_translate_6: .: (0.001645) test_translate_7: .: (0.001610) test_translate_given_codon_table: .: (0.188360) test_translate_n1: .: (0.001923) test_translate_n2: .: (0.007645) test_translate_n3: .: (0.001600) test_translate_unknown_o: .: (0.000811) test_translate_unknown_x: .: (0.000832) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.008332) test_convert_scores_from_phred_to_solexa: .: (0.009656) test_convert_scores_from_solexa_to_phred: .: (0.008197) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000694) test_convert_scores_from_phred: .: (0.000361) test_convert_scores_from_phred_to_solexa: .: (0.006960) test_convert_scores_from_solexa: .: (0.008054) test_convert_scores_from_solexa_to_phred: .: (0.008154) test_convert_scores_to_phred: .: (0.000385) test_convert_scores_to_solexa: .: (0.009040) test_p2q: .: (0.000643) test_phred_p2q: .: (0.007864) test_phred_q2p: .: (0.040970) test_q2p: .: (0.017327) test_quality_score_type: .: (0.000362) test_self_convert_scores_to_solexa: .: (0.001812) test_self_p2q: .: (0.000562) test_self_q2p: .: (0.017248) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000645) test_convert_scores_from_phred: .: (0.001529) test_convert_scores_from_phred_to_solexa: .: (0.001719) test_convert_scores_from_solexa: .: (0.000334) test_convert_scores_from_solexa_to_phred: .: (0.001805) test_convert_scores_to_phred: .: (0.000652) test_convert_scores_to_solexa: .: (0.000303) test_p2q: .: (0.000983) test_q2p: .: (0.019404) test_quality_score_type: .: (0.000352) test_self_convert_scores_to_phred: .: (0.000764) test_self_p2q: .: (0.000797) test_self_q2p: .: (0.019814) test_solexa_p2q: .: (0.000788) test_solexa_q2p: .: (0.018340) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.001236) test_center: .: (0.000448) test_chomp: .: (0.000504) test_chop: .: (0.000493) test_delete: .: (0.000414) test_delete_prefix: .: (0.000405) test_delete_suffix: .: (0.000423) test_downcase: .: (0.000383) test_each_char: .: (0.000696) test_each_char_enum: .: (0.000566) test_each_grapheme_cluster: .: (0.001057) test_each_grapheme_cluster_enum: .: (0.000974) test_each_line: .: (0.000618) test_each_line_enum: .: (0.000523) test_gsub: .: (0.000448) test_gsub_with_block: .: (0.001532) test_ljust: .: (0.000407) test_lstrip: .: (0.000441) test_multiply: .: (0.000368) test_next: .: (0.000385) test_reverse: .: (0.000376) test_rjust: .: (0.000469) test_rstrip: .: (0.000424) test_slice: .: (0.000381) test_slice2: .: (0.000383) test_split: .: (0.000478) test_squeeze: .: (0.000369) test_strip: .: (0.000369) test_sub: .: (0.000410) test_sub_with_block: .: (0.000824) test_succ: .: (0.000428) test_swapcase: .: (0.000385) test_tr: .: (0.000383) test_tr_s: .: (0.000327) test_upcase: .: (0.000369) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000804) test_partition_nomatch: .: (0.000523) test_partition_sep_TSeq: .: (0.000480) test_partition_sep_regexp: .: (0.000524) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000745) test_rpartition_nomatch: .: (0.000478) test_rpartition_sep_TSeq: .: (0.000440) test_rpartition_sep_regexp: .: (0.000500) Bio::TestShRNA: test_blocK_it: .: (0.082125) test_blocK_it_: .: (0.083252) test_blocK_it_BLOCK_IT: .: (0.082614) test_blocK_it_BLOCK_iT: .: (0.082143) test_blocK_it_piGene: .: (0.083064) test_bottom_strand: .: (0.080077) test_bottom_strand_class: .: (0.081510) test_bottom_strand_nil: .: (0.080434) test_design: .: (0.080685) test_design_BLOCK_IT: .: (0.081565) test_report: .: (0.083416) test_report_before_design: .: (0.079288) test_top_strand: .: (0.082125) test_top_strand_class: .: (0.079818) test_top_strand_nil: .: (0.082727) Bio::TestShRNANew: test_new: .: (0.001262) Bio::TestSiRNA: test_antisense_size: .: (0.000634) test_design: .: (0.079335) test_design_reynolds: .: (0.099814) test_design_uitei: .: (0.078091) test_max_gc_percent: .: (0.000400) test_min_gc_percent: .: (0.000363) test_reynolds: .: (0.100314) test_reynolds?: .: (0.000464) test_uitei: .: (0.079467) test_uitei?: .: (0.000469) Bio::TestSiRNANew: test_new: .: (0.001953) Bio::TestSiRNAPair: test_antisense: .: (0.081463) test_gc_percent: .: (0.082511) test_report: .: (0.082397) test_rule: .: (0.076393) test_sense: .: (0.070247) test_start: .: (0.070406) test_stop: .: (0.069526) test_target: .: (0.078271) Bio::TestSiRNAPairNew: test_new: .: (0.001977) Bio::TestSim4Report: test_all_hits: .: (0.001118) test_each: .: (0.000694) test_each_hit: .: (0.000755) test_hits: .: (0.000882) test_num_hits: .: (0.000622) test_query_def: .: (0.000592) test_query_id: .: (0.000571) test_query_len: .: (0.000631) test_seq1: .: (0.001355) Bio::TestSim4Report2: test_all_hits: .: (0.000994) test_each: .: (0.000674) test_each_hit: .: (0.000650) test_hits: .: (0.000701) test_num_hits: .: (0.000598) test_query_def: .: (0.000624) test_query_id: .: (0.000562) test_query_len: .: (0.000625) test_seq1: .: (0.001360) Bio::TestSim4Report4: test_all_hits: .: (0.001364) test_each: .: (0.000688) test_each_hit: .: (0.000661) test_hits: .: (0.000679) test_num_hits: .: (0.000590) test_query_def: .: (0.000589) test_query_id: .: (0.000604) test_query_len: .: (0.000590) test_seq1: .: (0.001449) Bio::TestSim4ReportHit: test_align: .: (0.001406) test_complement?: .: (0.000601) test_definition: .: (0.000623) test_each: .: (0.001121) test_exons: .: (0.001054) test_hit_id: .: (0.000581) test_hsps: .: (0.001575) test_introns: .: (0.001130) test_len: .: (0.000593) test_query_def: .: (0.000594) test_query_id: .: (0.000548) test_query_len: .: (0.000553) test_segmentpairs: .: (0.001052) test_seq1: .: (0.000726) test_seq2: .: (0.000701) test_target_def: .: (0.000550) test_target_id: .: (0.001241) test_target_len: .: (0.000541) Bio::TestSim4ReportHit2: test_align: .: (0.001024) test_complement?: .: (0.000522) test_definition: .: (0.000536) test_each: .: (0.000907) test_exons: .: (0.000984) test_hit_id: .: (0.000563) test_hsps: .: (0.001676) test_introns: .: (0.001219) test_len: .: (0.000560) test_query_def: .: (0.000595) test_query_id: .: (0.000550) test_query_len: .: (0.000548) test_segmentpairs: .: (0.001003) test_seq1: .: (0.000706) test_seq2: .: (0.000725) test_target_def: .: (0.001249) test_target_id: .: (0.000753) test_target_len: .: (0.000512) Bio::TestSim4ReportHit4: test_align: .: (0.001307) test_complement?: .: (0.000759) test_definition: .: (0.000595) test_each: .: (0.001350) test_exons: .: (0.001438) test_hit_id: .: (0.000788) test_hsps: .: (0.001293) test_introns: .: (0.001255) test_len: .: (0.000552) test_query_def: .: (0.000584) test_query_id: .: (0.000538) test_query_len: .: (0.000531) test_segmentpairs: .: (0.001897) test_seq1: .: (0.000931) test_seq2: .: (0.000769) test_target_def: .: (0.000629) test_target_id: .: (0.000577) test_target_len: .: (0.000561) Bio::TestSim4ReportSegment: test_from: .: (0.000603) test_self_new: .: (0.000465) test_seq: .: (0.000376) test_to: .: (0.000302) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.001902) test_direction: .: (0.000889) test_hit_from: .: (0.000921) test_hit_to: .: (0.000856) test_hseq: .: (0.000811) test_midline: .: (0.000863) test_percent_identity: .: (0.000812) test_qseq: .: (0.001390) test_query_from: .: (0.000930) test_query_to: .: (0.000857) test_seq1: .: (0.001002) test_seq2: .: (0.000984) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.001202) test_direction: .: (0.001467) test_hit_from: .: (0.001070) test_hit_to: .: (0.000853) test_hseq: .: (0.000874) test_midline: .: (0.000782) test_percent_identity: .: (0.000855) test_qseq: .: (0.000819) test_query_from: .: (0.000867) test_query_to: .: (0.001292) test_seq1: .: (0.001217) test_seq2: .: (0.000986) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.001414) test_direction: .: (0.001038) test_hit_from: .: (0.001668) test_hit_to: .: (0.001394) test_hseq: .: (0.000999) test_midline: .: (0.001069) test_percent_identity: .: (0.001101) test_qseq: .: (0.001727) test_query_from: .: (0.001048) test_query_to: .: (0.001089) test_seq1: .: (0.001170) test_seq2: .: (0.001661) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.001339) test_direction: .: (0.001058) test_hit_from: .: (0.001102) test_hit_to: .: (0.001494) test_hseq: .: (0.001208) test_midline: .: (0.001100) test_percent_identity: .: (0.001054) test_qseq: .: (0.001055) test_query_from: .: (0.001606) test_query_to: .: (0.001185) test_seq1: .: (0.001246) test_seq2: .: (0.001171) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.001340) test_direction: .: (0.001805) test_hit_from: .: (0.001085) test_hit_to: .: (0.001043) test_hseq: .: (0.001096) test_midline: .: (0.001041) test_percent_identity: .: (0.001610) test_qseq: .: (0.001179) test_query_from: .: (0.001104) test_query_to: .: (0.001196) test_seq1: .: (0.001284) test_seq2: .: (0.001714) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.001113) test_direction: .: (0.000918) test_hit_from: .: (0.000903) test_hit_to: .: (0.000915) test_hseq: .: (0.000895) test_midline: .: (0.001375) test_percent_identity: .: (0.001047) test_qseq: .: (0.000913) test_query_from: .: (0.000917) test_query_to: .: (0.000909) test_seq1: .: (0.001015) test_seq2: .: (0.001490) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.001213) test_direction: .: (0.000882) test_hit_from: .: (0.000846) test_hit_to: .: (0.000869) test_hseq: .: (0.000822) test_midline: .: (0.000837) test_percent_identity: .: (0.000856) test_qseq: .: (0.001283) test_query_from: .: (0.000921) test_query_to: .: (0.000825) test_seq1: .: (0.001006) test_seq2: .: (0.000935) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000734) test_entry_id: .: (0.000373) test_filename: .: (0.000340) test_len: .: (0.000345) test_self_new: .: (0.000372) test_self_parse: .: (0.000450) Bio::TestTMHMMReport: test_entry_id: .: (0.001365) test_exp_aas_in_tmhs: .: (0.000960) test_exp_first_60aa: .: (0.000955) test_helix: .: (0.001478) test_predicted_tmhs: .: (0.000917) test_query_len: .: (0.000909) test_tmhs: .: (0.000946) test_to_s: .: (0.001241) test_total_prob_of_N_in: .: (0.001334) Bio::TestTMHMMReport_reports: test_reports: .: (0.000644) Bio::TestTMHMMTMH: test_entry_id: .: (0.001258) test_pos: .: (0.000917) test_range: .: (0.000890) test_status: .: (0.001493) test_version: .: (0.000923) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.001011) test_cutoff: .: (0.000737) test_entry_id: .: (0.000608) test_length: .: (0.000630) test_loc: .: (0.000615) test_name: .: (0.000661) test_networks: .: (0.000644) test_prediction: .: (0.000719) test_query_len: .: (0.000761) test_query_sequences: .: (0.000653) test_rc: .: (0.000698) test_version: .: (0.000641) Bio::TestTargetPReportConst: test_delimiter: .: (0.000594) test_rs: .: (0.000301) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000912) test_togows_access_wait: .: (2.005831) Bio::TestTogoWSREST: test_debug: .: (0.001321) test_debug_default: .: (0.000533) test_internal_http: .: (0.000539) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.007765) test_entry: .: (0.000349) test_entry_database_list: .: (0.000273) test_new: .: (0.000820) test_new_with_uri_object: .: (0.000703) test_new_with_uri_string: .: (0.000660) test_retrieve: .: (0.000308) test_search: .: (0.000310) test_search_database_list: .: (0.000300) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.001118) test_prepare_return_value: .: (0.000692) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.001341) Bio::TestTree: test_get_edge_distance: .: (0.000726) test_get_edge_distance_string: .: (0.000463) test_get_node_name: .: (0.000364) test_initialize: .: (0.000391) test_options: .: (0.000331) test_root: .: (0.000279) test_root=: .: (0.000363) Bio::TestTree2: test_add_edge: .: (0.001506) test_add_node: .: (0.000824) test_adjacency_matrix: .: (0.000673) test_adjacency_matrix_with_block: .: (0.000899) test_adjacent_nodes: .: (0.000766) test_adjacent_nodes_nonexistent: .: (0.000524) test_ancestors: .: (0.000614) test_children: .: (0.000596) test_clear: .: (0.000660) test_clear_node: .: (0.000717) test_clear_node_nonexistent: .: (0.001786) test_collect_edge!: .: (0.000979) test_collect_node!: .: (0.000944) test_concat: .: (0.000908) test_descendents: .: (0.000654) test_distance_matrix: .: (0.001706) test_each_edge: .: (0.000691) test_each_node: .: (0.001517) test_each_out_edge: .: (0.000585) test_each_out_edge_chimpanzee: .: (0.000563) test_each_out_edge_human: .: (0.000558) test_each_out_edge_mammals: .: (0.000667) test_each_out_edge_nonexistent: .: (0.000497) test_each_out_edge_primates: .: (0.000963) test_each_out_edge_rat: .: (0.000566) test_each_out_edge_rodents: .: (0.000709) test_edges: .: (0.000560) test_get_edge: .: (0.001254) test_get_edge_indirect: .: (0.000510) test_get_edge_merged: .: (0.000529) test_get_edge_nonexistent: .: (0.000489) test_get_node_bootstrap: .: (0.000506) test_get_node_bootstrap_string=: .: (0.000556) test_get_node_by_name: .: (0.000741) test_get_node_by_name_noexistent: .: (0.000483) test_include?: .: (0.000666) test_include_nonexistent: .: (0.000534) test_insert_node: .: (0.001027) test_leaves: .: (0.000645) test_leaves_noargs: .: (0.000553) test_lowest_common_ancestor: .: (0.000581) test_nodes: .: (0.000546) test_number_of_edges: .: (0.000483) test_number_of_nodes: .: (0.000478) test_out_degree: .: (0.000661) test_out_degree_nonexistent: .: (0.000510) test_out_edges: .: (0.000702) test_out_edges_mammals: .: (0.000897) test_out_edges_nonexistent: .: (0.000502) test_out_edges_primates: .: (0.000781) test_out_edges_rodents: .: (0.000835) test_parent: .: (0.000600) test_path: .: (0.000590) test_remove_edge: .: (0.000616) test_remove_edge_if: .: (0.000637) test_remove_edge_if_nothing_removed: .: (0.001318) test_remove_edge_nonexistent: .: (0.000768) test_remove_node: .: (0.000737) test_remove_node_if: .: (0.000565) test_remove_node_if_false: .: (0.000618) test_remove_node_nonexistent: .: (0.000544) test_remove_nonsense_nodes: .: (0.000567) test_subtree: .: (0.000731) test_subtree_with_all_paths: .: (0.001124) test_total_distance: .: (0.000529) Bio::TestTreeEdge: test_distance: .: (0.001255) test_distance=: .: (0.000394) test_distance_string: .: (0.000276) test_distance_string=: .: (0.000417) test_initialize: .: (0.000417) test_inspect: .: (0.000280) test_to_s: .: (0.000261) Bio::TestTreeNode: test_bootstrap: .: (0.000514) test_bootstrap=: .: (0.000355) test_bootstrap_string: .: (0.000230) test_bootstrap_string=: .: (0.000468) test_initialize: .: (0.000368) test_inspect: .: (0.000327) test_name: .: (0.000915) test_to_s: .: (0.000274) Bio::TestUniProt: test_gene_name: .: (0.013604) Bio::TestUniProtKB: test_ac: .: (0.013583) test_accession: .: (0.013063) test_cc: .: (0.016798) test_cc_alternative_products: .: (0.017018) test_cc_database: .: (0.017806) test_cc_mass_spectrometry: .: (0.016834) test_de: .: (0.012582) test_dr: .: (0.017695) test_dr_with_key: .: (0.017802) test_dr_with_key_empty: .: (0.032760) test_dt: .: (0.039675) test_dt_annotation: .: (0.038709) test_dt_created: .: (0.062838) test_dt_sequence: .: (0.012123) test_entry: .: (0.012067) test_ft: .: (0.031866) test_gene_name: .: (0.012416) test_gene_names: .: (0.012128) test_gn: .: (0.011868) test_gn_old_parser: .: (0.012529) test_gn_uniprot_parser: .: (0.012075) test_id_line: .: (0.012926) test_id_line_data_class: .: (0.013003) test_id_line_entry_name: .: (0.012482) test_id_line_molecule_type: .: (0.012889) test_id_line_sequence_length: .: (0.011807) test_kw: .: (0.013065) test_molecule: .: (0.012276) test_oc: .: (0.012947) test_og_1: .: (0.015559) test_og_2: .: (0.012252) test_og_3: .: (0.012266) test_og_4: .: (0.012384) test_og_5: .: (0.013359) test_og_6: .: (0.012402) test_os: .: (0.012526) test_os_access: .: (0.012632) test_os_access2: .: (0.011935) test_ox: .: (0.012186) test_protein_name: .: (0.012409) test_ref: .: (0.029867) test_seq: .: (0.012582) test_sequence_length: .: (0.012135) test_sq: .: (0.013180) test_sq_crc64: .: (0.012034) test_sq_len: .: (0.012619) test_sq_mw: .: (0.015231) test_synonyms: .: (0.012977) Bio::TestUniProtKB_CC: test_allergen: .: (0.000906) test_alternative_products_access_as_hash: .: (0.000744) test_alternative_products_ai: .: (0.000857) test_alternative_products_apu: .: (0.001785) test_alternative_products_as: .: (0.001023) test_alternative_products_rf: .: (0.000344) test_biophysicochemical_properties: .: (0.001328) test_biotechnology: .: (0.000714) test_catalytic_activity: .: (0.000658) test_caution: .: (0.000672) test_cofactor: .: (0.000625) test_developmental_stage: .: (0.000728) test_disease: .: (0.001018) test_domain: .: (0.000952) test_enzyme_regulation: .: (0.000624) test_function: .: (0.000691) test_induction: .: (0.000578) test_interaction: .: (0.000791) test_mass_spectrometry: .: (0.000857) test_miscellaneous: .: (0.001190) test_pathway: .: (0.000782) test_pharmaceutical: .: (0.000624) test_polymorphism: .: (0.000892) test_ptm: .: (0.000583) test_rna_editing: .: (0.000727) test_similarity: .: (0.000622) test_subcellular_location: .: (0.000665) test_subunit: .: (0.000550) test_tissue_specificity: .: (0.000628) test_toxic_dose: .: (0.000598) test_web_resource: .: (0.000829) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.001126) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.001440) test_protein_name: .: (0.001582) test_synonyms: .: (0.001277) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000642) test_entry: .: (0.000384) test_entry_id: .: (0.000376) test_entry_name: .: (0.000365) test_id_line: .: (0.000426) test_molecule: .: (0.000406) test_sequence_length: .: (0.000351) Bio::TestUniProtKB_P28907: test_ac: .: (0.005674) test_accession: .: (0.004793) test_cc: .: (0.005805) test_cc_alternative_products: .: (0.007054) test_cc_database: .: (0.005936) test_cc_mass_spectrometry: .: (0.006180) test_de: .: (0.004928) test_dr: .: (0.012295) test_dr_with_key: .: (0.012642) test_dr_with_key_empty: .: (0.011496) test_dt: .: (0.004646) test_dt_annotation: .: (0.004382) test_dt_created: .: (0.004402) test_dt_sequence: .: (0.004526) test_entry: .: (0.004701) test_ft: .: (0.009186) test_gene_name: .: (0.004734) test_gene_names: .: (0.004791) test_gn: .: (0.005726) test_gn_old_parser: .: (0.004988) test_gn_uniprot_parser: .: (0.004828) test_id_line: .: (0.004859) test_id_line_data_class: .: (0.005360) test_id_line_entry_name: .: (0.004604) test_id_line_sequence_length: .: (0.004762) test_kw: .: (0.004794) test_oc: .: (0.004885) test_os: .: (0.004672) test_os_access: .: (0.004944) test_os_access2: .: (0.005309) test_ox: .: (0.004885) test_protein_name: .: (0.005483) test_protein_name_after_calling_de: .: (0.005699) test_ref: .: (0.008361) test_seq: .: (0.005262) test_sequence_length: .: (0.004951) test_sq: .: (0.004818) test_sq_crc64: .: (0.004557) test_sq_len: .: (0.010648) test_sq_mw: .: (0.004995) test_synonyms: .: (0.005232) test_synonyms_after_calling_de: .: (0.005931) Bio::TestUniProtKB_Ref: test_RA: .: (0.001206) test_RC: .: (0.000883) test_RG: .: (0.000846) test_RL: .: (0.001386) test_RN: .: (0.000964) test_RP: .: (0.000882) test_RT: .: (0.000792) test_RX: .: (0.000893) test_ref: .: (0.001424) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000757) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.001393) test_alternative_products_with_ft: .: (0.002023) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.001022) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000879) test_RL_lines: .: (0.000422) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.001644) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000693) test_RG_line: .: (0.000474) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.001368) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000829) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000608) test_RL_line: .: (0.000444) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.002405) test_RP_line: .: (0.000842) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000482) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000829) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000618) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000576) test_CC_interaction_isoform: .: (0.000547) test_CC_interaction_no_gene_name: .: (0.001187) test_CC_interaction_self_association: .: (0.000646) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000769) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000884) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.001130) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.001600) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000858) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000700) test_DT_line: .: (0.000532) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.010813) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.001730) test_CC_web_resource: .: (0.000308) test_FT_VER_SEQ: .: (0.000551) test_OH_line_exception: .: (0.000606) test_OH_lines: .: (0.001002) Bio::TestUtils: test_centreOfGravity: .: (0.002157) test_dihedral_angle: .: (0.001197) test_distance: .: (0.000998) test_geometricCentre: .: (0.001680) test_rad2deg: .: (0.000616) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000826) test_dijkstra_on_weighted_graph: .: (0.000420) Finished in 45.13335762 seconds. ------------------------------------------------------------------------------- 3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 85.46 tests/s, 476.06 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_armhf.buildinfo dpkg-genchanges --build=binary -O../ruby-bio_2.0.4-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/28272/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/28272/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/28272 and its subdirectories I: Current time: Thu Jun 1 20:56:18 +14 2023 I: pbuilder-time-stamp: 1685602578