W: cgroups are not available on the host, not using them.
I: pbuilder: network access will be disabled during build
I: Current time: Tue May 23 09:15:53 +14 2023
I: pbuilder-time-stamp: 1684782953
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: using eatmydata during job
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/24953/tmp/hooks/D01_modify_environment starting
debug: Running on ionos12-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 23 09:16 /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/24953/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/24953/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]="i686-pc-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=24953
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.wL4Zvxma/pbuilderrc_qtfn --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.wL4Zvxma/b2 --logfile b2/build.log --extrapackages usrmerge ruby-bio_2.0.4-1.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://78.137.99.97:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 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 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 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 42920 Sep 21 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 21 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 137160 Sep 21 2022 date
-rwxr-xr-x 1 root root 100364 Sep 21 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 21 2022 df
-rwxr-xr-x 1 root root 162152 Sep 21 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 24 00:20 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 38760 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 34664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount
-rwxr-xr-x 1 root root 218680 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 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 75756 Sep 21 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 24 01:43 login
-rwxr-xr-x 1 root root 162152 Sep 21 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk
-rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 24 00:20 more
-rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount
-rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint
-rwxr-xr-x 1 root root 157932 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 38792 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 21 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 May 23 09:16 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 21 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 24 00:20 su
-rwxr-xr-x 1 root root 38792 Sep 21 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 21 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 21 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount
-rwxr-xr-x 1 root root 38760 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 24 00:20 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/24953/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19604 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 49.0 MB of archives. After unpacking 169 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 netbase all 6.4 [12.8 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.8-1 [1412 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 libassuan0 i386 2.5.5-5 [50.3 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 gpgconf i386 2.2.40-1.1 [572 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libksba8 i386 1.6.3-2 [135 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libnpth0 i386 1.6-3 [19.1 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 dirmngr i386 2.2.40-1.1 [819 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 gnupg-l10n all 2.2.40-1.1 [1093 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 gnupg-utils i386 2.2.40-1.1 [973 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 gpg i386 2.2.40-1.1 [991 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 pinentry-curses i386 1.2.1-1 [79.0 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 gpg-agent i386 2.2.40-1.1 [715 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 gpg-wks-client i386 2.2.40-1.1 [551 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 gpg-wks-server i386 2.2.40-1.1 [541 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 gpgsm i386 2.2.40-1.1 [691 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 gnupg all 2.2.40-1.1 [846 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libfile-touch-perl all 0.12-2 [8816 B]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libio-pty-perl i386 1:1.17-1 [36.5 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libipc-run-perl all 20220807.0-1 [104 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libclass-method-modifiers-perl all 2.14-1 [18.1 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 libclass-xsaccessor-perl i386 1.19-4+b1 [38.0 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libb-hooks-op-check-perl i386 0.22-2+b1 [10.6 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 libdevel-callchecker-perl i386 0.008-2 [15.8 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 libparams-classify-perl i386 0.015-2+b1 [23.7 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libhttp-date-perl all 6.05-2 [10.5 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 libfile-listing-perl all 6.15-1 [12.6 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 86 http://deb.debian.org/debian bookworm/main i386 liburi-perl all 5.17-1 [90.4 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 libhtml-parser-perl i386 3.81-1 [102 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 libclone-perl i386 0.46-1 [13.8 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 libio-html-perl all 1.004-3 [16.2 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 libhttp-message-perl all 6.44-1 [81.7 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 libhttp-cookies-perl all 6.10-1 [19.6 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 perl-openssl-defaults i386 7+b1 [7920 B]
Get: 96 http://deb.debian.org/debian bookworm/main i386 libnet-ssleay-perl i386 1.92-2+b1 [318 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 libio-socket-ssl-perl all 2.081-2 [219 kB]
Get: 98 http://deb.debian.org/debian bookworm/main i386 libnet-http-perl all 6.22-1 [25.3 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 liblwp-protocol-https-perl all 6.10-1 [12.2 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 libwww-perl all 6.68-1 [186 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 patchutils i386 0.4.2-1 [79.6 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 wdiff i386 1.2.2-5 [120 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 devscripts i386 2.23.3 [1072 kB]
Get: 106 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 107 http://deb.debian.org/debian bookworm/main i386 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 108 http://deb.debian.org/debian bookworm/main i386 docbook all 4.5-10 [131 kB]
Get: 109 http://deb.debian.org/debian bookworm/main i386 libosp5 i386 1.5.2-13+b2 [968 kB]
Get: 110 http://deb.debian.org/debian bookworm/main i386 opensp i386 1.5.2-13+b2 [426 kB]
Get: 111 http://deb.debian.org/debian bookworm/main i386 docbook-to-man i386 1:2.0.0-45 [81.3 kB]
Get: 112 http://deb.debian.org/debian bookworm/main i386 rubygems-integration all 1.18 [6704 B]
Get: 113 http://deb.debian.org/debian bookworm/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 114 http://deb.debian.org/debian bookworm/main i386 ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 115 http://deb.debian.org/debian bookworm/main i386 ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get: 116 http://deb.debian.org/debian bookworm/main i386 libruby i386 1:3.1 [4968 B]
Get: 117 http://deb.debian.org/debian bookworm/main i386 ruby-sdbm i386 1.0.0-5+b1 [16.7 kB]
Get: 118 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 119 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB]
Get: 120 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-4 [111 kB]
Get: 121 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB]
Get: 122 http://deb.debian.org/debian bookworm/main i386 libruby3.1 i386 3.1.2-7 [5459 kB]
Get: 123 http://deb.debian.org/debian bookworm/main i386 ruby3.1 i386 3.1.2-7 [663 kB]
Get: 124 http://deb.debian.org/debian bookworm/main i386 ruby-rubygems all 3.3.15-2 [293 kB]
Get: 125 http://deb.debian.org/debian bookworm/main i386 ruby i386 1:3.1 [5872 B]
Get: 126 http://deb.debian.org/debian bookworm/main i386 rake all 13.0.6-3 [83.9 kB]
Get: 127 http://deb.debian.org/debian bookworm/main i386 gem2deb-test-runner i386 2.1 [16.9 kB]
Get: 128 http://deb.debian.org/debian bookworm/main i386 libgmpxx4ldbl i386 2:6.2.1+dfsg1-1.1 [339 kB]
Get: 129 http://deb.debian.org/debian bookworm/main i386 libgmp-dev i386 2:6.2.1+dfsg1-1.1 [661 kB]
Get: 130 http://deb.debian.org/debian bookworm/main i386 ruby3.1-dev i386 3.1.2-7 [1002 kB]
Get: 131 http://deb.debian.org/debian bookworm/main i386 ruby-all-dev i386 1:3.1 [5976 B]
Get: 132 http://deb.debian.org/debian bookworm/main i386 gem2deb i386 2.1 [53.5 kB]
Get: 133 http://deb.debian.org/debian bookworm/main i386 ruby-rd all 0.6.38-4.1 [64.0 kB]
Get: 134 http://deb.debian.org/debian bookworm/main i386 rdtool all 0.6.38-4.1 [44.5 kB]
Get: 135 http://deb.debian.org/debian bookworm/main i386 ruby-libxml i386 3.2.4-2 [88.6 kB]
Fetched 49.0 MB in 1s (34.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:i386.
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Setting up libpython3.11-minimal:i386 (3.11.2-6) ...
Setting up libexpat1:i386 (2.5.0-1) ...
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Unpacking readline-common (8.2-1.3) ...
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Unpacking libreadline8:i386 (8.2-1.3) ...
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Unpacking python3.11 (3.11.2-6) ...
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Setting up python3-minimal (3.11.2-1+b1) ...
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Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sgml-base.
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Selecting previously unselected package libmagic-mgc.
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Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
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Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
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Unpacking file (1:5.44-3) ...
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Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
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Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
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Selecting previously unselected package libpipeline1:i386.
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Unpacking autotools-dev (20220109.1) ...
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Unpacking debhelper (13.11.4) ...
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Unpacking libassuan0:i386 (2.5.5-5) ...
Selecting previously unselected package gpgconf.
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Unpacking gpgconf (2.2.40-1.1) ...
Selecting previously unselected package libksba8:i386.
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Unpacking libksba8:i386 (1.6.3-2) ...
Selecting previously unselected package libsasl2-modules-db:i386.
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Selecting previously unselected package libldap-2.5-0:i386.
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Selecting previously unselected package libnpth0:i386.
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Unpacking libnpth0:i386 (1.6-3) ...
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Unpacking dirmngr (2.2.40-1.1) ...
Selecting previously unselected package gnupg-l10n.
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Unpacking gnupg-l10n (2.2.40-1.1) ...
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Unpacking gnupg-utils (2.2.40-1.1) ...
Selecting previously unselected package gpg.
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Unpacking gpg (2.2.40-1.1) ...
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Unpacking gpgsm (2.2.40-1.1) ...
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Unpacking gnupg (2.2.40-1.1) ...
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Unpacking libfile-dirlist-perl (0.05-3) ...
Selecting previously unselected package libfile-which-perl.
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Unpacking libfile-which-perl (1.27-2) ...
Selecting previously unselected package libfile-homedir-perl.
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Selecting previously unselected package libclass-method-modifiers-perl.
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Unpacking libclass-method-modifiers-perl (2.14-1) ...
Selecting previously unselected package libclass-xsaccessor-perl.
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Selecting previously unselected package libb-hooks-op-check-perl:i386.
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Setting up libksba8:i386 (1.6.3-2) ...
Setting up media-types (10.0.0) ...
Setting up libpipeline1:i386 (1.5.7-1) ...
Setting up wdiff (1.2.2-5) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libicu72:i386 (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:i386 (0.46-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:i386 (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:i386 (1:5.44-3) ...
Setting up perl-openssl-defaults:i386 (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:i386 (1.6-3) ...
Setting up file (1:5.44-3) ...
Setting up libassuan0:i386 (2.5.5-5) ...
Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ...
Setting up libosp5 (1.5.2-13+b2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libgmpxx4ldbl:i386 (2:6.2.1+dfsg1-1.1) ...
Setting up gnupg-l10n (2.2.40-1.1) ...
Setting up libncurses6:i386 (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:i386 (0.22-2+b1) ...
Setting up libipc-run-perl (20220807.0-1) ...
Setting up libsasl2-2:i386 (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:i386 (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) ...
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Setting up libfile-homedir-perl (1.006-2) ...
Setting up openssl (3.0.8-1) ...
Setting up libbsd0:i386 (0.11.7-2) ...
Setting up libelf1:i386 (0.188-2.1) ...
Setting up readline-common (8.2-1.3) ...
Setting up ruby-xmlrpc (0.3.2-2) ...
Setting up libxml2:i386 (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:i386 (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:i386 (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:i386 (3.1-20221030-2) ...
Setting up libreadline8:i386 (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:i386 (0.008-2) ...
Setting up libldap-2.5-0:i386 (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:i386 (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:i386 (3.11.2-6) ...
Setting up libparams-classify-perl:i386 (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:i386 (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:i386 (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:i386 (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:i386 (3.1.2-7) ...
Setting up gem2deb-test-runner (2.1) ...
Setting up ruby3.1-dev:i386 (3.1.2-7) ...
Setting up ruby-libxml:i386 (3.2.4-2) ...
Setting up ruby-all-dev:i386 (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/24953/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/24953/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 <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
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/i386-linux-gnu/ruby/gems/3.1.0:/usr/share/rubygems-integration/3.1.0:/usr/share/rubygems-integration/all:/usr/lib/i386-linux-gnu/rubygems-integration/3.1.0 ruby3.1 -S rake -f debian/ruby-tests.rake
/usr/bin/ruby3.1 -w -I"test" /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader.rb "test/functional/bio/sequence/test_output_embl.rb" "test/functional/bio/test_command.rb" "test/unit/bio/appl/bl2seq/test_report.rb" "test/unit/bio/appl/blast/test_ncbioptions.rb" "test/unit/bio/appl/blast/test_report.rb" "test/unit/bio/appl/blast/test_rpsblast.rb" "test/unit/bio/appl/clustalw/test_report.rb" "test/unit/bio/appl/gcg/test_msf.rb" "test/unit/bio/appl/genscan/test_report.rb" "test/unit/bio/appl/hmmer/test_report.rb" "test/unit/bio/appl/iprscan/test_report.rb" "test/unit/bio/appl/mafft/test_report.rb" "test/unit/bio/appl/meme/mast/test_report.rb" "test/unit/bio/appl/meme/test_mast.rb" "test/unit/bio/appl/meme/test_motif.rb" "test/unit/bio/appl/paml/codeml/test_rates.rb" "test/unit/bio/appl/paml/codeml/test_report.rb" "test/unit/bio/appl/paml/codeml/test_report_single.rb" "test/unit/bio/appl/paml/test_codeml.rb" "test/unit/bio/appl/sim4/test_report.rb" "test/unit/bio/appl/sosui/test_report.rb" "test/unit/bio/appl/targetp/test_report.rb" "test/unit/bio/appl/test_blast.rb" "test/unit/bio/appl/test_fasta.rb" "test/unit/bio/appl/test_pts1.rb" "test/unit/bio/appl/tmhmm/test_report.rb" "test/unit/bio/data/test_aa.rb" "test/unit/bio/data/test_codontable.rb" "test/unit/bio/data/test_na.rb" "test/unit/bio/db/embl/test_common.rb" "test/unit/bio/db/embl/test_embl.rb" "test/unit/bio/db/embl/test_embl_rel89.rb" "test/unit/bio/db/embl/test_embl_to_bioseq.rb" "test/unit/bio/db/embl/test_uniprot.rb" "test/unit/bio/db/embl/test_uniprotkb.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_new_part.rb" "test/unit/bio/db/fasta/test_defline.rb" "test/unit/bio/db/fasta/test_defline_misc.rb" "test/unit/bio/db/fasta/test_format_qual.rb" "test/unit/bio/db/genbank/test_common.rb" "test/unit/bio/db/genbank/test_genbank.rb" "test/unit/bio/db/genbank/test_genpept.rb" "test/unit/bio/db/kegg/test_compound.rb" "test/unit/bio/db/kegg/test_drug.rb" "test/unit/bio/db/kegg/test_enzyme.rb" "test/unit/bio/db/kegg/test_genes.rb" "test/unit/bio/db/kegg/test_genome.rb" "test/unit/bio/db/kegg/test_glycan.rb" "test/unit/bio/db/kegg/test_kgml.rb" "test/unit/bio/db/kegg/test_module.rb" "test/unit/bio/db/kegg/test_orthology.rb" "test/unit/bio/db/kegg/test_pathway.rb" "test/unit/bio/db/kegg/test_reaction.rb" "test/unit/bio/db/pdb/test_pdb.rb" "test/unit/bio/db/sanger_chromatogram/test_abif.rb" "test/unit/bio/db/sanger_chromatogram/test_scf.rb" "test/unit/bio/db/test_aaindex.rb" "test/unit/bio/db/test_fasta.rb" "test/unit/bio/db/test_fastq.rb" "test/unit/bio/db/test_gff.rb" "test/unit/bio/db/test_go.rb" "test/unit/bio/db/test_lasergene.rb" "test/unit/bio/db/test_litdb.rb" "test/unit/bio/db/test_medline.rb" "test/unit/bio/db/test_nbrf.rb" "test/unit/bio/db/test_newick.rb" "test/unit/bio/db/test_nexus.rb" "test/unit/bio/db/test_prosite.rb" "test/unit/bio/db/test_qual.rb" "test/unit/bio/db/test_rebase.rb" "test/unit/bio/db/test_soft.rb" "test/unit/bio/io/flatfile/test_autodetection.rb" "test/unit/bio/io/flatfile/test_buffer.rb" "test/unit/bio/io/flatfile/test_splitter.rb" "test/unit/bio/io/test_fastacmd.rb" "test/unit/bio/io/test_flatfile.rb" "test/unit/bio/io/test_togows.rb" "test/unit/bio/sequence/test_aa.rb" "test/unit/bio/sequence/test_common.rb" "test/unit/bio/sequence/test_compat.rb" "test/unit/bio/sequence/test_dblink.rb" "test/unit/bio/sequence/test_na.rb" "test/unit/bio/sequence/test_quality_score.rb" "test/unit/bio/sequence/test_ruby3.rb" "test/unit/bio/sequence/test_sequence_masker.rb" "test/unit/bio/test_alignment.rb" "test/unit/bio/test_command.rb" "test/unit/bio/test_db.rb" "test/unit/bio/test_feature.rb" "test/unit/bio/test_location.rb" "test/unit/bio/test_map.rb" "test/unit/bio/test_pathway.rb" "test/unit/bio/test_reference.rb" "test/unit/bio/test_sequence.rb" "test/unit/bio/test_tree.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb" "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb" "test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb" "test/unit/bio/util/restriction_enzyme/test_analysis.rb" "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb" "test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb" "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand.rb" "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb" "test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb" "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb" "test/unit/bio/util/test_color_scheme.rb" "test/unit/bio/util/test_contingency_table.rb" "test/unit/bio/util/test_restriction_enzyme.rb" "test/unit/bio/util/test_sirna.rb" -v
/build/ruby-bio-2.0.4/test/functional/bio/test_command.rb:184: warning: assigned but unused variable - err
Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future.
Loaded suite /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader
Started
Bio::External2go:
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test_dbs: .: (0.000250)
test_go_ids: .: (0.000542)
test_go_terms: .: (0.000337)
test_parser: .: (0.000557)
test_set_date: .: (0.000253)
test_set_desc: .: (0.000245)
test_to_str: .: (0.000270)
Bio::FuncTestCommandBackports:
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test_mktmpdir_without_block: .: (0.000574)
test_remove_entry_secure: .: (0.000505)
Bio::FuncTestCommandCallMisc1:
test_call_command: .: (0.003884)
test_call_command_fork: .: (0.000150)
test_call_command_open3: .: (0.003359)
test_call_command_popen: .: (0.003168)
Bio::FuncTestCommandCallSimple:
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test_call_command_fork: .: (0.000146)
test_call_command_open3: .: (0.003254)
test_call_command_popen: .: (0.003044)
Bio::FuncTestCommandCallWithSpace:
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test_call_command_fork: .: (0.000148)
test_call_command_open3: .: (0.003099)
test_call_command_popen: .: (0.002837)
Bio::FuncTestCommandChdir:
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test_call_command_fork_chdir: .: (0.000268)
test_call_command_popen_chdir: .: (0.001691)
test_query_command_chdir: .: (0.001696)
test_query_command_fork_chdir: .: (0.000262)
test_query_command_popen_chdir: .: (0.001725)
Bio::FuncTestCommandQuery:
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test_query_command_fork: .: (0.002188)
test_query_command_open3: .: (0.004310)
test_query_command_popen: .: (0.004216)
Bio::FuncTestCommandTmpdir:
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test_initialize: .: (0.000421)
test_path: .: (0.000276)
test_path_after_close: .: (0.000479)
Bio::FuncTestSequenceOutputEMBL:
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test_output_fasta: .: (0.011553)
Bio::NCBIDB::TestCommon:
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test_accessions: .: (0.000197)
test_comment: .: (0.000280)
test_common_name: .: (0.000246)
test_definition: .: (0.000241)
test_features: .: (0.000399)
test_gi: .: (0.000203)
test_keywords: .: (0.000189)
test_locus: .: (0.000167)
test_nid: .: (0.000191)
test_organism: .: (0.000225)
test_origin: .: (0.000176)
test_references: .: (0.000720)
test_segment: .: (0.000189)
test_source: .: (0.000521)
test_taxonomy: .: (0.000227)
test_version: .: (0.000207)
test_versions: .: (0.000222)
Bio::TestAA:
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test_1n: .: (0.000111)
test_name2one: .: (0.000164)
test_name2three: .: (0.000146)
test_one2name: .: (0.000172)
test_one2three: .: (0.000113)
test_three2name: .: (0.000103)
test_three2one: .: (0.000139)
test_to_1_1: .: (0.000108)
test_to_1_3: .: (0.000139)
test_to_1_name: .: (0.000145)
test_to_3_1: .: (0.000132)
test_to_3_3: .: (0.000109)
test_to_3_name: .: (0.000139)
test_to_re: .: (0.000175)
Bio::TestAAConstants:
test_bio_aminoacid: .: (0.000236)
Bio::TestAAindex:
test_api: .: (0.000231)
test_auto_aax1: .: (0.000289)
test_auto_aax2: .: (0.000262)
Bio::TestAAindex1:
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test_comment: .: (0.000249)
test_correlation_coefficient: .: (0.000575)
test_dblinks: .: (0.000278)
test_definition: .: (0.000253)
test_entry_id: .: (0.000345)
test_index: .: (0.000395)
test_journal: .: (0.000296)
test_title: .: (0.000268)
Bio::TestAAindex2:
test_access_A_R: .: (0.001107)
test_access_R_A: .: (0.000940)
test_author: .: (0.000266)
test_cols: .: (0.000284)
test_comment: .: (0.000279)
test_dblinks: .: (0.000248)
test_definition: .: (0.000267)
test_entry_id: .: (0.000245)
test_journal: .: (0.000325)
test_matrix: .: (0.000946)
test_matrix_1_2: .: (0.000935)
test_matrix_2_2: .: (0.000947)
test_matrix_A_R: .: (0.000936)
test_matrix_R_A: .: (0.000956)
test_matrix_determinant: .: (0.006190)
test_matrix_rank: .: (0.006101)
test_matrix_transpose: .: (0.001230)
test_rows: .: (0.000251)
test_title: .: (0.000262)
Bio::TestAAindexConstant:
test_delimiter: .: (0.000293)
test_tagsize: .: (0.000105)
Bio::TestAbif:
test_complement: .: (0.015105)
test_seq: .: (0.014289)
test_to_biosequence: .: (0.015054)
Bio::TestActsLikeMap:
test_mixin: .: (0.000360)
Bio::TestActsLikeMapAndMarker:
test_mixin: .: (0.000455)
Bio::TestActsLikeMarker:
test_mixin: .: (0.000300)
Bio::TestAlignment:
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test_add_seq_using_seq_with_aaseq_method: .: (0.000173)
test_add_seq_using_seq_with_definition_method: .: (0.000133)
test_add_seq_using_seq_with_entry_id_method: .: (0.000143)
test_add_seq_using_seq_with_naseq_method: .: (0.000158)
test_add_seq_using_seq_with_seq_method: .: (0.000154)
test_consensus_iupac_gap_modes: .: (0.000553)
test_consensus_iupac_missing_char: .: (0.000266)
test_consensus_iupac_missing_char_option: .: (0.000271)
test_consensus_iupac_no_gaps: .: (0.000352)
test_consensus_iupac_of_ambiguous_bases: .: (0.000643)
test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.018771)
test_consensus_opt_gap_mode: .: (0.000996)
test_consensus_opt_missing_char: .: (0.000329)
test_consensus_string_no_gaps: .: (0.000326)
test_consensus_threshold_four_sequences: .: (0.000499)
test_consensus_threshold_two_sequences: .: (0.000763)
test_convert_match: .: (0.000282)
test_convert_unmatch: .: (0.000208)
test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000204)
test_convert_unmatch_different_match_char: .: (0.000181)
test_convert_unmatch_multiple_sequences: .: (0.000277)
test_default_gap_char: .: (0.000108)
test_default_gap_regexp_matches_default_gap_char: .: (0.000131)
test_default_missing_char: .: (0.000111)
test_each_site_equal_length: .: (0.000215)
test_each_site_unequal_length: .: (0.000216)
test_equals: .: (0.000237)
test_match_line_protein: .: (0.000585)
test_normalizebang_extends_sequences_with_gaps: .: (0.000185)
test_seq_length_is_max_seq_length: .: (0.000135)
test_seq_length_when_one_sequence: .: (0.000118)
test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000118)
test_seqclass_when_seqclass_set: .: (0.000127)
test_seqclass_when_sequence_used: .: (0.000118)
test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000220)
test_set_and_get_gap_char: .: (0.000205)
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test_store_with_nil_key_uses_next_number_for_key: .: (0.000131)
Bio::TestAlignmentEnumerableExtension:
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test_alignment_normalize!: .: (0.000121)
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test_consensus_each_site_gap_mode_1: .: (0.000191)
test_consensus_each_site_gap_mode_minus1: .: (0.000206)
test_consensus_iupac: .: (0.000518)
test_consensus_string_default: .: (0.000192)
test_consensus_string_half: .: (0.000184)
test_convert_match: .: (0.000151)
test_convert_unmatch: .: (0.000289)
test_each_seq: .: (0.000154)
test_each_site: .: (0.000242)
test_each_site_step: .: (0.000170)
test_each_window: .: (0.000217)
test_match_line: .: (0.001114)
test_match_line_amino: .: (0.002652)
test_match_line_nuc: .: (0.000237)
test_private_alignment_site: .: (0.000208)
test_remove_all_gaps!: .: (0.000176)
test_seqclass: .: (0.000119)
test_seqclass=: .: (0.000165)
test_seqclass_default: .: (0.000107)
Bio::TestAlignmentMultiFastaFormat:
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test_entries: .: (0.000418)
Bio::TestAlignmentOutput:
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Bio::TestAlignmentPropertyMethods:
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Bio::TestAlignmentSite:
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test_consensus_string_default_nil: .: (0.000120)
test_has_gap_false: .: (0.000120)
test_has_gap_true: .: (0.000113)
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test_match_line_nuc_missing: .: (0.000151)
test_remove_gaps!: .: (0.000122)
test_remove_gaps_bang_not_removed: .: (0.000109)
Bio::TestAtomFinder:
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Bio::TestBioFastaDefline:
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test_get_by_type: .: (0.000431)
test_gi: .: (0.000376)
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test_locus: .: (0.000335)
test_method_missing: .: (0.000717)
test_to_s: .: (0.000484)
test_words: .: (0.001166)
Bio::TestBioGOOntology:
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test_parse_goids: .: (0.000470)
Bio::TestBioGenBank:
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test_circular: .: (0.000330)
test_classification: .: (0.000397)
test_date: .: (0.000297)
test_date_modified: .: (0.000978)
test_division: .: (0.000311)
test_each_cds_feature: .: (0.001085)
test_each_cds_qualifiers: .: (0.001322)
test_each_gene: .: (0.001157)
test_entry_id: .: (0.000343)
test_length: .: (0.000338)
test_locus_circular: .: (0.000382)
test_locus_class: .: (0.000509)
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test_locus_natype: .: (0.000383)
test_locus_strand: .: (0.000376)
test_natype: .: (0.000341)
test_seq: .: (0.000414)
test_seq_len: .: (0.000436)
test_strand: .: (0.000338)
test_strandedness: .: (0.000342)
test_to_biosequence: .: (0.003009)
Bio::TestBioGenPept:
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test_date: .: (0.000269)
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test_length: .: (0.000272)
test_locus: .: (0.000267)
test_seq: .: (0.000288)
test_seq_len: .: (0.000279)
Bio::TestBioKEGGGENES_b0529:
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test_aaseq: .: (0.000365)
test_chromosome: .: (0.000308)
test_codon_usage: .: (0.000508)
test_cu_list: .: (0.000264)
test_dblinks_as_hash: .: (0.000352)
test_dblinks_as_strings: .: (0.000303)
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test_entry: .: (0.000306)
test_entry_id: .: (0.000277)
test_gbposition: .: (0.000304)
test_gene: .: (0.000297)
test_genes: .: (0.000293)
test_keggclass: .: (0.000340)
test_keggclasses: .: (0.000358)
test_locations: .: (0.000437)
test_motifs_as_hash: .: (0.000370)
test_motifs_as_strings: .: (0.000522)
test_name: .: (0.000364)
test_names_as_array: .: (0.000322)
test_new: .: (0.000270)
test_ntlen: .: (0.000386)
test_ntseq: .: (0.000444)
test_organism: .: (0.000271)
test_orthologs_as_hash: .: (0.000310)
test_orthologs_as_strings: .: (0.000279)
test_pathway: .: (0.000483)
test_pathway_after_pathways_as_strings: .: (0.000502)
test_pathway_before_pathways_as_strings: .: (0.000415)
test_pathways_as_hash: .: (0.000304)
test_pathways_as_strings: .: (0.000269)
test_position: .: (0.000277)
test_structure: .: (0.000281)
Bio::TestBioKEGGGENOME_T00005:
test_chromosomes: .: (0.002041)
test_comment: .: (0.000564)
test_data_source: .: (0.000638)
test_definition: .: (0.000521)
test_disease: .: (0.000527)
test_entry_id: .: (0.000515)
test_lineage: .: (0.000590)
test_nalen: .: (0.000828)
test_name: .: (0.000522)
test_new: .: (0.000496)
test_num_gene: .: (0.000500)
test_num_rna: .: (0.000496)
test_original_databases: .: (0.000501)
test_original_db: .: (0.000614)
test_plasmids: .: (0.000497)
test_references: .: (0.010784)
test_statistics: .: (0.000709)
test_taxid: .: (0.000576)
test_taxonomy: .: (0.000561)
Bio::TestBioKEGGGENOME_T00070:
test_chromosomes: .: (0.000789)
test_comment: .: (0.000352)
test_data_source: .: (0.000303)
test_definition: .: (0.000318)
test_disease: .: (0.000499)
test_entry_id: .: (0.000336)
test_lineage: .: (0.000346)
test_nalen: .: (0.000445)
test_name: .: (0.000316)
test_new: .: (0.000297)
test_num_gene: .: (0.000300)
test_num_rna: .: (0.000299)
test_original_databases: .: (0.000289)
test_original_db: .: (0.000298)
test_plasmids: .: (0.000738)
test_references: .: (0.000504)
test_statistics: .: (0.000319)
test_taxid: .: (0.000353)
test_taxonomy: .: (0.000348)
Bio::TestBioKEGGPATHWAY_ec00072:
test_compounds_as_hash: .: (0.000466)
test_compounds_as_strings: .: (0.000260)
test_dblinks_as_hash: .: (0.000512)
test_dblinks_as_strings: .: (0.000372)
test_description: .: (0.000280)
test_diseases_as_hash: .: (0.000232)
test_diseases_as_strings: .: (0.000223)
test_entry_id: .: (0.000260)
test_enzymes_as_strings: .: (0.000256)
test_genes_as_hash: .: (0.000227)
test_genes_as_strings: .: (0.000220)
test_keggclass: .: (0.000253)
test_ko_pathway: .: (0.000438)
test_modules_as_hash: .: (0.000267)
test_modules_as_strings: .: (0.000230)
test_name: .: (0.000491)
test_new: .: (0.000315)
test_organism: .: (0.000266)
test_orthologs_as_hash: .: (0.000237)
test_orthologs_as_strings: .: (0.000234)
test_pathways_as_hash: .: (0.000248)
test_pathways_as_strings: .: (0.000232)
test_reactions_as_hash: .: (0.000430)
test_reactions_as_strings: .: (0.000221)
test_references: .: (0.000226)
test_rel_pathways_as_hash: .: (0.000271)
test_rel_pathways_as_strings: .: (0.000245)
Bio::TestBioKEGGPATHWAY_hsa00790:
test_compounds_as_hash: .: (0.000697)
test_compounds_as_strings: .: (0.000399)
test_dblinks_as_hash: .: (0.000272)
test_dblinks_as_strings: .: (0.000485)
test_description: .: (0.000316)
test_diseases_as_hash: .: (0.000288)
test_diseases_as_strings: .: (0.000272)
test_entry_id: .: (0.000285)
test_enzymes_as_strings: .: (0.000256)
test_genes_as_hash: .: (0.000480)
test_genes_as_strings: .: (0.000330)
test_keggclass: .: (0.000676)
test_ko_pathway: .: (0.000280)
test_modules_as_hash: .: (0.000292)
test_modules_as_strings: .: (0.000271)
test_name: .: (0.000285)
test_new: .: (0.000273)
test_organism: .: (0.000287)
test_orthologs_as_hash: .: (0.000257)
test_orthologs_as_strings: .: (0.000368)
test_pathways_as_hash: .: (0.000621)
test_pathways_as_strings: .: (0.000340)
test_reactions_as_hash: .: (0.000261)
test_reactions_as_strings: .: (0.000259)
test_references: .: (0.000261)
test_rel_pathways_as_hash: .: (0.000314)
test_rel_pathways_as_strings: .: (0.000288)
Bio::TestBioKEGGPATHWAY_ko00312:
test_compounds_as_hash: .: (0.000390)
test_compounds_as_strings: .: (0.000499)
test_dblinks_as_hash: .: (0.000312)
test_dblinks_as_strings: .: (0.000218)
test_description: .: (0.000236)
test_diseases_as_hash: .: (0.000217)
test_diseases_as_strings: .: (0.000214)
test_entry_id: .: (0.000245)
test_enzymes_as_strings: .: (0.000214)
test_genes_as_hash: .: (0.000217)
test_genes_as_strings: .: (0.000209)
test_keggclass: .: (0.000246)
test_ko_pathway: .: (0.000229)
test_modules_as_hash: .: (0.000411)
test_modules_as_strings: .: (0.000233)
test_name: .: (0.000257)
test_new: .: (0.000223)
test_organism: .: (0.000235)
test_orthologs_as_hash: .: (0.000300)
test_orthologs_as_strings: .: (0.000258)
test_pathways_as_hash: .: (0.000230)
test_pathways_as_strings: .: (0.000221)
test_reactions_as_hash: .: (0.000212)
test_reactions_as_strings: .: (0.000209)
test_references: .: (0.000212)
test_rel_pathways_as_hash: .: (0.000383)
test_rel_pathways_as_strings: .: (0.000237)
Bio::TestBioKEGGPATHWAY_map00030:
test_compounds_as_hash: .: (0.000536)
test_compounds_as_strings: .: (0.000276)
test_dblinks_as_hash: .: (0.000284)
test_dblinks_as_strings: .: (0.000270)
test_description: .: (0.000472)
test_diseases_as_hash: .: (0.000292)
test_diseases_as_strings: .: (0.000313)
test_entry_id: .: (0.000537)
test_enzymes_as_strings: .: (0.000282)
test_genes_as_hash: .: (0.000258)
test_genes_as_strings: .: (0.000358)
test_keggclass: .: (0.000295)
test_ko_pathway: .: (0.000283)
test_modules_as_hash: .: (0.000393)
test_modules_as_strings: .: (0.000314)
test_name: .: (0.000286)
test_new: .: (0.000266)
test_organism: .: (0.000278)
test_orthologs_as_hash: .: (0.000553)
test_orthologs_as_strings: .: (0.000263)
test_pathways_as_hash: .: (0.000277)
test_pathways_as_strings: .: (0.000559)
test_reactions_as_hash: .: (0.000272)
test_reactions_as_strings: .: (0.000260)
test_references: .: (0.001299)
test_rel_pathways_as_hash: .: (0.000387)
test_rel_pathways_as_strings: .: (0.000295)
Bio::TestBioKeggDRUG:
test_activity: .: (0.000475)
test_comment: .: (0.000369)
test_dblinks_as_hash: .: (0.000410)
test_dblinks_as_strings: .: (0.000316)
test_entry_id: .: (0.000722)
test_formula: .: (0.000293)
test_kcf: .: (0.000269)
test_mass: .: (0.000294)
test_name: .: (0.000318)
test_names: .: (0.000327)
test_pathways_as_hash: .: (0.000417)
test_pathways_as_strings: .: (0.000336)
test_products: .: (0.000350)
test_remark: .: (0.000531)
Bio::TestBioKeggGLYCAN:
test_comment: .: (0.000473)
test_composition: .: (0.000320)
test_compounds: .: (0.000281)
test_dblinks_as_hash: .: (0.000536)
test_dblinks_as_strings: .: (0.000424)
test_entry_id: .: (0.000335)
test_enzymes: .: (0.000312)
test_kcf: .: (0.000431)
test_keggclass: .: (0.000318)
test_mass: .: (0.000291)
test_name: .: (0.000318)
test_orthologs_as_hash: .: (0.000393)
test_orthologs_as_strings: .: (0.000323)
test_pathways_as_hash: .: (0.000315)
test_pathways_as_strings: .: (0.000274)
test_reactions: .: (0.000413)
test_references: .: (0.000567)
test_remark: .: (0.000324)
Bio::TestBioKeggGLYCAN_G01366:
test_comment: .: (0.000397)
test_composition: .: (0.000262)
test_compounds: .: (0.000238)
test_dblinks_as_hash: .: (0.000294)
test_dblinks_as_strings: .: (0.000233)
test_entry_id: .: (0.000244)
test_enzymes: .: (0.000240)
test_kcf: .: (0.000352)
test_keggclass: .: (0.000309)
test_mass: .: (0.000499)
test_name: .: (0.000267)
test_orthologs_as_hash: .: (0.000238)
test_orthologs_as_strings: .: (0.000217)
test_pathways_as_hash: .: (0.000232)
test_pathways_as_strings: .: (0.000214)
test_reactions: .: (0.000227)
test_references: .: (0.000217)
test_remark: .: (0.000230)
Bio::TestBioKeggPathway_rn00250:
test_compounds_as_hash: .: (0.000769)
test_compounds_as_strings: .: (0.000622)
test_dblinks_as_hash: .: (0.000330)
test_dblinks_as_strings: .: (0.000279)
test_description: .: (0.000292)
test_diseases_as_hash: .: (0.000310)
test_diseases_as_strings: .: (0.000286)
test_entry_id: .: (0.000301)
test_enzymes_as_strings: .: (0.000273)
test_genes_as_hash: .: (0.000270)
test_genes_as_strings: .: (0.000625)
test_keggclass: .: (0.000311)
test_ko_pathway: .: (0.000294)
test_modules_as_hash: .: (0.000390)
test_modules_as_strings: .: (0.000332)
test_name: .: (0.000303)
test_new: .: (0.000282)
test_organism: .: (0.000289)
test_orthologs_as_hash: .: (0.000503)
test_orthologs_as_strings: .: (0.000269)
test_pathways_as_hash: .: (0.000385)
test_pathways_as_strings: .: (0.000286)
test_reactions_as_hash: .: (0.000664)
test_reactions_as_strings: .: (0.000723)
test_references: .: (0.000708)
test_rel_pathways_as_hash: .: (0.000477)
test_rel_pathways_as_strings: .: (0.000372)
Bio::TestBioLITDB:
test_author: .: (0.000433)
test_entry_id: .: (0.000237)
test_field: .: (0.000234)
test_journal: .: (0.000230)
test_keyword: .: (0.000463)
test_reference: .: (0.000475)
test_title: .: (0.000274)
test_volume: .: (0.000237)
Bio::TestBioNBRF:
test_aalen: .: (0.000341)
test_aaseq: .: (0.000180)
test_entry: .: (0.000228)
test_length: .: (0.000189)
test_nalen: .: (0.000241)
test_naseq: .: (0.000379)
test_seq: .: (0.000203)
test_seq_class: .: (0.000163)
test_to_nbrf: .: (0.000191)
Bio::TestBioTreeOutputPrivate:
test_to_newick_format_label: .: (0.000412)
test_to_newick_format_leaf: .: (0.000373)
test_to_newick_format_leaf_NHX: .: (0.000221)
Bio::TestBl2seqReport:
test_db_len: .: (0.000968)
test_db_num: .: (0.000656)
test_new: .: (0.000356)
test_undefed_methods: .: (0.001480)
test_undefed_methods_for_iteration: .: (0.001532)
Bio::TestBl2seqReportConstants:
test_rs: .: (0.000253)
Bio::TestBl2seqReportHit:
test_empty_hits: .: (0.000777)
test_hits: .: (0.000368)
Bio::TestBlast:
test_blast_reports_format0: .: (0.007736)
test_blast_reports_format0_with_block: .: (0.000902)
test_blast_reports_format7: .: (0.028237)
test_blast_reports_format7_with_block: .: (0.022655)
test_blast_reports_format7_with_parser: .: (0.022004)
test_blast_reports_format7_with_parser_with_block: .: (0.021431)
test_blast_reports_format8: .: (0.000958)
test_blast_reports_format8_with_block: .: (0.000564)
test_blast_reports_format8_with_parser: .: (0.000302)
test_blast_reports_format8_with_parser_with_block: .: (0.000426)
test_blast_reports_xml: .: (0.074474)
test_blast_reports_xml_with_block: .: (0.021648)
test_blastll: .: (0.000208)
test_db: .: (0.000345)
test_exec_genomenet: .: (0.000158)
test_exec_local: .: (0.000157)
test_exec_ncbi: .: (0.000156)
test_filter: .: (0.000178)
test_format: .: (0.000240)
test_make_command_line: .: (0.000534)
test_make_command_line_2: .: (0.000623)
test_matrix: .: (0.000184)
test_new: .: (0.000488)
test_new_opt_string: .: (0.000340)
test_option: .: (0.000202)
test_option_set: .: (0.000313)
test_option_set_m0: .: (0.000274)
test_options: .: (0.000180)
test_output: .: (0.000359)
test_parse_result: .: (0.020743)
test_parser: .: (0.000202)
test_program: .: (0.000220)
test_query: .: (0.000160)
test_self_local: .: (0.000607)
test_self_remote: .: (0.002457)
test_server: .: (0.000211)
Bio::TestBlastNCBIOptions:
test_add_options: .: (0.000589)
test_delete: .: (0.000528)
test_equal_equal: .: (0.000607)
test_get: .: (0.000470)
test_make_command_line_options: .: (0.000427)
test_normalize!: .: (0.000273)
test_parse: .: (0.000471)
test_set: .: (0.000631)
Bio::TestBlastReport:
test_db: .: (0.021421)
test_db_len: .: (0.020925)
test_db_num: .: (0.022946)
test_each_hit: .: (0.020804)
test_each_iteration: .: (0.020648)
test_eff_space: .: (0.020452)
test_entrez_query: .: (0.020360)
test_entropy: .: (0.021569)
test_expect: .: (0.020787)
test_filter: .: (0.020478)
test_gap_extend: .: (0.020324)
test_gap_open: .: (0.020619)
test_hits: .: (0.021506)
test_hsp_len: .: (0.020683)
test_inclusion: .: (0.020249)
test_iterations: .: (0.020271)
test_kappa: .: (0.020220)
test_lambda: .: (0.021441)
test_matrix: .: (0.020501)
test_message: .: (0.020196)
test_parameters: .: (0.020576)
test_pattern: .: (0.020195)
test_program: .: (0.021727)
test_query_def: .: (0.020690)
test_query_id: .: (0.020178)
test_query_len: .: (0.020213)
test_reference: .: (0.020228)
test_sc_match: .: (0.021259)
test_sc_mismatch: .: (0.020712)
test_statistics: .: (0.020348)
test_version: .: (0.020270)
Bio::TestBlastReportDefault:
test_db: .: (0.000896)
test_db_len: .: (0.000611)
test_db_num: .: (0.000556)
test_each_hit: .: (0.000548)
test_each_iteration: .: (0.000537)
test_eff_space: .: (0.000658)
test_entropy: .: (0.000563)
test_expect: .: (0.000813)
test_gap_extend: .: (0.000663)
test_gap_open: .: (0.000666)
test_gapped_entropy: .: (0.000552)
test_gapped_kappa: .: (0.000546)
test_gapped_lambda: .: (0.000545)
test_hits: .: (0.000529)
test_iterations: .: (0.000499)
test_kappa: .: (0.000805)
test_lambda: .: (0.000580)
test_matrix: .: (0.000642)
test_message: .: (0.000507)
test_pattern: .: (0.000505)
test_program: .: (0.000518)
test_query_def: .: (0.000544)
test_query_len: .: (0.000557)
test_reference: .: (0.020343)
test_sc_match: .: (0.000647)
test_sc_mismatch: .: (0.000630)
test_version: .: (0.000512)
Bio::TestBlastReportHit:
test_Hit_accession: .: (0.020574)
test_Hit_bit_score: .: (0.022294)
test_Hit_definition: .: (0.020531)
test_Hit_evalue: .: (0.020168)
test_Hit_hit_id: .: (0.020881)
test_Hit_hsps: .: (0.020553)
test_Hit_identity: .: (0.021334)
test_Hit_lap_at: .: (0.020723)
test_Hit_len: .: (0.020287)
test_Hit_midline: .: (0.020336)
test_Hit_num: .: (0.020242)
test_Hit_overlap: .: (0.021555)
test_Hit_query_def: .: (0.020275)
test_Hit_query_end: .: (0.020420)
test_Hit_query_id: .: (0.020341)
test_Hit_query_len: .: (0.020337)
test_Hit_query_seq: .: (0.021288)
test_Hit_query_start: .: (0.020550)
test_Hit_taeget_def: .: (0.020144)
test_Hit_target_end: .: (0.020342)
test_Hit_target_id: .: (0.020345)
test_Hit_target_len: .: (0.021388)
test_Hit_target_seq: .: (0.020380)
test_Hit_target_start: .: (0.020412)
Bio::TestBlastReportHitDefault:
test_Hit_bit_score: .: (0.000809)
test_Hit_definition: .: (0.000574)
test_Hit_evalue: .: (0.000557)
test_Hit_hsps: .: (0.000528)
test_Hit_identity: .: (0.000726)
test_Hit_lap_at: .: (0.000866)
test_Hit_len: .: (0.000552)
test_Hit_midline: .: (0.000813)
test_Hit_overlap: .: (0.000555)
test_Hit_query_end: .: (0.000772)
test_Hit_query_seq: .: (0.000985)
test_Hit_query_start: .: (0.000783)
test_Hit_taeget_def: .: (0.000544)
test_Hit_target_end: .: (0.000769)
test_Hit_target_id: .: (0.000549)
test_Hit_target_len: .: (0.000569)
test_Hit_target_seq: .: (0.000859)
test_Hit_target_start: .: (0.000782)
Bio::TestBlastReportHitMulti:
test_Hit_accession: .: (0.063003)
test_Hit_bit_score: .: (0.061492)
test_Hit_definition: .: (0.062044)
test_Hit_evalue: .: (0.062684)
test_Hit_hit_id: .: (0.060698)
test_Hit_hsps: .: (0.061916)
test_Hit_identity: .: (0.062721)
test_Hit_lap_at: .: (0.060545)
test_Hit_len: .: (0.061661)
test_Hit_midline: .: (0.062857)
test_Hit_num: .: (0.060668)
test_Hit_overlap: .: (0.061809)
test_Hit_query_def: .: (0.062554)
test_Hit_query_end: .: (0.060744)
test_Hit_query_id: .: (0.061733)
test_Hit_query_len: .: (0.062763)
test_Hit_query_seq: .: (0.060741)
test_Hit_query_start: .: (0.062109)
test_Hit_taeget_def: .: (0.062446)
test_Hit_target_end: .: (0.060936)
test_Hit_target_id: .: (0.062407)
test_Hit_target_len: .: (0.062065)
test_Hit_target_seq: .: (0.061040)
test_Hit_target_start: .: (0.062747)
Bio::TestBlastReportHitMultiREXML:
test_Hit_accession: .: (0.062785)
test_Hit_bit_score: .: (0.060958)
test_Hit_definition: .: (0.062912)
test_Hit_evalue: .: (0.061818)
test_Hit_hit_id: .: (0.060992)
test_Hit_hsps: .: (0.062801)
test_Hit_identity: .: (0.061787)
test_Hit_lap_at: .: (0.061034)
test_Hit_len: .: (0.065139)
test_Hit_midline: .: (0.062574)
test_Hit_num: .: (0.062107)
test_Hit_overlap: .: (0.063149)
test_Hit_query_def: .: (0.062183)
test_Hit_query_end: .: (0.061103)
test_Hit_query_id: .: (0.062722)
test_Hit_query_len: .: (0.061944)
test_Hit_query_seq: .: (0.061307)
test_Hit_query_start: .: (0.062472)
test_Hit_taeget_def: .: (0.062086)
test_Hit_target_end: .: (0.061160)
test_Hit_target_id: .: (0.062364)
test_Hit_target_len: .: (0.061826)
test_Hit_target_seq: .: (0.061105)
test_Hit_target_start: .: (0.062575)
Bio::TestBlastReportHitREXML:
test_Hit_accession: .: (0.020808)
test_Hit_bit_score: .: (0.020263)
test_Hit_definition: .: (0.021743)
test_Hit_evalue: .: (0.020529)
test_Hit_hit_id: .: (0.020359)
test_Hit_hsps: .: (0.020404)
test_Hit_identity: .: (0.020730)
test_Hit_lap_at: .: (0.021696)
test_Hit_len: .: (0.020930)
test_Hit_midline: .: (0.020701)
test_Hit_num: .: (0.020669)
test_Hit_overlap: .: (0.020535)
test_Hit_query_def: .: (0.021649)
test_Hit_query_end: .: (0.020900)
test_Hit_query_id: .: (0.020559)
test_Hit_query_len: .: (0.020449)
test_Hit_query_seq: .: (0.021599)
test_Hit_query_start: .: (0.020919)
test_Hit_taeget_def: .: (0.020252)
test_Hit_target_end: .: (0.020452)
test_Hit_target_id: .: (0.020672)
test_Hit_target_len: .: (0.022767)
test_Hit_target_seq: .: (0.020843)
test_Hit_target_start: .: (0.020364)
Bio::TestBlastReportHitTabular:
test_Hit_accession: .: (0.000415)
test_Hit_bit_score: .: (0.000181)
test_Hit_definition: .: (0.000275)
test_Hit_evalue: .: (0.000214)
test_Hit_hit_id: .: (0.000184)
test_Hit_hsps: .: (0.000320)
test_Hit_identity: .: (0.000191)
test_Hit_lap_at: .: (0.000179)
test_Hit_len: .: (0.000167)
test_Hit_midline: .: (0.000168)
test_Hit_num: .: (0.000170)
test_Hit_overlap: .: (0.000171)
test_Hit_query_def: .: (0.000179)
test_Hit_query_end: .: (0.000170)
test_Hit_query_id: .: (0.000174)
test_Hit_query_len: .: (0.000166)
test_Hit_query_seq: .: (0.000168)
test_Hit_query_start: .: (0.000171)
test_Hit_taeget_def: .: (0.000387)
test_Hit_target_end: .: (0.000223)
test_Hit_target_id: .: (0.000171)
test_Hit_target_len: .: (0.000166)
test_Hit_target_seq: .: (0.000167)
test_Hit_target_start: .: (0.000168)
Bio::TestBlastReportHsp:
test_Hsp_align_len: .: (0.020550)
test_Hsp_bit_score: .: (0.020519)
test_Hsp_density: .: (0.022270)
test_Hsp_evalue: .: (0.020480)
test_Hsp_gaps: .: (0.020642)
test_Hsp_hit_frame: .: (0.020914)
test_Hsp_hit_from: .: (0.021816)
test_Hsp_hit_to: .: (0.020698)
test_Hsp_hseq: .: (0.020307)
test_Hsp_identity: .: (0.020406)
test_Hsp_midline: .: (0.020385)
test_Hsp_mismatch_count: .: (0.021557)
test_Hsp_num: .: (0.020569)
test_Hsp_pattern_from: .: (0.020512)
test_Hsp_pattern_to: .: (0.020326)
test_Hsp_percent_identity: .: (0.020691)
test_Hsp_positive: .: (0.021578)
test_Hsp_qseq: .: (0.020339)
test_Hsp_query_frame: .: (0.020425)
test_Hsp_query_from: .: (0.020212)
test_Hsp_query_to: .: (0.021578)
test_Hsp_score: .: (0.020616)
Bio::TestBlastReportHspDefault:
test_Hsp_align_len: .: (0.000809)
test_Hsp_bit_score: .: (0.000529)
test_Hsp_evalue: .: (0.000539)
test_Hsp_gaps: .: (0.000535)
test_Hsp_hit_frame: .: (0.000533)
test_Hsp_hit_from: .: (0.000885)
test_Hsp_hit_to: .: (0.000875)
test_Hsp_hseq: .: (0.000805)
test_Hsp_identity: .: (0.000537)
test_Hsp_midline: .: (0.000788)
test_Hsp_percent_identity: .: (0.000625)
test_Hsp_positive: .: (0.000534)
test_Hsp_qseq: .: (0.000781)
test_Hsp_query_frame: .: (0.000670)
test_Hsp_query_from: .: (0.000767)
test_Hsp_query_to: .: (0.000819)
test_Hsp_score: .: (0.000529)
Bio::TestBlastReportHspMulti:
test_Hsp_align_len: .: (0.061063)
test_Hsp_bit_score: .: (0.063596)
test_Hsp_density: .: (0.116844)
test_Hsp_evalue: .: (0.061647)
test_Hsp_gaps: .: (0.062377)
test_Hsp_hit_frame: .: (0.062346)
test_Hsp_hit_from: .: (0.060914)
test_Hsp_hit_to: .: (0.062281)
test_Hsp_hseq: .: (0.060981)
test_Hsp_identity: .: (0.061928)
test_Hsp_midline: .: (0.062509)
test_Hsp_mismatch_count: .: (0.060900)
test_Hsp_num: .: (0.061822)
test_Hsp_pattern_from: .: (0.060573)
test_Hsp_pattern_to: .: (0.061344)
test_Hsp_percent_identity: .: (0.062638)
test_Hsp_positive: .: (0.060558)
test_Hsp_qseq: .: (0.061967)
test_Hsp_query_frame: .: (0.060488)
test_Hsp_query_from: .: (0.061628)
test_Hsp_query_to: .: (0.062273)
test_Hsp_score: .: (0.060289)
Bio::TestBlastReportHspMultiREXML:
test_Hsp_align_len: .: (0.062075)
test_Hsp_bit_score: .: (0.060539)
test_Hsp_density: .: (0.061706)
test_Hsp_evalue: .: (0.062097)
test_Hsp_gaps: .: (0.061226)
test_Hsp_hit_frame: .: (0.061979)
test_Hsp_hit_from: .: (0.061720)
test_Hsp_hit_to: .: (0.060765)
test_Hsp_hseq: .: (0.062535)
test_Hsp_identity: .: (0.060433)
test_Hsp_midline: .: (0.061880)
test_Hsp_mismatch_count: .: (0.061636)
test_Hsp_num: .: (0.061019)
test_Hsp_pattern_from: .: (0.062408)
test_Hsp_pattern_to: .: (0.060328)
test_Hsp_percent_identity: .: (0.062249)
test_Hsp_positive: .: (0.061923)
test_Hsp_qseq: .: (0.060698)
test_Hsp_query_frame: .: (0.062222)
test_Hsp_query_from: .: (0.060317)
test_Hsp_query_to: .: (0.061489)
test_Hsp_score: .: (0.062337)
Bio::TestBlastReportHspREXML:
test_Hsp_align_len: .: (0.020588)
test_Hsp_bit_score: .: (0.020126)
test_Hsp_density: .: (0.020775)
test_Hsp_evalue: .: (0.020370)
test_Hsp_gaps: .: (0.021692)
test_Hsp_hit_frame: .: (0.020584)
test_Hsp_hit_from: .: (0.020600)
test_Hsp_hit_to: .: (0.020622)
test_Hsp_hseq: .: (0.020471)
test_Hsp_identity: .: (0.021417)
test_Hsp_midline: .: (0.020688)
test_Hsp_mismatch_count: .: (0.020417)
test_Hsp_num: .: (0.020578)
test_Hsp_pattern_from: .: (0.020098)
test_Hsp_pattern_to: .: (0.021304)
test_Hsp_percent_identity: .: (0.020516)
test_Hsp_positive: .: (0.020375)
test_Hsp_qseq: .: (0.020357)
test_Hsp_query_frame: .: (0.020268)
test_Hsp_query_from: .: (0.021259)
test_Hsp_query_to: .: (0.020875)
test_Hsp_score: .: (0.020326)
Bio::TestBlastReportHspTabular:
test_Hsp_align_len: .: (0.000372)
test_Hsp_bit_score: .: (0.000178)
test_Hsp_density: .: (0.000179)
test_Hsp_evalue: .: (0.000177)
test_Hsp_gaps: .: (0.000172)
test_Hsp_hit_frame: .: (0.000168)
test_Hsp_hit_from: .: (0.000171)
test_Hsp_hit_to: .: (0.000405)
test_Hsp_hseq: .: (0.000169)
test_Hsp_identity: .: (0.000165)
test_Hsp_midline: .: (0.000166)
test_Hsp_mismatch_count: .: (0.000166)
test_Hsp_num: .: (0.000260)
test_Hsp_pattern_from: .: (0.000171)
test_Hsp_pattern_to: .: (0.000166)
test_Hsp_percent_identity: .: (0.000167)
test_Hsp_positive: .: (0.000165)
test_Hsp_qseq: .: (0.000167)
test_Hsp_query_frame: .: (0.000165)
test_Hsp_query_from: .: (0.000169)
test_Hsp_query_to: .: (0.000381)
test_Hsp_score: .: (0.000212)
Bio::TestBlastReportIteration:
test_hits: .: (0.020588)
test_message: .: (0.020349)
test_num: .: (0.021594)
test_statistics: .: (0.020601)
Bio::TestBlastReportIterationDefault:
test_hits: .: (0.000938)
test_message: .: (0.000518)
test_num: .: (0.000602)
Bio::TestBlastReportIterationMulti:
test_each: .: (0.060868)
test_hits: .: (0.062931)
test_message: .: (0.062269)
test_num: .: (0.060775)
test_query_def: .: (0.062410)
test_query_id: .: (0.060930)
test_query_len: .: (0.061806)
test_statistics: .: (0.062774)
Bio::TestBlastReportIterationMultiREXML:
test_each: .: (0.061175)
test_hits: .: (0.061857)
test_message: .: (0.062124)
test_num: .: (0.060998)
test_query_def: .: (0.062691)
test_query_id: .: (0.060682)
test_query_len: .: (0.063666)
test_statistics: .: (0.063720)
Bio::TestBlastReportIterationREXML:
test_hits: .: (0.020797)
test_message: .: (0.020961)
test_num: .: (0.020647)
test_statistics: .: (0.021808)
Bio::TestBlastReportIterationTabular:
test_hits: .: (0.000406)
test_message: .: (0.000180)
test_num: .: (0.000172)
test_statistics: .: (0.000174)
Bio::TestBlastReportMulti:
test_db: .: (0.061206)
test_db_len: .: (0.063199)
test_db_num: .: (0.060876)
test_each_hit: .: (0.061776)
test_each_iteration: .: (0.062753)
test_eff_space: .: (0.060632)
test_entropy: .: (0.062041)
test_expect: .: (0.062406)
test_filter: .: (0.060468)
test_gap_extend: .: (0.062067)
test_gap_open: .: (0.061846)
test_hits: .: (0.060829)
test_hsp_len: .: (0.062771)
test_iterations: .: (0.061497)
test_kappa: .: (0.061021)
test_lambda: .: (0.063028)
test_matrix: .: (0.061058)
test_message: .: (0.061635)
test_parameters: .: (0.063036)
test_pattern: .: (0.060544)
test_program: .: (0.061786)
test_query_def: .: (0.062531)
test_query_id: .: (0.060738)
test_query_len: .: (0.061959)
test_reference: .: (0.062533)
test_reports: .: (0.060992)
test_statistics: .: (0.062102)
test_version: .: (0.062560)
Bio::TestBlastReportMultiREXML:
test_db: .: (0.061069)
test_db_len: .: (0.061788)
test_db_num: .: (0.063006)
test_each_hit: .: (0.060661)
test_each_iteration: .: (0.061892)
test_eff_space: .: (0.062602)
test_entropy: .: (0.060751)
test_expect: .: (0.062250)
test_filter: .: (0.062531)
test_gap_extend: .: (0.060856)
test_gap_open: .: (0.061521)
test_hits: .: (0.062602)
test_hsp_len: .: (0.060655)
test_iterations: .: (0.061833)
test_kappa: .: (0.062686)
test_lambda: .: (0.061190)
test_matrix: .: (0.060986)
test_message: .: (0.062815)
test_parameters: .: (0.063257)
test_pattern: .: (0.061209)
test_program: .: (0.062636)
test_query_def: .: (0.062793)
test_query_id: .: (0.060436)
test_query_len: .: (0.062156)
test_reference: .: (0.062874)
test_reports: .: (0.061606)
test_statistics: .: (0.061487)
test_version: .: (0.062740)
Bio::TestBlastReportREXML:
test_db: .: (0.020946)
test_db_len: .: (0.020666)
test_db_num: .: (0.021869)
test_each_hit: .: (0.020318)
test_each_iteration: .: (0.020465)
test_eff_space: .: (0.020292)
test_entrez_query: .: (0.021458)
test_entropy: .: (0.020882)
test_expect: .: (0.020361)
test_filter: .: (0.020366)
test_gap_extend: .: (0.020332)
test_gap_open: .: (0.021734)
test_hits: .: (0.020700)
test_hsp_len: .: (0.020514)
test_inclusion: .: (0.020294)
test_iterations: .: (0.021203)
test_kappa: .: (0.020841)
test_lambda: .: (0.020366)
test_matrix: .: (0.020331)
test_message: .: (0.020291)
test_parameters: .: (0.021738)
test_pattern: .: (0.020526)
test_program: .: (0.020351)
test_query_def: .: (0.020520)
test_query_id: .: (0.021669)
test_query_len: .: (0.020888)
test_reference: .: (0.020321)
test_sc_match: .: (0.020749)
test_sc_mismatch: .: (0.020571)
test_statistics: .: (0.021460)
test_version: .: (0.020500)
Bio::TestBlastReportTabular:
test_db: .: (0.000514)
test_db_len: .: (0.000185)
test_db_num: .: (0.000169)
test_each_hit: .: (0.000173)
test_each_iteration: .: (0.000168)
test_eff_space: .: (0.000167)
test_entrez_query: .: (0.000174)
test_entropy: .: (0.000167)
test_expect: .: (0.000166)
test_filter: .: (0.000165)
test_gap_extend: .: (0.000285)
test_gap_open: .: (0.000191)
test_hits: .: (0.000174)
test_hsp_len: .: (0.000169)
test_inclusion: .: (0.000167)
test_iterations: .: (0.000166)
test_kappa: .: (0.000166)
test_lambda: .: (0.000228)
test_matrix: .: (0.000177)
test_message: .: (0.000170)
test_parameters: .: (0.000170)
test_pattern: .: (0.000170)
test_program: .: (0.000165)
test_query_def: .: (0.000180)
test_query_id: .: (0.000175)
test_query_len: .: (0.000198)
test_reference: .: (0.000200)
test_sc_match: .: (0.000168)
test_sc_mismatch: .: (0.000165)
test_statistics: .: (0.000171)
test_version: .: (0.000165)
Bio::TestChain:
test_aaseq: .: (0.000401)
test_addLigand: .: (0.000141)
test_addResidue: .: (0.000258)
test_atom_seq: .: (0.000152)
test_comp: .: (0.000181)
test_each: .: (0.000155)
test_each_heterogen: .: (0.000153)
test_each_residue: .: (0.000154)
test_get_heterogen_by_id: .: (0.000144)
test_get_residue_by_id: .: (0.000141)
test_inspect: .: (0.000173)
test_rehash: .: (0.000144)
test_rehash_heterogens: .: (0.000128)
test_rehash_residues: .: (0.000134)
test_square_brace: .: (0.000145)
test_to_s: .: (0.000159)
Bio::TestChainFinder:
test_chains: .: (0.000318)
test_each_chain: .: (0.000161)
test_find_chain: .: (0.000454)
Bio::TestClustalWReport::TestClustalWReport:
test_alignment: .: (0.014336)
test_header: .: (0.000837)
test_match_line: .: (0.001074)
test_sequence0: .: (0.001014)
test_sequence1: .: (0.000795)
Bio::TestClustalWReport::TestClustalWReportSeqnos:
test_alignment: .: (0.014808)
test_header: .: (0.001210)
test_match_line: .: (0.001118)
test_sequence0: .: (0.001240)
test_sequence1: .: (0.001073)
Bio::TestClustalWReport::TestClustalWReportWith2ndArgument:
test_alignment: .: (0.020368)
test_header: .: (0.000992)
test_match_line: .: (0.000846)
test_sequence0: .: (0.000807)
test_sequence1: .: (0.000782)
Bio::TestCodonTable:
test_Tables: .: (0.000278)
test_accessor: .: (0.000352)
test_definition: .: (0.000198)
test_each: .: (0.000172)
test_revtrans: .: (0.000247)
test_self_accessor: .: (0.000121)
test_self_copy: .: (0.001123)
test_set_accessor: .: (0.211750)
test_start: .: (0.000139)
test_start_codon?: .: (0.000141)
test_stop: .: (0.000114)
test_stop_codon?: .: (0.000133)
test_table: .: (0.000113)
Bio::TestCodonTableConstants:
test_Definitions: .: (0.000285)
test_Starts: .: (0.000260)
test_Tables: .: (0.000107)
test_stops: .: (0.000125)
Bio::TestColorScheme:
test_buried: .: (0.001392)
Bio::TestCommand:
test_command_constants: .: (0.000281)
test_escape_shell: .: (0.000183)
test_escape_shell_unix: .: (0.000149)
test_escape_shell_windows: .: (0.000154)
test_make_cgi_params_by_array_of_array: .: (0.000545)
test_make_cgi_params_by_array_of_hash: .: (0.000409)
test_make_cgi_params_by_array_of_string: .: (0.000205)
test_make_cgi_params_by_hash_in_string: .: (0.000781)
test_make_cgi_params_by_hash_in_symbol: .: (0.000593)
test_make_cgi_params_by_string: .: (0.000331)
test_make_command_line: .: (0.000151)
test_make_command_line_unix: .: (0.000139)
test_make_command_line_windows: .: (0.000142)
test_safe_command_line_array: .: (0.000159)
test_safe_command_line_array_passthrough: .: (0.000166)
Bio::TestContingencyTable:
test_lite_example: .: (0.256516)
Bio::TestDB:
test_entry_id: .: (0.000307)
test_exists: .: (0.000165)
test_fetch: .: (0.000217)
test_get: .: (0.000113)
test_open: .: (0.000109)
test_tags: .: (0.000109)
Bio::TestDataType:
test_const_like_method: .: (0.000582)
test_pdb_achar: .: (0.000250)
test_pdb_atom: .: (0.000226)
test_pdb_character: .: (0.000342)
test_pdb_date: .: (0.000239)
test_pdb_idcode: .: (0.000225)
test_pdb_integer: .: (0.000112)
test_pdb_list: .: (0.000119)
test_pdb_lstring: .: (0.000203)
test_pdb_real: .: (0.000302)
test_pdb_resudue_name: .: (0.000272)
test_pdb_slist: .: (0.000125)
test_pdb_string: .: (0.000232)
test_pdb_stringrj: .: (0.000120)
test_pdb_symop: .: (0.000224)
test_specification_list: .: (0.000139)
Bio::TestEMBL:
test_ac: .: (0.000843)
test_accession: .: (0.000471)
test_cc: .: (0.000432)
test_de: .: (0.000646)
test_division: .: (0.000625)
test_dr: .: (0.000435)
test_dt: .: (0.000453)
test_dt_created: .: (0.000462)
test_dt_iterator: .: (0.000440)
test_dt_updated: .: (0.000579)
test_each_cds: .: (0.000885)
test_each_gene: .: (0.000657)
test_entry: .: (0.000655)
test_fh: .: (0.000465)
test_ft: .: (0.000676)
test_ft_accessor: .: (0.000925)
test_ft_iterator: .: (0.000911)
test_id_line: .: (0.000502)
test_id_line_data_class: .: (0.000499)
test_id_line_division: .: (0.000496)
test_id_line_entry_name: .: (0.000494)
test_id_line_iterator: .: (0.000634)
test_id_line_molecule_type: .: (0.000493)
test_id_line_sequence_length: .: (0.000489)
test_kw: .: (0.000583)
test_molecule: .: (0.000519)
test_oc: .: (0.000561)
test_og: .: (0.000437)
test_os: .: (0.000873)
test_ref: .: (0.000656)
test_references: .: (0.000852)
test_seq: .: (0.001003)
test_sequence_length: .: (0.000527)
test_sq: .: (0.000526)
test_sq_get: .: (0.000490)
test_sv: .: (0.000463)
test_version: .: (0.000615)
Bio::TestEMBL89:
test_ac: .: (0.000638)
test_accession: .: (0.000453)
test_cc: .: (0.000518)
test_de: .: (0.000630)
test_division: .: (0.000513)
test_dr: .: (0.000432)
test_dt: .: (0.000442)
test_dt_created: .: (0.000437)
test_dt_iterator: .: (0.000588)
test_dt_updated: .: (0.000498)
test_each_cds: .: (0.000689)
test_each_gene: .: (0.000643)
test_entry: .: (0.000531)
test_fh: .: (0.000529)
test_ft: .: (0.000669)
test_ft_accessor: .: (0.003110)
test_ft_iterator: .: (0.000717)
test_id_line: .: (0.000506)
test_id_line_data_class: .: (0.000799)
test_id_line_division: .: (0.000667)
test_id_line_entry_name: .: (0.000486)
test_id_line_iterator: .: (0.000489)
test_id_line_molecule_type: .: (0.000489)
test_id_line_sequence_length: .: (0.000610)
test_id_line_sequence_version: .: (0.000625)
test_kw: .: (0.000472)
test_molecule: .: (0.000509)
test_oc: .: (0.000617)
test_og: .: (0.000426)
test_os: .: (0.000488)
test_ref: .: (0.000834)
test_references: .: (0.000826)
test_seq: .: (0.000813)
test_sequence_length: .: (0.000508)
test_sq: .: (0.000596)
test_sq_get: .: (0.000472)
test_sv: .: (0.000648)
test_version: .: (0.000519)
Bio::TestEMBLAPI:
test_ac: .: (0.000483)
test_accessions: .: (0.000206)
Bio::TestEMBLCommon:
test_ac: .: (0.000253)
test_accession: .: (0.000115)
test_accessions: .: (0.000117)
test_de: .: (0.000112)
test_definition: .: (0.000116)
test_description: .: (0.000121)
test_dr: .: (0.000116)
test_keywords: .: (0.000118)
test_kw: .: (0.000112)
test_oc: .: (0.000118)
test_og: .: (0.000109)
test_os: .: (0.000139)
test_ref: .: (0.000262)
test_references: .: (0.000125)
Bio::TestEMBLDB:
test_fetch: .: (0.000339)
test_p_entry2hash: .: (0.000111)
Bio::TestEMBLToBioSequence:
test_classification: .: (0.004892)
test_date_created: .: (0.000724)
test_date_modified: .: (0.000627)
test_definition: .: (0.000675)
test_division: .: (0.000560)
test_entry_id: .: (0.000550)
test_entry_version: .: (0.000552)
test_features: .: (0.000842)
test_keywords: .: (0.000591)
test_molecule_type: .: (0.000580)
test_primary_accession: .: (0.000508)
test_references: .: (0.000939)
test_release_created: .: (0.000510)
test_release_modified: .: (0.000510)
test_secondary_accessions: .: (0.000611)
test_sequence_version: .: (0.000609)
test_species: .: (0.000624)
test_topology: .: (0.000544)
Bio::TestEMBLToBioSequenceRoundTrip:
test_classification: .: (0.004458)
test_date_created: .: (0.004128)
test_date_modified: .: (0.003934)
test_definition: .: (0.004075)
test_division: .: (0.003706)
test_entry_id: .: (0.004272)
test_entry_version: .: (0.003975)
test_features: .: (0.004486)
test_keywords: .: (0.004233)
test_molecule_type: .: (0.003987)
test_primary_accession: .: (0.004160)
test_references: .: (0.004235)
test_release_created: .: (0.007282)
test_release_modified: .: (0.004237)
test_secondary_accessions: .: (0.004137)
test_sequence_version: .: (0.003971)
test_species: .: (0.004266)
test_topology: .: (0.004057)
Bio::TestFasta:
test_db: .: (0.000296)
test_format: .: (0.000112)
test_format_arg_integer: .: (0.000137)
test_format_arg_str: .: (0.000127)
test_ktup: .: (0.000126)
test_matrix: .: (0.000126)
test_option: .: (0.000167)
test_options: .: (0.000136)
test_output: .: (0.000108)
test_program: .: (0.000127)
test_server: .: (0.000128)
Bio::TestFastaDeflineEmb:
test_acc_version: .: (0.000293)
test_accession: .: (0.000173)
test_accessions: .: (0.000161)
test_description: .: (0.000147)
test_descriptions: .: (0.000140)
test_entry_id: .: (0.000137)
test_get_all_by_type: .: (0.000139)
test_gi: .: (0.000139)
test_id_strings: .: (0.000202)
test_list_ids: .: (0.000140)
test_locus: .: (0.000138)
test_words: .: (0.000188)
Bio::TestFastaDeflineGI1:
test_acc_version: .: (0.000286)
test_accession: .: (0.000381)
test_accessions: .: (0.000167)
test_description: .: (0.000150)
test_descriptions: .: (0.000149)
test_emb: .: (0.000248)
test_entry_id: .: (0.000167)
test_get_all_by_type: .: (0.000172)
test_get_emb: .: (0.000165)
test_gi: .: (0.000151)
test_id_strings: .: (0.000210)
test_list_ids: .: (0.000153)
test_locus: .: (0.000153)
test_words: .: (0.000215)
Bio::TestFastaDeflineGI2:
test_acc_version: .: (0.000530)
test_accession: .: (0.000154)
test_accessions: .: (0.000146)
test_description: .: (0.000134)
test_descriptions: .: (0.000134)
test_entry_id: .: (0.000134)
test_get_all_by_type: .: (0.000137)
test_gi: .: (0.000136)
test_id_strings: .: (0.000278)
test_list_ids: .: (0.000153)
test_locus: .: (0.000146)
test_sp: .: (0.000150)
test_words: .: (0.000179)
Bio::TestFastaDeflineGIMultiple:
test_acc_version: .: (0.000360)
test_accession: .: (0.000209)
test_accessions: .: (0.000492)
test_description: .: (0.000193)
test_descriptions: .: (0.000199)
test_entry_id: .: (0.000192)
test_get_all_by_type: .: (0.000197)
test_gi: .: (0.000190)
test_id_strings: .: (0.000441)
test_list_ids: .: (0.000228)
test_locus: .: (0.000208)
test_words: .: (0.000569)
Bio::TestFastaDeflineSce:
test_acc_version: .: (0.000350)
test_accession: .: (0.000176)
test_accessions: .: (0.000169)
test_description: .: (0.000162)
test_descriptions: .: (0.000164)
test_entry_id: .: (0.000162)
test_get_all_by_type: .: (0.000167)
test_gi: .: (0.000166)
test_id_strings: .: (0.000277)
test_list_ids: .: (0.000169)
test_locus: .: (0.000284)
test_words: .: (0.000292)
Bio::TestFastaDeflineSimple:
test_acc_version: .: (0.000275)
test_accession: .: (0.000130)
test_accessions: .: (0.000123)
test_description: .: (0.000121)
test_descriptions: .: (0.000121)
test_entry_id: .: (0.000119)
test_get_all_by_type: .: (0.000120)
test_gi: .: (0.000122)
test_id_strings: .: (0.000152)
test_list_ids: .: (0.000121)
test_locus: .: (0.000121)
test_words: .: (0.000147)
Bio::TestFastaDeflineSwissProt:
test_acc_version: .: (0.000294)
test_accession: .: (0.000225)
test_accessions: .: (0.000179)
test_description: .: (0.000151)
test_descriptions: .: (0.000138)
test_entry_id: .: (0.000134)
test_get: .: (0.000144)
test_get_all_by_type: .: (0.000135)
test_id_strings: .: (0.000224)
test_list_ids: .: (0.000136)
test_locus: .: (0.000133)
test_sp: .: (0.000146)
test_words: .: (0.000241)
Bio::TestFastaDeflineTrembl:
test_acc_version: .: (0.000490)
test_accession: .: (0.000152)
test_accessions: .: (0.000143)
test_description: .: (0.000134)
test_descriptions: .: (0.000135)
test_entry_id: .: (0.000221)
test_get: .: (0.000154)
test_get_all_by_type: .: (0.000156)
test_id_strings: .: (0.000273)
test_list_ids: .: (0.000138)
test_locus: .: (0.000137)
test_tr: .: (0.000146)
test_words: .: (0.000282)
Bio::TestFastaFirstName:
test_first_name1: .: (0.000256)
test_first_name_multi_identifier: .: (0.000314)
test_first_name_single_worded_defintion: .: (0.000123)
test_no_definition: .: (0.000119)
test_space_before_first_name: .: (0.000123)
test_tabbed_defintion: .: (0.000122)
Bio::TestFastaFormat:
test_aalen: .: (0.000304)
test_aaseq: .: (0.000142)
test_acc_version: .: (0.000350)
test_accession: .: (0.000218)
test_accessions: .: (0.000190)
test_data: .: (0.000131)
test_definition: .: (0.000128)
test_entry: .: (0.000132)
test_entry_id: .: (0.000174)
test_entry_overrun: .: (0.000128)
test_first_name: .: (0.000133)
test_gi: .: (0.000448)
test_identifiers: .: (0.000224)
test_length: .: (0.000141)
test_query: .: (0.000161)
test_seq: .: (0.000140)
Bio::TestFastaFormatConst:
test_delimiter: .: (0.000251)
Bio::TestFastaFormatKeggGenesAA:
test_acc_version: .: (0.000411)
test_data: .: (0.000162)
test_definition: .: (0.000132)
test_entry: .: (0.000132)
test_entry_id: .: (0.000190)
test_first_name: .: (0.000434)
Bio::TestFastaFormatKeggGenesNT:
test_nalen: .: (0.000264)
test_naseq: .: (0.000132)
test_naseq_class: .: (0.000133)
Bio::TestFastaFormatSwissProt:
test_locus: .: (0.000282)
Bio::TestFastaInitialize:
test_new_1: .: (0.000658)
test_option: .: (0.000120)
test_option_backward_compatibility: .: (0.000226)
Bio::TestFastaNumericFormat:
test_arg: .: (0.000373)
test_data: .: (0.000177)
test_definition: .: (0.000122)
test_each: .: (0.000168)
test_entry: .: (0.000121)
test_entry_id: .: (0.000141)
test_length: .: (0.000171)
test_to_biosequence: .: (0.000962)
Bio::TestFastaQuery:
test_query: .: (0.000207)
test_self_local: .: (0.000085)
test_self_parser: .: (0.000083)
test_self_remote: .: (0.000083)
Bio::TestFastacmd:
test_database: .: (0.000318)
test_fastacmd: .: (0.000112)
test_methods: .: (0.000158)
Bio::TestFastq::TestFastq_error_diff_ids:
test_validate_format: .: (0.001076)
Bio::TestFastq::TestFastq_error_double_qual:
test_validate_format: .: (0.000618)
Bio::TestFastq::TestFastq_error_double_seq:
test_validate_format: .: (0.000585)
Bio::TestFastq::TestFastq_error_long_qual:
test_validate_format: .: (0.001031)
Bio::TestFastq::TestFastq_error_no_qual:
test_validate_format: .: (0.000720)
Bio::TestFastq::TestFastq_error_qual_del:
test_validate_format: .: (0.000603)
Bio::TestFastq::TestFastq_error_qual_escape:
test_validate_format: .: (0.000589)
Bio::TestFastq::TestFastq_error_qual_null:
test_validate_format: .: (0.000871)
Bio::TestFastq::TestFastq_error_qual_space:
test_validate_format: .: (0.000684)
Bio::TestFastq::TestFastq_error_qual_tab:
test_validate_format: .: (0.000590)
Bio::TestFastq::TestFastq_error_qual_unit_sep:
test_validate_format: .: (0.000621)
Bio::TestFastq::TestFastq_error_qual_vtab:
test_validate_format: .: (0.000818)
Bio::TestFastq::TestFastq_error_short_qual:
test_validate_format: .: (0.000722)
Bio::TestFastq::TestFastq_error_spaces:
test_validate_format: .: (0.001775)
Bio::TestFastq::TestFastq_error_tabs:
test_validate_format: .: (0.001650)
Bio::TestFastq::TestFastq_error_trunc_at_plus:
test_validate_format: .: (0.000841)
Bio::TestFastq::TestFastq_error_trunc_at_qual:
test_validate_format: .: (0.000610)
Bio::TestFastq::TestFastq_error_trunc_at_seq:
test_validate_format: .: (0.000566)
Bio::TestFastq::TestFastq_illumina_full_range:
test_error_probabilities_as_illumina: .: (0.013104)
test_error_probabilities_as_sanger: .: (0.008684)
test_error_probabilities_as_solexa: .: (0.008767)
test_quality_scores_as_illumina: .: (0.000534)
test_quality_scores_as_sanger: .: (0.000409)
test_quality_scores_as_solexa: .: (0.000500)
test_validate_format: .: (0.000710)
Bio::TestFastq::TestFastq_longreads_original_sanger:
test_definition: .: (0.001633)
test_entry_id: .: (0.001617)
test_error_probabilities: .: (0.276888)
test_nalen: .: (0.001661)
test_naseq: .: (0.001376)
test_quality_scores: .: (0.003093)
test_quality_string: .: (0.001227)
test_roundtrip: .: (0.233786)
test_seq: .: (0.001434)
test_sequence_string: .: (0.001542)
test_to_biosequence: .: (0.219595)
test_to_biosequence_and_output: .: (0.007727)
test_to_s: .: (0.001478)
test_validate_format: .: (0.001298)
test_validate_format_with_array: .: (0.001793)
Bio::TestFastq::TestFastq_mask:
test_mask_20: .: (0.000673)
test_mask_20_with_empty_string: .: (0.000503)
test_mask_20_with_longer_string: .: (0.000474)
test_mask_20_with_x: .: (0.000455)
test_mask_60: .: (0.001105)
Bio::TestFastq::TestFastq_sanger_full_range:
test_error_probabilities_as_illumina: .: (0.011833)
test_error_probabilities_as_sanger: .: (0.011821)
test_error_probabilities_as_solexa: .: (0.013373)
test_quality_scores_as_illumina: .: (0.000492)
test_quality_scores_as_sanger: .: (0.000382)
test_quality_scores_as_solexa: .: (0.000608)
test_validate_format: .: (0.001001)
Bio::TestFastq::TestFastq_solexa_full_range:
test_error_probabilities_as_illumina: .: (0.009223)
test_error_probabilities_as_sanger: .: (0.008967)
test_error_probabilities_as_solexa: .: (0.008663)
test_quality_scores_as_illumina: .: (0.000762)
test_quality_scores_as_sanger: .: (0.000506)
test_quality_scores_as_solexa: .: (0.000354)
test_validate_format: .: (0.000716)
Bio::TestFeature:
test_append: .: (0.000288)
test_append_nil: .: (0.000130)
test_assoc: .: (0.000299)
test_each: .: (0.000113)
test_feature: .: (0.000108)
test_locations: .: (0.000208)
test_new: .: (0.000109)
test_position: .: (0.000107)
test_qualifiers: .: (0.000108)
Bio::TestFeatures:
test_append: .: (0.000325)
test_arg: .: (0.000128)
test_each: .: (0.000125)
test_features: .: (0.000129)
Bio::TestFlatFile::TestDefaultAutoDetect:
test_aaindex1: .: (0.001299)
test_aaindex2: .: (0.000305)
test_blast: .: (0.000320)
test_blastxml: .: (0.000741)
test_embl: .: (0.000317)
test_embl_oldrelease: .: (0.000298)
test_fastaformat: .: (0.000470)
test_fastanumericformat: .: (0.000221)
test_fastq: .: (0.000219)
test_genbank: .: (0.000299)
test_genpept: .: (0.000320)
test_hmmer: .: (0.000260)
test_maxml_cluster: .: (0.004165)
test_maxml_sequence: .: (0.000261)
test_medline: .: (0.000205)
test_prosite: .: (0.004031)
test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future.
.: (0.003525)
test_transfac: .: (0.002264)
Bio::TestFlatFile::TestFlatFileClassMethod:
test_auto_0arg: .: (0.000328)
test_auto_1arg_filename: .: (0.000467)
test_auto_1arg_io: .: (0.000509)
test_auto_1arg_io_with_block: .: (0.000894)
test_auto_1arg_with_block: .: (0.000923)
test_auto_2arg_filename_mode: .: (0.000419)
test_auto_2arg_filename_mode_with_block: .: (0.000778)
test_auto_3arg: .: (0.000468)
test_auto_3arg_with_block: .: (0.000839)
test_foreach: .: (0.000819)
test_new_2arg_class: .: (0.000205)
test_new_2arg_nil: .: (0.000379)
test_open_0arg: .: (0.000145)
test_open_1arg_class: .: (0.000140)
test_open_1arg_filename: .: (0.000390)
test_open_1arg_io: .: (0.000394)
test_open_1arg_io_with_block: .: (0.001099)
test_open_1arg_nil: .: (0.000145)
test_open_1arg_with_block: .: (0.000787)
test_open_2arg_autodetect: .: (0.000385)
test_open_2arg_autodetect_io: .: (0.000392)
test_open_2arg_autodetect_io_with_block: .: (0.000973)
test_open_2arg_autodetect_with_block: .: (0.000873)
test_open_2arg_class: .: (0.000211)
test_open_2arg_class_io: .: (0.000211)
test_open_2arg_class_io_with_block: .: (0.000617)
test_open_2arg_class_with_block: .: (0.000588)
test_open_2arg_filename_mode: .: (0.000483)
test_open_2arg_filename_mode_with_block: .: (0.001064)
test_open_3arg: .: (0.000888)
test_open_3arg_with_block: .: (0.002167)
test_open_4arg: .: (0.001946)
test_to_a: .: (0.000663)
Bio::TestFlatFile::TestFlatFileFastaFormat:
test_autodetect: .: (0.000542)
test_close: .: (0.000172)
test_dbclass: .: (0.000170)
test_dbclass_eq: .: (0.000213)
test_dbclass_nil: .: (0.000261)
test_each: .: (0.000354)
test_each_entry: .: (0.000498)
test_ended_pos: .: (0.000400)
test_entry_pos_flag: .: (0.000213)
test_entry_raw: .: (0.000406)
test_eof?: .: (0.000562)
test_next_entry: .: (0.000452)
test_path: .: (0.000170)
test_pos: .: (0.000246)
test_raw: .: (0.000398)
test_rewind: .: (0.000264)
test_start_pos: .: (0.000289)
test_start_pos_ended_pos_not_recorded: .: (0.000321)
test_to_io: .: (0.000223)
Bio::TestFlatFile::TestFlatFileWithCustomClass:
test_simpleformat: .: (0.000358)
test_simpleformat2: .: (0.000235)
Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream:
test_close: .: (0.000260)
test_eof_false_after_prefetch: .: (0.000271)
test_eof_false_first: .: (0.000128)
test_eof_true: .: (0.000251)
test_getc: .: (0.000135)
test_getc_after_prefetch: .: (0.000134)
test_gets: .: (0.000136)
test_gets_equal_prefetch_gets: .: (0.000337)
test_gets_paragraph_mode: .: (0.000219)
test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000474)
test_gets_paragraph_mode_within_buffer: .: (0.000446)
test_gets_rs: .: (0.000186)
test_gets_rs_equal_prefetch_gets: .: (0.000200)
test_gets_rs_within_buffer: .: (0.000401)
test_pos: .: (0.000139)
test_pos=: .: (0.000155)
test_prefetch_buffer: .: (0.000136)
test_prefetch_gets: .: (0.000154)
test_prefetch_gets_with_arg: .: (0.000171)
test_rewind: .: (0.000130)
test_skip_spaces: .: (0.000153)
test_to_io: .: (0.000321)
test_ungetc: .: (0.000166)
test_ungetc_after_prefetch: .: (0.000161)
test_ungets: .: (0.000478)
Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod:
test_self_for_io: .: (0.000311)
test_self_open_file: .: (0.000160)
test_self_open_file_with_block: .: (0.000188)
Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg:
test_parse_file_open_arg_int_opt: .: (0.000273)
test_parse_file_open_arg_int_perm: .: (0.000116)
test_parse_file_open_arg_int_perm_opt: .: (0.000116)
test_parse_file_open_arg_integer: .: (0.000151)
test_parse_file_open_arg_nil: .: (0.000112)
test_parse_file_open_arg_opt: .: (0.000344)
test_parse_file_open_arg_opt_with_integer_mode: .: (0.000136)
test_parse_file_open_arg_str: .: (0.000126)
test_parse_file_open_arg_str_opt: .: (0.000134)
test_parse_file_open_arg_str_perm: .: (0.000126)
test_parse_file_open_arg_str_perm_opt: .: (0.000127)
test_parse_file_open_arg_str_with_enc: .: (0.000215)
test_parse_file_open_arg_str_with_ext_enc: .: (0.000149)
test_parse_file_open_mode_integer: .: (0.000130)
test_parse_file_open_mode_nil: .: (0.000125)
test_parse_file_open_mode_str: .: (0.000121)
test_parse_file_open_mode_str_with_enc: .: (0.000126)
test_parse_file_open_mode_str_with_ext_enc: .: (0.000123)
Bio::TestFlatFileSplitter::TestTemplate:
test_dbclass: .: (0.000260)
test_entry: .: (0.000133)
test_entry_ended_pos: .: (0.000131)
test_entry_pos_flag: .: (0.000150)
test_entry_start_pos: .: (0.000124)
test_get_entry: .: (0.000155)
test_rewind: .: (0.000140)
test_skip_leader: .: (0.000141)
test_stream: .: (0.000115)
test_stream_pos: .: (0.000151)
Bio::TestFlatFileSplitter::TestDefault:
test_delimiter: .: (0.000286)
test_delimiter_overrun: .: (0.000276)
test_entry: .: (0.000190)
test_entry_ended_pos: .: (0.000154)
test_entry_ended_pos_default_nil: .: (0.000145)
test_entry_start_pos: .: (0.000147)
test_entry_start_pos_default_nil: .: (0.000143)
test_get_entry: .: (0.000451)
test_get_parsed_entry: .: (0.000310)
test_header: .: (0.000120)
test_skip_leader: .: (0.000171)
test_skip_leader_without_header: .: (0.000181)
Bio::TestFlatFileSplitter::TestLineOriented:
test_dbclass: .: (0.000373)
test_entry_ended_pos: .: (0.000297)
test_entry_start_pos: .: (0.000358)
test_flag_to_fetch_header: .: (0.000523)
test_get_entry: .: (0.000406)
test_get_parsed_entry: .: (0.000399)
test_rewind: .: (0.000297)
test_skip_leader: .: (0.000172)
Bio::TestGCGMsf:
test_alignment: .: (0.001544)
test_checksum: .: (0.000413)
test_compcheck: .: (0.000308)
test_date: .: (0.000296)
test_description: .: (0.000297)
test_entry_id: .: (0.000295)
test_gap_length_weight: .: (0.000468)
test_gap_weight: .: (0.000304)
test_heading: .: (0.000294)
test_length: .: (0.000288)
test_seq_type: .: (0.000291)
test_symbol_comparison_table: .: (0.000415)
test_validate_checksum: .: (0.002492)
Bio::TestGFF:
test_record_class: .: (0.000662)
test_records: .: (0.000543)
Bio::TestGFF2:
test_const_version: .: (0.000925)
test_gff_version: .: (0.000540)
test_metadata: .: (0.000551)
test_metadata_size: .: (0.000533)
test_records_size: .: (0.000698)
test_to_s: .: (0.001135)
Bio::TestGFF2ComplexAttributes:
test_attributes_case1: .: (0.000305)
test_attributes_case2: .: (0.000417)
test_attributes_incompatible_backslash_semicolon: .: (0.000279)
Bio::TestGFF2MetaData:
test_data: .: (0.000238)
test_directive: .: (0.000109)
test_parse: .: (0.000121)
Bio::TestGFF2Record:
test_attribute: .: (0.000597)
test_attribute_nonexistent: .: (0.000465)
test_attributes: .: (0.000571)
test_attributes_to_hash: .: (0.000381)
test_comment_only?: .: (0.000326)
test_delete_attribute: .: (0.000380)
test_delete_attribute_multiple: .: (0.000396)
test_delete_attribute_multiple2: .: (0.000445)
test_delete_attribute_multiple_nil: .: (0.000583)
test_delete_attribute_nil: .: (0.000529)
test_delete_attribute_nonexistent: .: (0.000413)
test_delete_attributes: .: (0.000388)
test_delete_attributes_multiple: .: (0.000389)
test_delete_attributes_nonexistent: .: (0.000378)
test_end: .: (0.000493)
test_eqeq: .: (0.000849)
test_eqeq_false: .: (0.000916)
test_feature: .: (0.000327)
test_frame: .: (0.000508)
test_get_attribute: .: (0.000452)
test_get_attribute_nonexistent: .: (0.000348)
test_get_attributes: .: (0.000497)
test_get_attributes_nonexistent: .: (0.000331)
test_replace_attributes: .: (0.000394)
test_replace_attributes_multiple_multiple_over: .: (0.000498)
test_replace_attributes_multiple_multiple_same: .: (0.000531)
test_replace_attributes_multiple_multiple_two: .: (0.000387)
test_replace_attributes_multiple_single: .: (0.000388)
test_replace_attributes_nonexistent: .: (0.000377)
test_replace_attributes_nonexistent_multiple: .: (0.000386)
test_replace_attributes_single_multiple: .: (0.000633)
test_score: .: (0.000430)
test_self_parse: .: (0.000804)
test_seqname: .: (0.000324)
test_set_attribute: .: (0.000699)
test_set_attribute_multiple: .: (0.000403)
test_set_attribute_nonexistent: .: (0.000372)
test_sort_attributes_by_tag!: .: (0.000480)
test_sort_attributes_by_tag_bang_test2: .: (0.000959)
test_sort_attributes_by_tag_bang_with_block: .: (0.000555)
test_source: .: (0.000672)
test_start: .: (0.000327)
test_strand: .: (0.000327)
test_to_s: .: (0.000596)
Bio::TestGFF2RecordEmpty:
test_comment: .: (0.000313)
test_comment_eq: .: (0.000136)
test_comment_only?: .: (0.000128)
test_comment_only_false: .: (0.000123)
test_to_s: .: (0.000137)
test_to_s_not_empty: .: (0.000451)
Bio::TestGFF3:
test_const_version: .: (0.001008)
test_gff_version: .: (0.000927)
test_records: .: (0.001263)
test_sequence_regions: .: (0.000951)
test_sequences: .: (0.000841)
test_to_s: .: (0.001764)
Bio::TestGFF3MetaData:
test_data: .: (0.000248)
test_directive: .: (0.000107)
test_parse: .: (0.000124)
Bio::TestGFF3Record:
test_attributes: .: (0.000470)
test_end: .: (0.000299)
test_feature: .: (0.000371)
test_frame: .: (0.000294)
test_id: .: (0.004409)
test_score: .: (0.000313)
test_seqname: .: (0.000446)
test_source: .: (0.000311)
test_start: .: (0.000310)
test_strand: .: (0.000593)
test_to_s: .: (0.000520)
test_to_s_attr_order_changed: .: (0.000614)
Bio::TestGFF3RecordEscape:
test_escape: .: (0.000308)
test_escape_attribute: .: (0.000187)
test_escape_seqid: .: (0.000604)
test_unescape: .: (0.000189)
Bio::TestGFF3RecordGap:
test___scan_gap: .: (0.000458)
test_eqeq: .: (0.000279)
test_new_from_sequences_na: .: (0.000278)
test_new_from_sequences_na_aa: .: (0.000435)
test_new_from_sequences_na_aa_boundary_gap: .: (0.000895)
test_new_from_sequences_na_aa_example: .: (0.000468)
test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000480)
test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000366)
test_process_sequences_na: .: (0.000266)
test_process_sequences_na_aa: .: (0.000268)
test_process_sequences_na_aa_reverse_frameshift: .: (0.000527)
test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000290)
test_process_sequences_na_aa_tooshort: .: (0.000406)
test_process_sequences_na_tooshort: .: (0.000346)
test_to_s: .: (0.000270)
Bio::TestGFF3RecordMisc:
test_attributes_none: .: (0.000454)
test_attributes_one: .: (0.000165)
test_attributes_with_escaping: .: (0.000456)
test_id_multiple: .: (0.000329)
test_id_multiple2: .: (0.000313)
test_id_replace: .: (0.000200)
test_id_set: .: (0.000236)
test_initialize_9: .: (0.000115)
test_phase: .: (0.000200)
test_score: .: (0.000171)
test_to_s_void: .: (0.000143)
Bio::TestGFF3RecordTarget:
test_end: .: (0.000530)
test_parse: .: (0.000426)
test_start: .: (0.000193)
test_strand: .: (0.000147)
test_target_id: .: (0.000149)
test_to_s: .: (0.000238)
Bio::TestGFF3SequenceRegion:
test_end: .: (0.000286)
test_parse: .: (0.000248)
test_seqid: .: (0.000147)
test_start: .: (0.000139)
test_to_s: .: (0.000230)
Bio::TestGFFRecord:
test_attributes: .: (0.000303)
test_comment: .: (0.000157)
test_end: .: (0.000152)
test_feature: .: (0.000153)
test_frame: .: (0.000244)
test_score: .: (0.000154)
test_seqname: .: (0.000153)
test_source: .: (0.000150)
test_start: .: (0.000153)
test_strand: .: (0.000150)
Bio::TestGFFRecordConstruct:
test_add_seqname: .: (0.000256)
Bio::TestGeneAssociation:
test_aspect: .: (0.000643)
test_assigned_by: .: (0.000147)
test_date: .: (0.000146)
test_db: .: (0.000142)
test_db_object_id: .: (0.000145)
test_db_object_name: .: (0.000145)
test_db_object_symbol: .: (0.000143)
test_db_object_synonym: .: (0.000146)
test_db_object_type: .: (0.000313)
test_db_reference: .: (0.000177)
test_evidence: .: (0.000149)
test_goid: .: (0.000167)
test_parser: .: (0.000960)
test_qualifier: .: (0.000146)
test_taxon: .: (0.000141)
test_to_str: .: (0.000151)
test_with: .: (0.000139)
Bio::TestGenscanReport:
test_date_run: .: (0.001536)
test_gccontent: .: (0.000939)
test_genscan_version: .: (0.000938)
test_isochore: .: (0.001146)
test_length: .: (0.001001)
test_matrix: .: (0.001113)
test_predictions_size: .: (0.000887)
test_query_name: .: (0.001039)
test_time: .: (0.001039)
Bio::TestGenscanReportExon:
test_acceptor_score: .: (0.001035)
test_donor_score: .: (0.001061)
test_exon_type: .: (0.001064)
test_exon_type_long: .: (0.001208)
test_first: .: (0.000985)
test_initiation_score: .: (0.001121)
test_last: .: (0.000960)
test_number: .: (0.000939)
test_p_value: .: (0.001133)
test_phase: .: (0.000967)
test_range: .: (0.001172)
test_score: .: (0.000988)
test_strand: .: (0.000940)
test_t_score: .: (0.001183)
test_termination_score: .: (0.000941)
Bio::TestGenscanReportGene:
test_aaseq: .: (0.001328)
test_naseq: .: (0.001028)
test_number: .: (0.000933)
test_polyA: .: (0.000989)
test_promoter: .: (0.000966)
Bio::TestHMMERReportClassMethods:
test_reports_ary: .: (0.001393)
test_reports_ary_contents: .: (0.000987)
Bio::TestHMMERReportConstants:
test_rs: .: (0.000346)
Bio::TestHMMERReportHit:
test_accession: .: (0.008211)
test_append_hsp: .: (0.001024)
test_bit_score: .: (0.007324)
test_definition: .: (0.006714)
test_description: .: (0.001034)
test_each: .: (0.007347)
test_each_hsp: .: (0.006389)
test_entry_id: .: (0.001016)
test_evalue: .: (0.007381)
test_hit: .: (0.001011)
test_hit_id: .: (0.005751)
test_hsps: .: (0.005771)
test_num: .: (0.001051)
test_score: .: (0.001090)
test_target_def: .: (0.000991)
test_target_id: .: (0.001056)
Bio::TestHMMERReportHmmpfam:
test_domain_top_hits: .: (0.001438)
test_each: .: (0.000992)
test_each_hit: .: (0.001014)
test_histogram: .: (0.001239)
test_hits: .: (0.001016)
test_hsps: .: (0.000977)
test_parameter: .: (0.001052)
test_program: .: (0.001381)
test_query_info: .: (0.001075)
test_statistical_detail: .: (0.001013)
test_total_seq_searched: .: (0.001246)
test_whole_seq_top_hits: .: (0.001002)
Bio::TestHMMERReportHmmsearch:
test_domain_top_hits: .: (0.001367)
test_histogram: .: (0.001116)
test_statistical_detail: .: (0.001236)
test_total_seq_searched: .: (0.001174)
test_whole_seq_top_hit: .: (0.001190)
Bio::TestHMMERReportHsp:
test_accession: .: (0.001402)
test_bit_score: .: (0.001017)
test_csline: .: (0.000963)
test_domain: .: (0.001184)
test_evalue: .: (0.001025)
test_flatseq: .: (0.000983)
test_hmm_f: .: (0.001012)
test_hmm_t: .: (0.001202)
test_hmmseq: .: (0.001012)
test_hsp: .: (0.000964)
test_midline: .: (0.001179)
test_query_frame: .: (0.001020)
test_query_from: .: (0.000968)
test_query_seq: .: (0.000977)
test_query_to: .: (0.001256)
test_rfline: .: (0.001086)
test_score: .: (0.000992)
test_seq_f: .: (0.000963)
test_seq_ft: .: (0.001274)
test_seq_t: .: (0.001018)
test_set_alignment: .: (0.000954)
test_targat_to: .: (0.001235)
test_target_frame: .: (0.001050)
test_target_from: .: (0.000975)
test_target_seq: .: (0.001009)
Bio::TestHetatmFinder:
test_each_hetatm: .: (0.000965)
test_find_hetatm: .: (0.000395)
test_hetatms: .: (0.000493)
Bio::TestHeterogen:
test_addAtom: .: (0.000522)
test_each: .: (0.000585)
test_each_hetatm: .: (0.000333)
test_get_residue_id_from_atom: .: (0.000292)
test_het_atom: .: (0.000261)
test_iCode: .: (0.000264)
test_inspect: .: (0.000286)
test_resSeq: .: (0.000264)
test_sort: .: (0.000317)
test_square_bracket: .: (0.000525)
test_to_s: .: (0.000478)
test_update_resudue_id: .: (0.000272)
Bio::TestHeterogenFinder:
test_each_heterogen: .: (0.000376)
test_find_heterogen: .: (0.000211)
test_heterogens: .: (0.000263)
Bio::TestIprscanPTxtReport:
test_match_accession: .: (0.000419)
test_match_description: .: (0.000266)
test_match_evalue: .: (0.000499)
test_match_ipr_description: .: (0.000269)
test_match_ipr_id: .: (0.000258)
test_match_match_end: .: (0.000255)
test_match_match_start: .: (0.000259)
test_match_method: .: (0.000268)
test_matches_size: .: (0.000281)
test_query_id: .: (0.000272)
test_query_length: .: (0.000262)
Bio::TestIprscanRawReport:
test_entry_id: .: (0.003714)
test_match_accession: .: (0.003021)
test_match_crc64: .: (0.003256)
test_match_date: .: (0.003148)
test_match_description: .: (0.003133)
test_match_evalue: .: (0.003173)
test_match_go_terms: .: (0.006008)
test_match_ipr_description: .: (0.003303)
test_match_ipr_id: .: (0.003340)
test_match_match_end: .: (0.003604)
test_match_match_start: .: (0.003243)
test_match_method: .: (0.003113)
test_match_query_id: .: (0.003232)
test_match_query_length: .: (0.003042)
test_match_status: .: (0.003043)
test_obj: .: (0.003098)
test_query_id: .: (0.003018)
test_query_length: .: (0.003018)
test_self_reports_in_raw: .: (0.007869)
Bio::TestIprscanReport:
test_output_raw: .: (0.000937)
test_to_raw: .: (0.001013)
Bio::TestIprscanTxtEntry:
test_iprscan_report_class: .: (0.000832)
test_match_accession: .: (0.000701)
test_match_date: .: (0.000990)
test_match_description: .: (0.000712)
test_match_evalue: .: (0.000696)
test_match_go_terms: .: (0.000701)
test_match_ipr_description: .: (0.000903)
test_match_ipr_id: .: (0.000750)
test_match_match_end: .: (0.000687)
test_match_match_start: .: (0.000676)
test_match_method: .: (0.000915)
test_match_status: .: (0.000708)
test_matches_size: .: (0.000708)
test_query_id: .: (0.000685)
test_query_length: .: (0.000907)
Bio::TestIprscanTxtEntryList:
test_to_hash: .: (0.000963)
test_to_hash_match?: .: (0.001000)
Bio::TestIprscanTxtReport:
test_parse_txt: .: (0.002090)
Bio::TestKeggCompound:
test_comment: .: (0.000600)
test_dblinks_as_hash: .: (0.000542)
test_dblinks_as_strings: .: (0.000419)
test_entry_id: .: (0.000643)
test_enzymes: .: (0.000882)
test_formula: .: (0.000398)
test_kcf: .: (0.000368)
test_mass: .: (0.000416)
test_name: .: (0.000442)
test_names: .: (0.000421)
test_pathways_as_hash: .: (0.000886)
test_pathways_as_strings: .: (0.000508)
test_reactions: .: (0.000897)
test_remark: .: (0.000427)
test_rpairs: .: (0.000615)
Bio::TestKeggEnzyme:
test_all_reac: .: (0.000891)
test_classes: .: (0.000672)
test_cofactors: .: (0.000638)
test_comment: .: (0.000702)
test_dblinks_as_hash: .: (0.000721)
test_dblinks_as_strings: .: (0.000898)
test_diseases: .: (0.000711)
test_entry: .: (0.000805)
test_entry_id: .: (0.000809)
test_genes: .: (0.019973)
test_genes_as_hash: .: (0.023929)
test_genes_as_strings: .: (0.006388)
test_inhibitors: .: (0.000675)
test_iubmb_reactions: .: (0.000689)
test_kegg_reactions: .: (0.000678)
test_motifs: .: (0.000588)
test_name: .: (0.000778)
test_names: .: (0.001109)
test_obsolete?: .: (0.000714)
test_orthologs_as_hash: .: (0.000829)
test_orthologs_as_strings: .: (0.000796)
test_pathways_as_hash: .: (0.000922)
test_pathways_as_strings: .: (0.000847)
test_products: .: (0.001162)
test_reaction: .: (0.000791)
test_structures: .: (0.001101)
test_substrates: .: (0.000792)
test_sysname: .: (0.000782)
Bio::TestKeggGenesDblinks:
test_data: .: (0.000690)
test_dblinks_0: .: (0.000230)
test_dblinks_1: .: (0.000222)
test_dblinks_2: .: (0.000217)
Bio::TestKeggGenesStructure:
test_data: .: (0.000468)
test_ids: .: (0.000277)
test_ids_in_array: .: (0.000240)
Bio::TestKeggKGML::TestKGMLEntry1:
test_components: .: (0.053563)
test_graphics__size: .: (0.031062)
test_id: .: (0.012630)
test_link: .: (0.012209)
test_name: .: (0.012241)
test_reaction: .: (0.012543)
test_type: .: (0.012595)
Bio::TestKeggKGML::TestKGMLEntry1234:
test_components: .: (0.012174)
test_graphics__size: .: (0.012502)
test_id: .: (0.011721)
test_link: .: (0.011596)
test_name: .: (0.011494)
test_reaction: .: (0.011682)
test_type: .: (0.011624)
Bio::TestKeggKGML::TestKGMLEntry1Deprecated:
test_bgcolor=: .: (0.011837)
test_category: .: (0.012599)
test_entry_id: .: (0.011665)
test_fgcolor=: .: (0.011775)
test_height=: .: (0.011637)
test_label=: .: (0.011753)
test_shape=: .: (0.011635)
test_width=: .: (0.011702)
test_x=: .: (0.012455)
test_y=: .: (0.011875)
Bio::TestKeggKGML::TestKGMLEntry567:
test_components: .: (0.011961)
test_graphics__size: .: (0.011481)
test_id: .: (0.011467)
test_link: .: (0.011501)
test_name: .: (0.011542)
test_reaction: .: (0.011403)
test_type: .: (0.012449)
Bio::TestKeggKGML::TestKGMLEntrySetter:
test_components=: .: (0.000375)
test_graphics=: .: (0.000411)
test_id=: .: (0.000226)
test_link=: .: (0.000220)
test_name=: .: (0.000227)
test_reaction=: .: (0.000215)
test_type=: .: (0.000217)
Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated:
test_bgcolor=: .: (0.000440)
test_category=: .: (0.000262)
test_entry_id=: .: (0.000254)
test_fgcolor=: .: (0.000466)
test_height=: .: (0.000279)
test_label=: .: (0.000279)
test_pathway=: .: (0.000236)
test_shape=: .: (0.000271)
test_width=: .: (0.000250)
test_x=: .: (0.000244)
test_y=: .: (0.000243)
Bio::TestKeggKGML::TestKGMLGraphics1234:
test_bgcolor: .: (0.011748)
test_coords: .: (0.011489)
test_fgcolor: .: (0.011598)
test_height: .: (0.011589)
test_name: .: (0.011567)
test_type: .: (0.012520)
test_width: .: (0.011674)
test_x: .: (0.011558)
test_y: .: (0.011471)
Bio::TestKeggKGML::TestKGMLGraphics1_0:
test_bgcolor: .: (0.011910)
test_coords: .: (0.011518)
test_fgcolor: .: (0.011542)
test_height: .: (0.011358)
test_name: .: (0.012577)
test_type: .: (0.011501)
test_width: .: (0.011497)
test_x: .: (0.011537)
test_y: .: (0.011531)
Bio::TestKeggKGML::TestKGMLGraphicsSetter:
test_bgcolor=: .: (0.000378)
test_coords=: .: (0.000212)
test_fgcolor=: .: (0.000220)
test_height=: .: (0.000241)
test_name=: .: (0.000216)
test_type=: .: (0.000219)
test_width=: .: (0.000217)
test_x=: .: (0.000212)
test_y=: .: (0.000203)
Bio::TestKeggKGML::TestKGMLPathway:
test_entries=: .: (0.011855)
test_entries__size: .: (0.011344)
test_image: .: (0.012605)
test_link: .: (0.011663)
test_name: .: (0.011518)
test_number: .: (0.011484)
test_org: .: (0.011632)
test_reactions=: .: (0.011533)
test_reactions__size: .: (0.011456)
test_relations=: .: (0.012418)
test_relations__size: .: (0.011602)
test_title: .: (0.011491)
Bio::TestKeggKGML::TestKGMLProduct:
test_id: .: (0.023228)
test_name: .: (0.022832)
Bio::TestKeggKGML::TestKGMLProductSetter:
test_id=: .: (0.000380)
test_initialize_0: .: (0.000294)
test_initialize_1: .: (0.000183)
test_initialize_2: .: (0.000179)
test_name=: .: (0.000255)
Bio::TestKeggKGML::TestKGMLReaction:
test_id: .: (0.012714)
test_name: .: (0.011800)
test_products: .: (0.011549)
test_substrates: .: (0.011587)
test_type: .: (0.011383)
Bio::TestKeggKGML::TestKGMLReactionSetter:
test_id=: .: (0.000572)
test_name=: .: (0.000226)
test_products=: .: (0.000223)
test_substraces=: .: (0.000224)
test_type=: .: (0.000230)
Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated:
test_direction=: .: (0.000399)
test_entry_id=: .: (0.000256)
Bio::TestKeggKGML::TestKGMLRelation:
test_entry1: .: (0.011654)
test_entry2: .: (0.012500)
test_name: .: (0.011660)
test_type: .: (0.011622)
test_value: .: (0.011619)
Bio::TestKeggKGML::TestKGMLRelationDeprecated:
test_edge: .: (0.000323)
test_node1=: .: (0.000261)
test_node2=: .: (0.000417)
test_rel=: .: (0.000265)
Bio::TestKeggKGML::TestKGMLRelationSetter:
test_entry1=: .: (0.000363)
test_entry2=: .: (0.000224)
test_name=: .: (0.000229)
test_type=: .: (0.000227)
test_value=: .: (0.000230)
Bio::TestKeggKGML::TestKGMLSubstrate:
test_id: .: (0.023242)
test_name: .: (0.024081)
Bio::TestKeggKGML::TestKGMLSubstrateProductSetter:
test_id=: .: (0.000371)
test_initialize_0: .: (0.000336)
test_initialize_1: .: (0.000172)
test_initialize_2: .: (0.000178)
test_name=: .: (0.000255)
Bio::TestKeggKGML::TestKGMLSubstrateSetter:
test_id=: .: (0.000356)
test_initialize_0: .: (0.000183)
test_initialize_1: .: (0.000173)
test_initialize_2: .: (0.000185)
test_name=: .: (0.000234)
Bio::TestKeggModule:
test_compounds: .: (0.000640)
test_compounds_as_hash: .: (0.000545)
test_compounds_as_strings: .: (0.000372)
test_definition: .: (0.000384)
test_entry_id: .: (0.000322)
test_keggclass: .: (0.000323)
test_name: .: (0.000320)
test_new: .: (0.000300)
test_orthologs: .: (0.000462)
test_orthologs_as_array: .: (0.000645)
test_orthologs_as_hash: .: (0.000438)
test_orthologs_as_strings: .: (0.000382)
test_pathways: .: (0.000310)
test_pathways_as_hash: .: (0.000305)
test_pathways_as_strings: .: (0.000296)
test_reactions: .: (0.000433)
test_reactions_as_hash: .: (0.000426)
test_reactions_as_strings: .: (0.000601)
Bio::TestKeggOrthology:
test_dblinks: .: (0.000802)
test_dblinks_as_hash: .: (0.000578)
test_dblinks_as_strings: .: (0.000539)
test_definition: .: (0.000561)
test_entry_id: .: (0.000559)
test_genes_as_hash: .: (0.017285)
test_genes_as_strings: .: (0.005774)
test_keggclass: .: (0.000724)
test_keggclasses: .: (0.000717)
test_modules: .: (0.000569)
test_modules_as_hash: .: (0.000675)
test_modules_as_strings: .: (0.000528)
test_name: .: (0.000609)
test_names: .: (0.000669)
test_pathways_as_strings: .: (0.000661)
test_pathways_in_keggclass: .: (0.000845)
test_references: .: (0.000849)
Bio::TestKeggPathway_map00052:
test_compounds_as_hash: .: (0.000698)
test_compounds_as_strings: .: (0.000319)
test_dblinks_as_hash: .: (0.000315)
test_dblinks_as_strings: .: (0.000312)
test_description: .: (0.000338)
test_diseases_as_hash: .: (0.000315)
test_diseases_as_strings: .: (0.000308)
test_entry_id: .: (0.000344)
test_enzymes_as_strings: .: (0.000308)
test_genes_as_hash: .: (0.000527)
test_genes_as_strings: .: (0.000358)
test_keggclass: .: (0.000337)
test_ko_pathway: .: (0.000328)
test_modules_as_hash: .: (0.000417)
test_modules_as_strings: .: (0.000337)
test_name: .: (0.000338)
test_organism: .: (0.000330)
test_orthologs_as_hash: .: (0.000318)
test_orthologs_as_strings: .: (0.000454)
test_pathways_as_hash: .: (0.000355)
test_pathways_as_strings: .: (0.000313)
test_reactions_as_hash: .: (0.000305)
test_reactions_as_strings: .: (0.000331)
test_references: .: (0.000313)
test_rel_pathways_as_hash: .: (0.000377)
test_rel_pathways_as_strings: .: (0.000335)
Bio::TestKeggReaction:
test_definition: .: (0.000537)
test_entry_id: .: (0.000503)
test_enzymes: .: (0.000380)
test_equation: .: (0.000380)
test_name: .: (0.000381)
test_orthologs_as_hash: .: (0.000400)
test_orthologs_as_strings: .: (0.000352)
test_pathways_as_hash: .: (0.000376)
test_pathways_as_strings: .: (0.000333)
test_rpairs_as_hash: .: (0.000408)
test_rpairs_as_strings: .: (0.000542)
test_rpairs_as_tokens: .: (0.000408)
Bio::TestLasergene:
test_methods: .: (0.013065)
Bio::TestLocations:
test_complement: .: (0.000429)
test_hat: .: (0.000240)
test_normal: .: (0.000231)
test_replace_single_base: .: (0.000203)
test_should_not_modify_argument: .: (0.000193)
Bio::TestLocationsRoundTrip:
test_locations_roundtrip: .: (0.005537)
test_locations_to_s: .: (0.002633)
Bio::TestMEDLINE:
test_authors: .: (0.001378)
test_authors_with_last_name_all_caps: .: (0.000194)
test_authors_with_suffix: .: (0.000204)
Bio::TestMEDLINE_20146148:
test_ab: .: (0.000817)
test_ad: .: (0.000565)
test_au: .: (0.000965)
test_authors: .: (0.000643)
test_doi: .: (0.000563)
test_dp: .: (0.000562)
test_ip: .: (0.000840)
test_mh: .: (0.000683)
test_pages: .: (0.000561)
test_pg: .: (0.000558)
test_pii: .: (0.000775)
test_pmid: .: (0.000589)
test_pt: .: (0.000565)
test_reference: .: (0.001068)
test_self_new: .: (0.000611)
test_so: .: (0.000556)
test_ta: .: (0.000572)
test_ti: .: (0.000584)
test_ui: .: (0.000759)
test_vi: .: (0.000576)
test_year: .: (0.000559)
Bio::TestMapSimple:
test_attributes: .: (0.000482)
Bio::TestMapping:
test_add_mapping_as_map: .: (0.000693)
test_add_mapping_as_marker: .: (0.000295)
test_contains_marker?: .: (0.000218)
test_mapped_to?: .: (0.000211)
test_mapping_location_comparison: .: (0.000457)
test_mappings_as_map_each: .: (0.000205)
test_mappings_as_marker_each: .: (0.000263)
test_mappings_on: .: (0.000271)
test_multiple_mappings_between_same_marker_and_map: .: (0.000704)
test_positions_on: .: (0.000306)
test_raise_error_kind_of: .: (0.000480)
Bio::TestMast:
test_check_options_with_empty_opts: .: (0.000470)
test_check_options_with_invalid_opts: .: (0.000303)
test_check_options_with_valid_opts: .: (0.000317)
test_command_to_be_run: .: (0.000306)
test_config_defaults: .: (0.000245)
test_minimal_config: .: (0.000267)
test_more_config: .: (0.000481)
test_run: .: (0.000188)
Bio::TestMastReport:
test_parse_hit_list_with_bad_data: .: (0.000672)
test_report_has_motifs: .: (0.000363)
Bio::TestModel:
test_addChain: .: (0.000324)
test_comp: .: (0.000209)
test_each: .: (0.000204)
test_each_chain: .: (0.000201)
test_inspect: .: (0.000178)
test_rehash: .: (0.000175)
test_square_brace: .: (0.000410)
test_to_s: .: (0.000186)
Bio::TestModelFinder:
test_find_model: .: (0.000362)
Bio::TestMotif:
test_creation_and_attributes: .: (0.000394)
test_length: .: (0.000166)
Bio::TestMyGraph:
test_cliquishness: .: (0.000734)
Bio::TestNA:
test_accessor: .: (0.000299)
test_na: .: (0.000176)
test_name: .: (0.000161)
test_names: .: (0.000163)
test_to_re: .: (0.000367)
test_weight: .: (0.000191)
test_weight_rna: .: (0.000184)
Bio::TestNAConstants:
test_NAMES: .: (0.000294)
test_NAMES_1_to_name: .: (0.000171)
test_WEIGHT: .: (0.000179)
Bio::TestNATranslate:
test_translate: .: (0.000580)
test_translate_1: .: (0.000241)
test_translate_2: .: (0.000182)
test_translate_3: .: (0.000188)
test_translate_4: .: (0.000268)
test_translate_5: .: (0.000485)
test_translate_6: .: (0.000197)
Bio::TestNCBIDB:
test_fetch: .: (0.000347)
test_p_entry2hash: .: (0.000151)
test_p_subtag2array: .: (0.000153)
test_p_toptag2array: .: (0.000153)
Bio::TestNewick:
test_reparse: .: (0.001818)
test_reparse_before_lazy_parsing: .: (0.000969)
test_string_tree: .: (0.001185)
Bio::TestNewick2:
test_string_tree: .: (0.000964)
Bio::TestNewickPrivate:
test_parse_newick_get_tokens_for_leaf: .: (0.000365)
test_parse_newick_leaf: .: (0.000623)
test_parse_newick_tokenize: .: (0.000517)
Bio::TestNexus:
test_nexus: .: (0.017862)
Bio::TestOSLine:
test_period_trancation_O63147: .: (0.000388)
test_uncapitalized_letter_Q32725_9POAL: .: (0.000216)
Bio::TestPAMLCodeml::TestCodeml:
test_dump_parameters: .: (0.000324)
test_load_parameters: .: (0.000193)
test_parameters: .: (0.000164)
test_set_default_parameters: .: (0.000200)
Bio::TestPAMLCodeml::TestCodemlControlGeneration:
test_control_file_generated: .: (0.011887)
test_expected_parameters_set_in_control_file: .: (0.002349)
Bio::TestPAMLCodeml::TestCodemlInitialize:
test_new_with_one_argument: .: (0.000313)
test_new_with_parameters: .: (0.000166)
test_new_with_two_argument: .: (0.000158)
test_new_without_argument: .: (0.000139)
Bio::TestPAMLCodeml::TestCodemlRates:
test_rates_first_position: .: (0.002347)
test_rates_hundred_and_fiftieth_position: .: (0.006090)
test_rates_last_position: .: (0.002101)
Bio::TestPAMLCodeml::TestCodemlReport:
test_alpha: .: (0.015063)
test_tree: .: (0.014696)
test_tree_length: .: (0.014176)
test_tree_log_likelihood: .: (0.014530)
Bio::TestPAMLCodeml::TestControlFileUsage:
test_correct_parameters_should_be_loaded: .: (0.000713)
test_parameters_should_be_loaded_from_control: .: (0.000372)
Bio::TestPAMLCodeml::TestExpectedErrorsThrown:
test_error_thrown_if_seqfile_does_not_specified: .: (0.002028)
Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3:
test_alpha: .: (0.000364)
test_dN_dS: .: (0.000302)
test_kappa: .: (0.000216)
test_lnL: .: (0.000199)
test_m3_classes: .: (0.000315)
test_m3_lnL: .: (0.000200)
test_m3_to_s: .: (0.000197)
test_m3_tree: .: (0.001052)
test_omega: .: (0.000196)
test_to_s: .: (0.000193)
test_tree: .: (0.000930)
test_tree_length: .: (0.000656)
Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3:
test_dN_dS: .: (0.000668)
test_p: .: (0.000495)
test_position: .: (0.000915)
test_probability: .: (0.000490)
test_w: .: (0.000583)
Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3:
test_graph: .: (0.001188)
test_graph_omega: .: (0.000642)
Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3:
test_descr: .: (0.000340)
test_footer: .: (0.000197)
test_header: .: (0.000194)
test_initialize: .: (0.000211)
test_models: .: (0.000687)
test_nb_sites: .: (0.000886)
test_num_codons: .: (0.000223)
test_num_sequences: .: (0.000217)
test_significant: .: (0.000220)
Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8:
test_models: .: (0.000388)
test_nb_sites: .: (0.000592)
test_significant: .: (0.000267)
test_sites: .: (0.001850)
Bio::TestPDB:
test_accession: .: (0.001590)
test_addModel: .: (0.001455)
test_authors: .: (0.001078)
test_bracket: .: (0.001281)
test_classification: .: (0.001505)
test_dbref: .: (0.001506)
test_definition: .: (0.001087)
test_each: .: (0.001835)
test_each_model: .: (0.001087)
test_entry_id: .: (0.001483)
test_helix: .: (0.001186)
test_inspect: .: (0.001366)
test_jrnl: .: (0.001071)
test_keywords: .: (0.001556)
test_record: .: (0.001088)
test_remark: .: (0.001636)
test_seqres: .: (0.001442)
test_sheet: .: (0.001760)
test_ssbond: .: (0.001270)
test_to_s: .: (0.010148)
test_turn: .: (0.011923)
test_version: .: (0.017595)
Bio::TestPDBRecord::TestANISOU:
test_U11: .: (0.000374)
test_U12: .: (0.000182)
test_U13: .: (0.000177)
test_U22: .: (0.000175)
test_U23: .: (0.000174)
test_U33: .: (0.000239)
test_altLoc: .: (0.000264)
test_chainID: .: (0.000186)
test_charge: .: (0.000180)
test_element: .: (0.000178)
test_iCode: .: (0.000176)
test_name: .: (0.007566)
test_resName: .: (0.000201)
test_resSeq: .: (0.000182)
test_segID: .: (0.000180)
test_serial: .: (0.000177)
Bio::TestPDBRecord::TestATOM:
test_altLoc: .: (0.000389)
test_anisou: .: (0.000138)
test_chainID: .: (0.000133)
test_charge: .: (0.000132)
test_comparable: .: (0.000175)
test_do_parse: .: (0.000136)
test_element: .: (0.000134)
test_iCode: .: (0.000130)
test_name: .: (0.000129)
test_occupancy: .: (0.000300)
test_original_data: .: (0.000139)
test_record_name: .: (0.000135)
test_resName: .: (0.000390)
test_resSeq: .: (0.000127)
test_residue: .: (0.000128)
test_segID: .: (0.000127)
test_serial: .: (0.000124)
test_sigatm: .: (0.000125)
test_tempFactor: .: (0.000168)
test_ter: .: (0.000126)
test_to_a: .: (0.000134)
test_to_s: .: (0.000170)
test_x: .: (0.000171)
test_xyz: .: (0.000221)
test_y: .: (0.000171)
test_z: .: (0.000415)
Bio::TestPDBRecord::TestAUTHOR:
test_authorList: .: (0.000295)
Bio::TestPDBRecord::TestCAVEAT:
test_comment: .: (0.000269)
test_idcode: .: (0.000127)
Bio::TestPDBRecord::TestCISPEP:
test_chainID1: .: (0.000339)
test_chainID2: .: (0.000165)
test_icode1: .: (0.000160)
test_icode2: .: (0.000158)
test_measure: .: (0.000160)
test_modNum: .: (0.000158)
test_pep1: .: (0.000417)
test_pep2: .: (0.000161)
test_seqNum1: .: (0.000158)
test_seqNum2: .: (0.000157)
test_serNum: .: (0.000158)
Bio::TestPDBRecord::TestCOMPND:
test_compound: .: (0.000313)
Bio::TestPDBRecord::TestCONECT:
test_serial: .: (0.000280)
Bio::TestPDBRecord::TestCRYST1:
test_a: .: (0.000291)
test_alpha: .: (0.000144)
test_b: .: (0.000137)
test_beta: .: (0.000138)
test_c: .: (0.000428)
test_gamma: .: (0.000141)
test_sGroup: .: (0.000140)
test_z: .: (0.000137)
Bio::TestPDBRecord::TestDBREF:
test_chainID: .: (0.000347)
test_database: .: (0.000188)
test_dbAccession: .: (0.000183)
test_dbIdCode: .: (0.000198)
test_dbseqBegin: .: (0.000184)
test_dbseqEnd: .: (0.000187)
test_idCode: .: (0.000188)
test_idbnsBeg: .: (0.000188)
test_insertBegin: .: (0.000409)
test_insertEnd: .: (0.000194)
test_seqBegin: .: (0.000184)
test_seqEnd: .: (0.000187)
Bio::TestPDBRecord::TestDefault:
test_text: .: (0.000268)
Bio::TestPDBRecord::TestENDMDL:
test_serial: .: (0.000261)
Bio::TestPDBRecord::TestEXPDTA:
test_technique: .: (0.000271)
Bio::TestPDBRecord::TestEnd:
test_serial: .: (0.000348)
Bio::TestPDBRecord::TestHEADER:
test_classification: .: (0.000273)
test_depDate: .: (0.000353)
test_idCode: .: (0.000142)
Bio::TestPDBRecord::TestHET:
test_ChainID: .: (0.000300)
test_hetID: .: (0.000149)
test_iCode: .: (0.000148)
test_numHetAtoms: .: (0.000181)
test_seqNum: .: (0.000150)
test_text: .: (0.000147)
Bio::TestPDBRecord::TestHETATM:
test_altLoc: .: (0.000280)
test_anisou: .: (0.000130)
test_chainID: .: (0.000127)
test_charge: .: (0.000125)
test_comparable: .: (0.000166)
test_do_parse: .: (0.000522)
test_element: .: (0.000134)
test_iCode: .: (0.000127)
test_name: .: (0.000125)
test_occupancy: .: (0.000186)
test_original_data: .: (0.000131)
test_record_name: .: (0.000127)
test_resName: .: (0.000126)
test_resSeq: .: (0.000125)
test_residue: .: (0.000126)
test_segID: .: (0.000129)
test_serial: .: (0.000124)
test_sigatm: .: (0.000125)
test_tempFactor: .: (0.000168)
test_ter: .: (0.000126)
test_to_a: .: (0.000439)
test_to_s: .: (0.000167)
test_x: .: (0.000225)
test_xyz: .: (0.000156)
test_y: .: (0.000167)
test_z: .: (0.000166)
Bio::TestPDBRecord::TestHYDBND:
test_Chain1: .: (0.000428)
test_ChainH: .: (0.000209)
test_ICode1: .: (0.000204)
test_altLoc1: .: (0.000206)
test_altLoc2: .: (0.000208)
test_altLocH: .: (0.000205)
test_chainID2: .: (0.000449)
test_iCode2: .: (0.000214)
test_iCodeH: .: (0.000207)
test_name1: .: (0.000206)
test_name2: .: (0.000288)
test_nameH: .: (0.000246)
test_resName1: .: (0.000207)
test_resName2: .: (0.000207)
test_resSeq1: .: (0.000207)
test_resSeq2: .: (0.000206)
test_resSeqH: .: (0.000454)
test_sym1: .: (0.000212)
test_sym2: .: (0.000206)
Bio::TestPDBRecord::TestKEYWDS:
test_keywds: .: (0.000276)
Bio::TestPDBRecord::TestLINK:
test_altLoc1: .: (0.000347)
test_altLoc2: .: (0.000182)
test_chainID1: .: (0.000180)
test_chainID2: .: (0.000199)
test_iCode1: .: (0.000183)
test_iCode2: .: (0.000180)
test_name1: .: (0.000180)
test_name2: .: (0.000182)
test_resName1: .: (0.000428)
test_resName2: .: (0.000180)
test_resSeq1: .: (0.000181)
test_resSeq2: .: (0.000177)
test_sym1: .: (0.000179)
test_sym2: .: (0.000179)
Bio::TestPDBRecord::TestMASTER:
test_numConect: .: (0.000297)
test_numCoord: .: (0.000143)
test_numHelix: .: (0.000139)
test_numHet: .: (0.000140)
test_numRemark: .: (0.000222)
test_numSeq: .: (0.000143)
test_numSheet: .: (0.000140)
test_numSite: .: (0.000139)
test_numTer: .: (0.000139)
test_numTurn: .: (0.000144)
test_numXform: .: (0.000140)
Bio::TestPDBRecord::TestMODEL:
test_serial: .: (0.000253)
Bio::TestPDBRecord::TestMODRES:
test_chainID: .: (0.000328)
test_comment: .: (0.000156)
test_iCode: .: (0.000152)
test_idCode: .: (0.000154)
test_resName: .: (0.000155)
test_seqNum: .: (0.000151)
test_stdRes: .: (0.000155)
Bio::TestPDBRecord::TestMTRIX1:
test_Mn1: .: (0.000584)
test_Mn2: .: (0.000144)
test_Mn3: .: (0.000135)
test_Vn: .: (0.000133)
test_iGiven: .: (0.000134)
test_serial: .: (0.000131)
Bio::TestPDBRecord::TestMTRIX2:
test_Mn1: .: (0.000273)
test_Mn2: .: (0.000133)
test_Mn3: .: (0.000131)
test_Vn: .: (0.000131)
test_iGiven: .: (0.000134)
test_serial: .: (0.000134)
Bio::TestPDBRecord::TestMTRIX3:
test_Mn1: .: (0.000272)
test_Mn2: .: (0.000133)
test_Mn3: .: (0.000137)
test_Vn: .: (0.000131)
test_iGiven: .: (0.000423)
test_serial: .: (0.000158)
Bio::TestPDBRecord::TestOBSLTE:
test_idCode: .: (0.000307)
test_rIdCode: .: (0.000146)
test_repDate: .: (0.000143)
Bio::TestPDBRecord::TestORIGX1:
test_On1: .: (0.000286)
test_On2: .: (0.000131)
test_On3: .: (0.000128)
test_Tn: .: (0.000126)
Bio::TestPDBRecord::TestREVDAT:
test_modDate: .: (0.000479)
test_modId: .: (0.000146)
test_modNum: .: (0.000141)
test_modType: .: (0.000139)
test_record: .: (0.000142)
Bio::TestPDBRecord::TestRemarkN:
test_remarkNum: .: (0.000296)
test_text: .: (0.000130)
Bio::TestPDBRecord::TestSCALE1:
test_Sn1: .: (0.000275)
test_Sn2: .: (0.000129)
test_Sn3: .: (0.000127)
test_Un: .: (0.000126)
Bio::TestPDBRecord::TestSCALE2:
test_Sn1: .: (0.000267)
test_Sn2: .: (0.000402)
test_Sn3: .: (0.000128)
test_Un: .: (0.000126)
Bio::TestPDBRecord::TestSCALE3:
test_Sn1: .: (0.000265)
test_Sn2: .: (0.000126)
test_Sn3: .: (0.000124)
test_Un: .: (0.000122)
Bio::TestPDBRecord::TestSEQADV:
test_chainID: .: (0.000426)
test_conflict: .: (0.000171)
test_database: .: (0.000164)
test_dbIdCode: .: (0.000163)
test_dbRes: .: (0.000166)
test_dbSeq: .: (0.000167)
test_iCode: .: (0.000496)
test_idCode: .: (0.000185)
test_resName: .: (0.000166)
test_seqNum: .: (0.000164)
Bio::TestPDBRecord::TestSEQRES:
test_chainID: .: (0.000306)
test_numRes: .: (0.000175)
test_resName: .: (0.000174)
Bio::TestPDBRecord::TestSHEET:
test_curAtom: .: (0.000438)
test_curChainId: .: (0.000222)
test_curICode: .: (0.000216)
test_curResName: .: (0.000217)
test_curResSeq: .: (0.000238)
test_endChainID: .: (0.000216)
test_endICode: .: (0.000214)
test_endResName: .: (0.000241)
test_endSeqNum: .: (0.000213)
test_initChainID: .: (0.000217)
test_initICode: .: (0.000217)
test_initResName: .: (0.000221)
test_initSeqNum: .: (0.000216)
test_numStrands: .: (0.000214)
test_prevAtom: .: (0.000453)
test_prevChainId: .: (0.000217)
test_prevICode: .: (0.000215)
test_prevResName: .: (0.000214)
test_prevResSeq: .: (0.000216)
test_sense: .: (0.000215)
test_sheetID: .: (0.000215)
test_strand: .: (0.000214)
Bio::TestPDBRecord::TestSIGATM:
test_altLoc: .: (0.000340)
test_chainID: .: (0.000174)
test_charge: .: (0.000376)
test_element: .: (0.000175)
test_iCode: .: (0.000267)
test_name: .: (0.000188)
test_resName: .: (0.000172)
test_resSeq: .: (0.000170)
test_segID: .: (0.000173)
test_serial: .: (0.000170)
test_sigOcc: .: (0.000172)
test_sigTemp: .: (0.000171)
test_sigX: .: (0.000169)
test_sigY: .: (0.000171)
test_sigZ: .: (0.000168)
Bio::TestPDBRecord::TestSIGUIJ:
test_SigmaU11: .: (0.000520)
test_SigmaU12: .: (0.000177)
test_SigmaU13: .: (0.000176)
test_SigmaU22: .: (0.000173)
test_SigmaU23: .: (0.000171)
test_SigmaU33: .: (0.000250)
test_altLoc: .: (0.000183)
test_chainID: .: (0.000175)
test_charge: .: (0.000174)
test_element: .: (0.000173)
test_iCode: .: (0.000173)
test_name: .: (0.000174)
test_resName: .: (0.000171)
test_resSeq: .: (0.000172)
test_segID: .: (0.000343)
test_serial: .: (0.000173)
Bio::TestPDBRecord::TestSITE:
test_chainID1: .: (0.000361)
test_chainID2: .: (0.000193)
test_chainID3: .: (0.000190)
test_chainID4: .: (0.000192)
test_iCode1: .: (0.000282)
test_iCode2: .: (0.000197)
test_iCode3: .: (0.000191)
test_iCode4: .: (0.000190)
test_numRes: .: (0.000191)
test_resName1: .: (0.000371)
test_resName2: .: (0.000196)
test_resName3: .: (0.000192)
test_resName4: .: (0.000192)
test_seq1: .: (0.000191)
test_seq2: .: (0.000189)
test_seq3: .: (0.000193)
test_seq4: .: (0.000192)
test_seqNum: .: (0.000193)
test_siteID: .: (0.000191)
Bio::TestPDBRecord::TestSLTBRG:
test_altLoc1: .: (0.000503)
test_altLoc2: .: (0.000170)
test_atom1: .: (0.000166)
test_atom2: .: (0.000165)
test_chainID1: .: (0.000164)
test_chainID2: .: (0.000161)
test_iCode1: .: (0.000168)
test_iCode2: .: (0.000165)
test_resName1: .: (0.000163)
test_resName2: .: (0.000162)
test_resSeq1: .: (0.000180)
test_resSeq2: .: (0.000163)
test_sym1: .: (0.000164)
test_sym2: .: (0.000163)
Bio::TestPDBRecord::TestSOURCE:
test_srcName: .: (0.000302)
Bio::TestPDBRecord::TestSPRSDE:
test_idCode: .: (0.000291)
test_sIdCode: .: (0.000147)
test_sprsdeDate: .: (0.000139)
Bio::TestPDBRecord::TestTER:
test_chainID: .: (0.000285)
test_iCode: .: (0.000141)
test_resName: .: (0.000140)
test_resSeq: .: (0.000140)
test_serial: .: (0.000140)
Bio::TestPDBRecord::TestTITLE:
test_title: .: (0.000816)
Bio::TestPDBRecord::TestTVECT:
test_serial: .: (0.000309)
test_t1: .: (0.000146)
test_t2: .: (0.000142)
test_t3: .: (0.000138)
test_text: .: (0.000141)
Bio::TestPROSITE:
test_ac: .: (0.002779)
test_cc: .: (0.002339)
test_de: .: (0.002367)
test_division: .: (0.002611)
test_dr: .: (0.024742)
test_dt: .: (0.002481)
test_false_neg: .: (0.002658)
test_false_pos: .: (0.002506)
test_false_positive_sequences: .: (0.002291)
test_list_falsenegative: .: (0.023701)
test_list_falsepositive: .: (0.024484)
test_list_potentialhit: .: (0.024370)
test_list_truepositive: .: (0.025871)
test_list_unknown: .: (0.024697)
test_list_xref: .: (0.030105)
test_ma: .: (0.002526)
test_max_repeat: .: (0.002536)
test_name: .: (0.002928)
test_nr: .: (0.002927)
test_pa: .: (0.002429)
test_pa2re: .: (0.002990)
test_partial: .: (0.002908)
test_pdb_xref: .: (0.002559)
test_pdoc_xref: .: (0.002578)
test_positive: .: (0.002541)
test_positive_hits: .: (0.002349)
test_positive_sequences: .: (0.002624)
test_release: .: (0.002462)
test_ru: .: (0.002832)
test_self_pa2re: .: (0.002593)
test_site: .: (0.002917)
test_skip_flag: .: (0.002711)
test_swissprot_release_number: .: (0.002726)
test_swissprot_release_sequences: .: (0.002606)
test_taxon_range: .: (0.002533)
test_total: .: (0.002251)
test_total_hits: .: (0.002898)
test_total_sequences: .: (0.002749)
test_unknown: .: (0.002709)
test_unknown_hits: .: (0.002746)
test_unknown_sequences: .: (0.002486)
Bio::TestPROSITEConst:
test_delimiter: .: (0.000380)
test_tagsize: .: (0.000110)
Bio::TestPTS1:
test_function_set: .: (0.000267)
test_function_set_number_1: .: (0.000136)
test_function_set_number_2: .: (0.000125)
test_function_set_number_3: .: (0.000126)
test_function_show: .: (0.000117)
Bio::TestPTS1Constant:
test_FUNCTION: .: (0.000236)
Bio::TestPTS1New:
test_fungi: .: (0.000239)
test_general: .: (0.000122)
test_metazoa: .: (0.000119)
Bio::TestQualifier:
test_qualifier: .: (0.000547)
test_value: .: (0.000109)
Bio::TestREBASE:
test_methods: .: (0.001194)
Bio::TestRPSBlast::TestRPSBlastHSP:
test_align_len: .: (0.001107)
test_bit_score: .: (0.000757)
test_evalue: .: (0.001534)
test_gaps: .: (0.000757)
test_hit_from: .: (0.000800)
test_hit_to: .: (0.000790)
test_hseq: .: (0.000794)
test_identity: .: (0.001322)
test_midline: .: (0.000913)
test_percent_identity: .: (0.000745)
test_positive: .: (0.000740)
test_qseq: .: (0.000901)
test_query_from: .: (0.000790)
test_query_to: .: (0.000919)
test_score: .: (0.000732)
Bio::TestRPSBlast::TestRPSBlastReport:
test_db: .: (0.000808)
test_hits_size: .: (0.001644)
test_iterations_size: .: (0.002101)
test_program: .: (0.000642)
test_query_def: .: (0.001555)
test_query_len: .: (0.001921)
test_version: .: (0.000635)
test_version_date: .: (0.000628)
test_version_number: .: (0.000628)
Bio::TestRPSBlast::TestRPSBlastReportHit:
test_bit_score: .: (0.001018)
test_definition: .: (0.000976)
test_evalue: .: (0.000786)
test_hsps_size: .: (0.000701)
test_identity: .: (0.000779)
test_lap_at: .: (0.000965)
test_len: .: (0.000786)
test_midline: .: (0.001423)
test_overlap: .: (0.000784)
test_query_end: .: (0.000954)
test_query_seq: .: (0.000845)
test_query_start: .: (0.001343)
test_target_def: .: (0.000986)
test_target_end: .: (0.000844)
test_target_len: .: (0.000776)
test_target_seq: .: (0.000842)
test_target_start: .: (0.001645)
Bio::TestRPSBlast::TestRPSBlastSplitter:
test_entry_pos: .: (0.000813)
test_get_entry: .: (0.000621)
test_rewind: .: (0.000133)
test_skip_leader: .: (0.000262)
Bio::TestReference:
test_abstract: .: (0.000256)
test_affiliations: .: (0.000127)
test_authors: .: (0.000125)
test_format_bibitem: .: (0.000200)
test_format_bibtex: .: (0.000854)
test_format_bibtex_with_arguments: .: (0.000291)
test_format_cell: .: (0.000149)
test_format_current: .: (0.000149)
test_format_endnote: .: (0.000188)
test_format_general: .: (0.000183)
test_format_genome_biol: .: (0.000164)
test_format_genome_res: .: (0.000162)
test_format_nar: .: (0.000162)
test_format_nature: .: (0.000189)
test_format_rd: .: (0.000166)
test_format_science: .: (0.000443)
test_format_trends: .: (0.000132)
test_issue: .: (0.000119)
test_journal: .: (0.000207)
test_mesh: .: (0.000133)
test_pages: .: (0.000120)
test_pubmed: .: (0.000116)
test_pubmed_url: .: (0.000124)
test_url: .: (0.000117)
test_volume: .: (0.000117)
test_year: .: (0.000114)
Bio::TestReference_noURL:
test_format_endnote: .: (0.000317)
test_url: .: (0.000121)
Bio::TestReferences:
test_append: .: (0.000730)
test_each: .: (0.000151)
Bio::TestRelation:
test_comparison_operator: .: (0.000329)
test_uniq: .: (0.000175)
Bio::TestResidue:
test_addAtom: .: (0.000566)
test_each: .: (0.000281)
test_each_atom: .: (0.000267)
test_get_residue_id_from_atom: .: (0.000236)
test_het_atom: .: (0.000204)
test_iCode: .: (0.000698)
test_inspect: .: (0.000228)
test_resSeq: .: (0.000208)
test_sort: .: (0.000255)
test_square_bracket: .: (0.000234)
test_to_s: .: (0.000315)
test_update_resudue_id: .: (0.000301)
Bio::TestResidueFinder:
test_each_residue: .: (0.000306)
test_find_residue: .: (0.000156)
test_residues: .: (0.000683)
Bio::TestRestrictionEnzyme::TestAnalysis:
test_cut: .: (0.194923)
test_cut_from_bio_sequence_na: .: (0.046979)
test_cut_without_permutations: .: (0.031778)
test_view_ranges: .: (0.032123)
Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts:
test_cuts: .: (0.002016)
test_cuts_after_remove_incomplete_cuts: .: (0.001147)
test_strands_for_display: .: (0.004516)
test_strands_for_display_current: .: (0.001039)
Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange:
test_fragments: .: (0.001022)
test_fragments_for_display_1: .: (0.001242)
test_fragments_for_display_10: .: (0.001653)
test_fragments_for_display_2: .: (0.001293)
test_fragments_for_display_3: .: (0.001973)
test_fragments_for_display_4: .: (0.001757)
test_fragments_for_display_5: .: (0.000965)
test_fragments_for_display_6: .: (0.001292)
test_fragments_for_display_7: .: (0.001050)
test_fragments_for_display_8: .: (0.000892)
test_fragments_for_display_9: .: (0.001084)
Bio::TestRestrictionEnzyme::TestCutRanges:
test_obj_2: .: (0.000846)
test_obj_3: .: (0.000395)
test_obj_7: .: (0.000329)
test_obj_z: .: (0.000387)
Bio::TestRestrictionEnzyme::TestCutSymbol:
test_methods: .: (0.000488)
Bio::TestRestrictionEnzyme::TestDenseIntArray:
test_bracket: .: (0.000407)
test_bracket_eq: .: (0.000206)
test_concat: .: (0.000204)
test_delete: .: (0.000382)
test_dup: .: (0.000219)
test_each: .: (0.000244)
test_eqeq: .: (0.000161)
test_eqeq_false: .: (0.000141)
test_eqeq_other: .: (0.000128)
test_eqeq_self: .: (0.000128)
test_include?: .: (0.000149)
test_internal_data: .: (0.000140)
test_internal_data_eq: .: (0.000159)
test_length: .: (0.000133)
test_ltlt: .: (0.000154)
test_ltlt_larger: .: (0.002822)
test_ltlt_middle: .: (0.000174)
test_plus: .: (0.000184)
test_plus_error: .: (0.000175)
test_push: .: (0.000169)
test_reverse_each: .: (0.000250)
test_self_bracket: .: (0.000138)
test_self_new: .: (0.000156)
test_size: .: (0.000137)
test_sort!: .: (0.000132)
test_to_a: .: (0.000245)
test_uniq!: .: (0.000185)
test_unshift: .: (0.000178)
Bio::TestRestrictionEnzyme::TestDoubleStranded:
test_argument_error: .: (0.006898)
test_complement: .: (0.005847)
test_complement_with_cut_symbols: .: (0.006201)
test_cut_locations: .: (0.006002)
test_cut_locations_in_enzyme_notation: .: (0.005957)
test_primary: .: (0.006153)
test_primary_with_cut_symbols: .: (0.006190)
test_to_re: .: (0.005864)
Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands:
test_align: .: (0.001521)
test_align_with_cuts: .: (0.001311)
test_argument_error: .: (0.001601)
test_ds: .: (0.001307)
Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair:
test_argument_error: .: (0.000600)
test_complement: .: (0.000425)
test_contents: .: (0.000286)
test_primary: .: (0.000284)
Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation:
test_argument_error: .: (0.000489)
test_complement: .: (0.000281)
test_contents: .: (0.000271)
test_primary: .: (0.000431)
Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations:
test_complement: .: (0.000470)
test_contents: .: (0.000214)
test_primary: .: (0.000201)
Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation:
test_complement: .: (0.000371)
test_complement_to_array_index: .: (0.000343)
test_complement_to_array_index_class: .: (0.000311)
test_contents: .: (0.000236)
test_primary: .: (0.000223)
test_primary_to_array_index: .: (0.000329)
test_primary_to_array_index_class: .: (0.000500)
test_to_array_index: .: (0.000904)
test_to_array_index_class: .: (0.000608)
Bio::TestRestrictionEnzyme::TestRestrictionEnzyme:
test_enzyme_name: .: (0.000631)
test_rebase: .: (0.000194)
Bio::TestRestrictionEnzyme::TestSingleStrand:
test_argument_error: .: (0.001535)
test_creation_with_no_cuts: .: (0.000677)
test_cut_locations: .: (0.000681)
test_cut_locations_in_enzyme_notation: .: (0.000721)
test_orientation: .: (0.000757)
test_pattern: .: (0.000943)
test_pattern_palindromic?: .: (0.000819)
test_stripped: .: (0.000765)
test_to_re: .: (0.000555)
test_with_cut_symbols: .: (0.000685)
test_with_spaces: .: (0.001024)
Bio::TestRestrictionEnzyme::TestSingleStrandComplement:
test_argument_error: .: (0.001149)
test_creation_with_no_cuts: .: (0.000675)
test_cut_locations: .: (0.000817)
test_cut_locations_in_enzyme_notation: .: (0.000942)
test_orientation: .: (0.000643)
test_pattern: .: (0.000832)
test_pattern_palindromic?: .: (0.000792)
test_stripped: .: (0.000630)
test_to_re: .: (0.000768)
test_with_cut_symbols: .: (0.000681)
test_with_spaces: .: (0.000752)
Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation:
test_argument_error: .: (0.000754)
test_initialize_with_pattern: .: (0.000494)
test_max: .: (0.000198)
test_min: .: (0.000278)
test_to_array_index: .: (0.000249)
Bio::TestRestrictionEnzyme::TestSortedNumArray:
test_bracket: .: (0.000345)
test_bracket_eq: .: (0.000162)
test_concat: .: (0.000306)
test_delete: .: (0.000136)
test_dup: .: (0.000183)
test_each: .: (0.000283)
test_eqeq: .: (0.000136)
test_eqeq_false: .: (0.000126)
test_eqeq_other: .: (0.000118)
test_eqeq_self: .: (0.000115)
test_include?: .: (0.000134)
test_internal_data_hash: .: (0.000122)
test_internal_data_hash_eq: .: (0.000147)
test_length: .: (0.000120)
test_ltlt: .: (0.000143)
test_ltlt_noeffect: .: (0.000156)
test_plus: .: (0.000134)
test_plus_error: .: (0.000155)
test_private_push_element: .: (0.000137)
test_private_push_element_intermediate: .: (0.000145)
test_private_push_element_last: .: (0.000140)
test_private_push_element_noeffect: .: (0.000137)
test_private_sorted_keys: .: (0.000121)
test_private_unshift_element: .: (0.000135)
test_private_unshift_element_first: .: (0.000143)
test_private_unshift_element_intermediate: .: (0.000141)
test_private_unshift_element_noeffect: .: (0.000137)
test_push: .: (0.000144)
test_reverse_each: .: (0.000243)
test_self_bracket: .: (0.000118)
test_self_new: .: (0.000134)
test_size: .: (0.000115)
test_sort!: .: (0.000242)
test_to_a: .: (0.000122)
test_uniq!: .: (0.000213)
test_unshift: .: (0.000145)
Bio::TestRestrictionEnzyme::TestStringFormatting:
test_add_spacing: .: (0.000306)
test_left_padding: .: (0.000174)
test_right_padding: .: (0.000172)
test_strip_padding: .: (0.000179)
Bio::TestSOFT:
test_dataset: .: (0.010971)
test_series: .: (0.015442)
Bio::TestSOSUIReport:
test_entry_id: .: (0.000371)
test_prediction: .: (0.000198)
test_tmh: .: (0.000379)
test_tmhs: .: (0.000222)
Bio::TestSOSUIReportConst:
test_delimiter: .: (0.000227)
test_rs: .: (0.000107)
Bio::TestSOSUITMH:
test_grade: .: (0.000318)
test_range: .: (0.000194)
test_sequence: .: (0.000192)
Bio::TestSampleGraph:
test_bellman_ford: .: (0.000907)
test_bfs_shortest_path: .: (0.000327)
test_breadth_first_search: .: (0.000449)
test_depth_first_search: .: (0.000470)
test_dijkstra: .: (0.000355)
test_dump_list: .: (0.000381)
test_dump_matrix: .: (0.000482)
test_extract_subgraph_by_label: .: (0.000307)
test_extract_subgraph_by_list: .: (0.000330)
test_extract_subgraph_retains_disconnected_nodes: .: (0.000518)
test_small_world_aka_node_degree_histogram: .: (0.000223)
test_to_matrix: .: (0.000540)
test_to_matrix_fixed_index: .: (0.000383)
test_undirected_cliquishness: .: (0.000466)
Bio::TestScf_version_2:
test_complement: .: (0.017965)
test_seq: .: (0.017283)
test_to_biosequence: .: (0.017314)
Bio::TestScf_version_3:
test_complement: .: (0.052069)
test_seq: .: (0.050524)
test_to_biosequence: .: (0.050474)
Bio::TestSequence:
test_AA_new_blank_sequence: .: (0.000457)
test_AA_new_sequence_all_legal_symbols: .: (0.000127)
test_AA_new_sequence_removes_whitespace: .: (0.000121)
test_AA_new_sequence_upcases_symbols: .: (0.000121)
test_DNA_new_blank_sequence: .: (0.000117)
test_DNA_new_sequence_downcases_symbols: .: (0.000120)
test_DNA_new_sequence_removes_whitespace: .: (0.000116)
test_NA_randomize_with_counts: .: (0.001168)
test_NA_randomize_with_counts_and_block: .: (0.001686)
test_RNA_new_sequence: .: (0.000306)
test_ambiguous_dna_sequence_complement: .: (0.000131)
test_ambiguous_rna_sequence_complement: .: (0.000126)
test_amino_acid_codes: .: (0.000166)
test_amino_acid_molecular_weight: .: (0.000257)
test_amino_acid_names: .: (0.000169)
test_amino_acid_randomize_can_be_chained: .: (0.001945)
test_amino_acid_randomize_has_same_composition: .: (0.000878)
test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000948)
test_dna_composition: .: (0.000161)
test_dna_gc_percent: .: (0.000185)
test_dna_molecular_weight: .: (0.000364)
test_dna_pikachu: .: (0.000131)
test_dna_sequence_complement: .: (0.000121)
test_dna_sequence_translate: .: (0.000556)
test_dna_to_re: .: (0.000210)
test_element_reference_operator_with_one_argument: .: (0.000125)
test_element_reference_operator_with_two_arguments: .: (0.000122)
test_invalid_nucleic_acid_illegal_bases: .: (0.000166)
test_invalid_nucleic_acid_illegal_bases_more: .: (0.000196)
test_nucleic_acid_names: .: (0.000148)
test_randomize_dna_can_be_chained: .: (0.000699)
test_randomize_dna_retains_composition: .: (0.000380)
test_randomize_dna_with_block: .: (0.000450)
test_rna_composition: .: (0.000157)
test_rna_gc_percent: .: (0.000185)
test_rna_molecular_weight: .: (0.000350)
test_rna_pikachu: .: (0.000139)
test_rna_sequence_complement: .: (0.000127)
test_rna_sequence_translate: .: (0.000560)
test_rna_to_re: .: (0.000207)
test_total: .: (0.000141)
test_two_consecutive_dna_randomizations_not_equal: .: (0.000383)
test_valid_dna_sequence_illegal_bases: .: (0.000118)
Bio::TestSequenceAA:
test_codes: .: (0.000276)
test_molecular_weight: .: (0.000228)
test_names: .: (0.000157)
test_to_re: .: (0.000179)
test_to_s: .: (0.000110)
Bio::TestSequenceAACompat:
test_aa_self_randomize: .: (0.000415)
Bio::TestSequenceAANew:
test_new: .: (0.000237)
test_new_n: .: (0.000116)
test_new_r: .: (0.000110)
test_new_t: .: (0.000107)
Bio::TestSequenceCommon::TestSequenceCommon:
test_composition: .: (0.000298)
test_concat: .: (0.000117)
test_push: .: (0.000110)
test_seq: .: (0.000106)
test_splicing: .: (0.000212)
test_sum: .: (0.000111)
test_to_s: .: (0.000107)
test_to_str: .: (0.000106)
test_total: .: (0.000124)
test_window_search: .: (0.000404)
Bio::TestSequenceCommon::TestSequenceCommonNormalize:
test_no_normalize: .: (0.000302)
test_normalize_A: .: (0.000137)
test_normalize_a: .: (0.000126)
Bio::TestSequenceCommon::TestSequenceCommonRandomize:
test_randomize: .: (0.001676)
test_randomize_with_block: .: (0.006285)
test_randomize_with_hash: .: (0.001927)
test_randomize_with_hash_block: .: (0.008076)
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'
===============================================================================
: (0.001540)
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'
===============================================================================
: (0.001016)
Bio::TestSequenceCommon::TestSequenceCommonSubseq:
test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000294)
test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000141)
test_subseq_returns_subsequence: .: (0.000116)
test_to_s_returns_self_as_string: .: (0.000139)
Bio::TestSequenceCommon::TestSequenceCommonWindowSearch:
test_window_search_with_width_3_default_step_no_residual: .: (0.000262)
test_window_search_with_width_3_step_two_with_residual: .: (0.000137)
Bio::TestSequenceCompat::TestSequenceCommonCompat:
test_to_fasta: .: (0.000265)
Bio::TestSequenceCompat::TestSequenceCompat:
test_to_s: .: (0.000356)
Bio::TestSequenceCompat::TestSequenceNACompat:
test_aa_self_randomize: .: (0.000388)
test_na_self_randomize: .: (0.000221)
Bio::TestSequenceDBLink:
test_database: .: (0.000240)
test_id: .: (0.000112)
test_secondary_ids: .: (0.000112)
Bio::TestSequenceDBLinkClassMethods:
test_parse_embl_DR_line: .: (0.000290)
test_parse_uniprot_DR_line: .: (0.000174)
Bio::TestSequenceFormatFormatterFasta_numeric:
test_output: .: (0.001775)
test_output_width_35: .: (0.000508)
test_output_width_nil: .: (0.000724)
Bio::TestSequenceFormatFormatterQual:
test_output: .: (0.000691)
test_output_after_adding_sequence: .: (0.000446)
test_output_after_truncating_sequence: .: (0.000477)
test_output_from_error_probabilities: .: (0.005744)
test_output_width45: .: (0.000337)
test_output_with_converting_score_phred2solexa: .: (0.001054)
test_output_with_converting_score_solexa2phred: .: (0.000913)
test_output_with_default_score: .: (0.000364)
Bio::TestSequenceMasker:
test_mask: .: (0.000373)
test_mask_with_enumerator: .: (0.000241)
test_mask_with_enumerator_empty_mask_char: .: (0.000260)
test_mask_with_enumerator_excess: .: (0.001053)
test_mask_with_enumerator_longer_mask_char: .: (0.000231)
test_mask_with_enumerator_shorter: .: (0.000544)
test_mask_with_error_probability: .: (0.000244)
test_mask_with_quality_score: .: (0.000220)
Bio::TestSequenceNA:
test_at_content: .: (0.000625)
test_at_skew: .: (0.000372)
test_codon_usage: .: (0.000314)
test_complement: .: (0.000144)
test_dna: .: (0.000134)
test_dna!: .: (0.000129)
test_forward_complement: .: (0.000208)
test_gc_content: .: (0.000375)
test_gc_percent: .: (0.000347)
test_gc_skew: .: (0.000532)
test_iliegal_bases: .: (0.000127)
test_molecular_weight: .: (0.000216)
test_names: .: (0.000169)
test_reverse_complement: .: (0.000456)
test_rna: .: (0.000129)
test_rna!: .: (0.000125)
test_splicing: .: (0.000193)
test_to_re: .: (0.000208)
test_to_s: .: (0.000109)
Bio::TestSequenceNACommon:
test_composition: .: (0.000303)
test_concat: .: (0.000117)
test_push: .: (0.000114)
test_seq: .: (0.000113)
test_splicing: .: (0.000503)
test_sum: .: (0.000127)
test_to_s: .: (0.000113)
test_to_str: .: (0.000113)
test_total: .: (0.000130)
test_window_search: .: (0.000545)
Bio::TestSequenceNANew:
test_new: .: (0.000241)
test_new_n: .: (0.000117)
test_new_r: .: (0.000109)
test_new_t: .: (0.000109)
Bio::TestSequenceNATranslation:
test_translate: .: (0.000488)
test_translate_0: .: (0.001163)
test_translate_1: .: (0.000310)
test_translate_2: .: (0.000519)
test_translate_3: .: (0.000317)
test_translate_4: .: (0.000305)
test_translate_5: .: (0.000277)
test_translate_6: .: (0.000275)
test_translate_7: .: (0.000670)
test_translate_given_codon_table: .: (0.150584)
test_translate_n1: .: (0.000752)
test_translate_n2: .: (0.001336)
test_translate_n3: .: (0.000743)
test_translate_unknown_o: .: (0.000322)
test_translate_unknown_x: .: (0.000313)
Bio::TestSequenceQualityScore::TestConverter:
test_convert_nothing: .: (0.000279)
test_convert_scores_from_phred_to_solexa: .: (0.001018)
test_convert_scores_from_solexa_to_phred: .: (0.000343)
Bio::TestSequenceQualityScore::TestPhred:
test_convert_nothing: .: (0.000282)
test_convert_scores_from_phred: .: (0.000125)
test_convert_scores_from_phred_to_solexa: .: (0.000970)
test_convert_scores_from_solexa: .: (0.000335)
test_convert_scores_from_solexa_to_phred: .: (0.000507)
test_convert_scores_to_phred: .: (0.000107)
test_convert_scores_to_solexa: .: (0.000726)
test_p2q: .: (0.000662)
test_phred_p2q: .: (0.000266)
test_phred_q2p: .: (0.008787)
test_q2p: .: (0.008756)
test_quality_score_type: .: (0.000122)
test_self_convert_scores_to_solexa: .: (0.000725)
test_self_p2q: .: (0.000547)
test_self_q2p: .: (0.009076)
Bio::TestSequenceQualityScore::TestSolexa:
test_convert_nothing: .: (0.000272)
test_convert_scores_from_phred: .: (0.000743)
test_convert_scores_from_phred_to_solexa: .: (0.000969)
test_convert_scores_from_solexa: .: (0.000114)
test_convert_scores_from_solexa_to_phred: .: (0.000339)
test_convert_scores_to_phred: .: (0.000727)
test_convert_scores_to_solexa: .: (0.000112)
test_p2q: .: (0.000411)
test_q2p: .: (0.009106)
test_quality_score_type: .: (0.000120)
test_self_convert_scores_to_phred: .: (0.000345)
test_self_p2q: .: (0.000356)
test_self_q2p: .: (0.009707)
test_solexa_p2q: .: (0.000372)
test_solexa_q2p: .: (0.008930)
Bio::TestSequenceRuby3::TestSequenceCommon:
test_capitalize: .: (0.000446)
test_center: .: (0.000157)
test_chomp: .: (0.000182)
test_chop: .: (0.000270)
test_delete: .: (0.000161)
test_delete_prefix: .: (0.000165)
test_delete_suffix: .: (0.000139)
test_downcase: .: (0.000139)
test_each_char: .: (0.000263)
test_each_char_enum: .: (0.000216)
test_each_grapheme_cluster: .: (0.000462)
test_each_grapheme_cluster_enum: .: (0.000215)
test_each_line: .: (0.000385)
test_each_line_enum: .: (0.000192)
test_gsub: .: (0.000167)
test_gsub_with_block: .: (0.000605)
test_ljust: .: (0.000236)
test_lstrip: .: (0.000156)
test_multiply: .: (0.000166)
test_next: .: (0.000145)
test_reverse: .: (0.000138)
test_rjust: .: (0.000140)
test_rstrip: .: (0.000136)
test_slice: .: (0.000138)
test_slice2: .: (0.000283)
test_split: .: (0.000190)
test_squeeze: .: (0.000137)
test_strip: .: (0.000137)
test_sub: .: (0.000151)
test_sub_with_block: .: (0.000299)
test_succ: .: (0.000138)
test_swapcase: .: (0.000137)
test_tr: .: (0.000140)
test_tr_s: .: (0.000134)
test_upcase: .: (0.000138)
Bio::TestSequenceRuby3::TestSequenceCommonPartition:
test_partition: .: (0.000424)
test_partition_nomatch: .: (0.000307)
test_partition_sep_TSeq: .: (0.000183)
test_partition_sep_regexp: .: (0.000192)
Bio::TestSequenceRuby3::TestSequenceCommonRpartition:
test_rpartition: .: (0.000327)
test_rpartition_nomatch: .: (0.000189)
test_rpartition_sep_TSeq: .: (0.000185)
test_rpartition_sep_regexp: .: (0.000192)
Bio::TestShRNA:
test_blocK_it: .: (0.041655)
test_blocK_it_: .: (0.039094)
test_blocK_it_BLOCK_IT: .: (0.039533)
test_blocK_it_BLOCK_iT: .: (0.039544)
test_blocK_it_piGene: .: (0.040814)
test_bottom_strand: .: (0.039526)
test_bottom_strand_class: .: (0.040125)
test_bottom_strand_nil: .: (0.040309)
test_design: .: (0.039714)
test_design_BLOCK_IT: .: (0.039643)
test_report: .: (0.039703)
test_report_before_design: .: (0.041119)
test_top_strand: .: (0.040162)
test_top_strand_class: .: (0.039820)
test_top_strand_nil: .: (0.040536)
Bio::TestShRNANew:
test_new: .: (0.000535)
Bio::TestSiRNA:
test_antisense_size: .: (0.000253)
test_design: .: (0.039888)
test_design_reynolds: .: (0.049167)
test_design_uitei: .: (0.040777)
test_max_gc_percent: .: (0.000131)
test_min_gc_percent: .: (0.000120)
test_reynolds: .: (0.050230)
test_reynolds?: .: (0.000185)
test_uitei: .: (0.040050)
test_uitei?: .: (0.000168)
Bio::TestSiRNANew:
test_new: .: (0.000523)
Bio::TestSiRNAPair:
test_antisense: .: (0.040454)
test_gc_percent: .: (0.040656)
test_report: .: (0.039422)
test_rule: .: (0.039770)
test_sense: .: (0.041217)
test_start: .: (0.039914)
test_stop: .: (0.039992)
test_target: .: (0.040671)
Bio::TestSiRNAPairNew:
test_new: .: (0.000735)
Bio::TestSim4Report:
test_all_hits: .: (0.000590)
test_each: .: (0.000266)
test_each_hit: .: (0.000255)
test_hits: .: (0.000269)
test_num_hits: .: (0.000216)
test_query_def: .: (0.000532)
test_query_id: .: (0.000281)
test_query_len: .: (0.000208)
test_seq1: .: (0.000402)
Bio::TestSim4Report2:
test_all_hits: .: (0.000415)
test_each: .: (0.000253)
test_each_hit: .: (0.000250)
test_hits: .: (0.000255)
test_num_hits: .: (0.000208)
test_query_def: .: (0.000505)
test_query_id: .: (0.000278)
test_query_len: .: (0.000205)
test_seq1: .: (0.000278)
Bio::TestSim4Report4:
test_all_hits: .: (0.000510)
test_each: .: (0.000304)
test_each_hit: .: (0.000263)
test_hits: .: (0.000270)
test_num_hits: .: (0.000227)
test_query_def: .: (0.000554)
test_query_id: .: (0.000305)
test_query_len: .: (0.000219)
test_seq1: .: (0.000305)
Bio::TestSim4ReportHit:
test_align: .: (0.000467)
test_complement?: .: (0.000291)
test_definition: .: (0.000265)
test_each: .: (0.000457)
test_exons: .: (0.000703)
test_hit_id: .: (0.000213)
test_hsps: .: (0.000393)
test_introns: .: (0.000382)
test_len: .: (0.000212)
test_query_def: .: (0.000212)
test_query_id: .: (0.000208)
test_query_len: .: (0.000209)
test_segmentpairs: .: (0.000817)
test_seq1: .: (0.000294)
test_seq2: .: (0.000283)
test_target_def: .: (0.000211)
test_target_id: .: (0.000208)
test_target_len: .: (0.000207)
Bio::TestSim4ReportHit2:
test_align: .: (0.000444)
test_complement?: .: (0.000445)
test_definition: .: (0.000254)
test_each: .: (0.000493)
test_exons: .: (0.000458)
test_hit_id: .: (0.000210)
test_hsps: .: (0.000396)
test_introns: .: (0.000378)
test_len: .: (0.000448)
test_query_def: .: (0.000260)
test_query_id: .: (0.000203)
test_query_len: .: (0.000203)
test_segmentpairs: .: (0.000409)
test_seq1: .: (0.000349)
test_seq2: .: (0.000327)
test_target_def: .: (0.000212)
test_target_id: .: (0.000204)
test_target_len: .: (0.000203)
Bio::TestSim4ReportHit4:
test_align: .: (0.000794)
test_complement?: .: (0.000224)
test_definition: .: (0.000223)
test_each: .: (0.000535)
test_exons: .: (0.000538)
test_hit_id: .: (0.000354)
test_hsps: .: (0.000789)
test_introns: .: (0.000559)
test_len: .: (0.000223)
test_query_def: .: (0.000220)
test_query_id: .: (0.000220)
test_query_len: .: (0.000218)
test_segmentpairs: .: (0.000767)
test_seq1: .: (0.000467)
test_seq2: .: (0.000337)
test_target_def: .: (0.000224)
test_target_id: .: (0.000221)
test_target_len: .: (0.000219)
Bio::TestSim4ReportSegment:
test_from: .: (0.000244)
test_self_new: .: (0.000153)
test_seq: .: (0.000109)
test_to: .: (0.000104)
Bio::TestSim4ReportSegmentPair2_exon:
test_align_len: .: (0.000740)
test_direction: .: (0.000330)
test_hit_from: .: (0.000539)
test_hit_to: .: (0.000593)
test_hseq: .: (0.000341)
test_midline: .: (0.000347)
test_percent_identity: .: (0.000335)
test_qseq: .: (0.000712)
test_query_from: .: (0.000330)
test_query_to: .: (0.000344)
test_seq1: .: (0.000541)
test_seq2: .: (0.000406)
Bio::TestSim4ReportSegmentPair2_intron:
test_align_len: .: (0.000842)
test_direction: .: (0.000331)
test_hit_from: .: (0.000323)
test_hit_to: .: (0.000334)
test_hseq: .: (0.000323)
test_midline: .: (0.000332)
test_percent_identity: .: (0.000770)
test_qseq: .: (0.000438)
test_query_from: .: (0.000325)
test_query_to: .: (0.000324)
test_seq1: .: (0.000390)
test_seq2: .: (0.000381)
Bio::TestSim4ReportSegmentPair4_exon:
test_align_len: .: (0.000823)
test_direction: .: (0.000586)
test_hit_from: .: (0.000455)
test_hit_to: .: (0.000429)
test_hseq: .: (0.000428)
test_midline: .: (0.000473)
test_percent_identity: .: (0.000425)
test_qseq: .: (0.000426)
test_query_from: .: (0.000424)
test_query_to: .: (0.000746)
test_seq1: .: (0.000551)
test_seq2: .: (0.000489)
Bio::TestSim4ReportSegmentPair4_intron:
test_align_len: .: (0.000560)
test_direction: .: (0.000638)
test_hit_from: .: (0.000472)
test_hit_to: .: (0.000572)
test_hseq: .: (0.000441)
test_midline: .: (0.000425)
test_percent_identity: .: (0.000648)
test_qseq: .: (0.000500)
test_query_from: .: (0.000427)
test_query_to: .: (0.000420)
test_seq1: .: (0.000844)
test_seq2: .: (0.000557)
Bio::TestSim4ReportSegmentPair4_intron1:
test_align_len: .: (0.000569)
test_direction: .: (0.000428)
test_hit_from: .: (0.000425)
test_hit_to: .: (0.000684)
test_hseq: .: (0.000518)
test_midline: .: (0.000477)
test_percent_identity: .: (0.000431)
test_qseq: .: (0.000634)
test_query_from: .: (0.000471)
test_query_to: .: (0.000425)
test_seq1: .: (0.000490)
test_seq2: .: (0.000841)
Bio::TestSim4ReportSegmentPair_exon:
test_align_len: .: (0.000521)
test_direction: .: (0.000324)
test_hit_from: .: (0.000319)
test_hit_to: .: (0.000323)
test_hseq: .: (0.000318)
test_midline: .: (0.000318)
test_percent_identity: .: (0.000370)
test_qseq: .: (0.000325)
test_query_from: .: (0.000461)
test_query_to: .: (0.000334)
test_seq1: .: (0.000383)
test_seq2: .: (0.000373)
Bio::TestSim4ReportSegmentPair_intron:
test_align_len: .: (0.000752)
test_direction: .: (0.000322)
test_hit_from: .: (0.000325)
test_hit_to: .: (0.000319)
test_hseq: .: (0.000438)
test_midline: .: (0.000352)
test_percent_identity: .: (0.000321)
test_qseq: .: (0.000317)
test_query_from: .: (0.000535)
test_query_to: .: (0.000401)
test_seq1: .: (0.000388)
test_seq2: .: (0.000373)
Bio::TestSim4ReportSeqDesc:
test_definition: .: (0.000258)
test_entry_id: .: (0.000125)
test_filename: .: (0.000214)
test_len: .: (0.000136)
test_self_new: .: (0.000161)
test_self_parse: .: (0.000177)
Bio::TestTMHMMReport:
test_entry_id: .: (0.000793)
test_exp_aas_in_tmhs: .: (0.000418)
test_exp_first_60aa: .: (0.000406)
test_helix: .: (0.000457)
test_predicted_tmhs: .: (0.000655)
test_query_len: .: (0.000569)
test_tmhs: .: (0.000441)
test_to_s: .: (0.000541)
test_total_prob_of_N_in: .: (0.000410)
Bio::TestTMHMMReport_reports:
test_reports: .: (0.000259)
Bio::TestTMHMMTMH:
test_entry_id: .: (0.000744)
test_pos: .: (0.000413)
test_range: .: (0.000698)
test_status: .: (0.000435)
test_version: .: (0.000843)
Bio::TestTargetPReport:
test_cleavage_site_prediction: .: (0.000608)
test_cutoff: .: (0.000294)
test_entry_id: .: (0.000281)
test_length: .: (0.000289)
test_loc: .: (0.000374)
test_name: .: (0.000294)
test_networks: .: (0.000284)
test_prediction: .: (0.000319)
test_query_len: .: (0.000286)
test_query_sequences: .: (0.000282)
test_rc: .: (0.000574)
test_version: .: (0.000279)
Bio::TestTargetPReportConst:
test_delimiter: .: (0.000235)
test_rs: .: (0.000107)
Bio::TestTogoWSAccessWait:
test_reset_togows_access_wait: .: (0.000232)
test_togows_access_wait: .: (2.005385)
Bio::TestTogoWSREST:
test_debug: .: (0.000599)
test_debug_default: .: (0.000206)
test_internal_http: .: (0.000493)
Bio::TestTogoWSRESTclassMethod:
test_convert: .: (0.000238)
test_entry: .: (0.000111)
test_entry_database_list: .: (0.000110)
test_new: .: (0.000381)
test_new_with_uri_object: .: (0.000288)
test_new_with_uri_string: .: (0.000259)
test_retrieve: .: (0.000111)
test_search: .: (0.000109)
test_search_database_list: .: (0.000108)
Bio::TestTogoWSRESTprivate:
test_make_path: .: (0.000429)
test_prepare_return_value: .: (0.000616)
Bio::TestTopologicalSort:
test_dfs_topological_sort: .: (0.000565)
Bio::TestTree:
test_get_edge_distance: .: (0.000312)
test_get_edge_distance_string: .: (0.000181)
test_get_node_name: .: (0.000215)
test_initialize: .: (0.000171)
test_options: .: (0.000133)
test_root: .: (0.000109)
test_root=: .: (0.000129)
Bio::TestTree2:
test_add_edge: .: (0.000540)
test_add_node: .: (0.000308)
test_adjacency_matrix: .: (0.000548)
test_adjacency_matrix_with_block: .: (0.000316)
test_adjacent_nodes: .: (0.000338)
test_adjacent_nodes_nonexistent: .: (0.000209)
test_ancestors: .: (0.000268)
test_children: .: (0.000312)
test_clear: .: (0.000244)
test_clear_node: .: (0.000307)
test_clear_node_nonexistent: .: (0.000266)
test_collect_edge!: .: (0.000626)
test_collect_node!: .: (0.000416)
test_concat: .: (0.000381)
test_descendents: .: (0.000274)
test_distance_matrix: .: (0.000746)
test_each_edge: .: (0.000336)
test_each_node: .: (0.000305)
test_each_out_edge: .: (0.000490)
test_each_out_edge_chimpanzee: .: (0.000268)
test_each_out_edge_human: .: (0.000267)
test_each_out_edge_mammals: .: (0.000337)
test_each_out_edge_nonexistent: .: (0.000225)
test_each_out_edge_primates: .: (0.000531)
test_each_out_edge_rat: .: (0.000268)
test_each_out_edge_rodents: .: (0.000354)
test_edges: .: (0.000508)
test_get_edge: .: (0.000574)
test_get_edge_indirect: .: (0.000215)
test_get_edge_merged: .: (0.000221)
test_get_edge_nonexistent: .: (0.000202)
test_get_node_bootstrap: .: (0.000207)
test_get_node_bootstrap_string=: .: (0.000212)
test_get_node_by_name: .: (0.000335)
test_get_node_by_name_noexistent: .: (0.000203)
test_include?: .: (0.000502)
test_include_nonexistent: .: (0.000207)
test_insert_node: .: (0.000408)
test_leaves: .: (0.000289)
test_leaves_noargs: .: (0.000226)
test_lowest_common_ancestor: .: (0.000252)
test_nodes: .: (0.000214)
test_number_of_edges: .: (0.000203)
test_number_of_nodes: .: (0.000202)
test_out_degree: .: (0.000304)
test_out_degree_nonexistent: .: (0.000426)
test_out_edges: .: (0.000275)
test_out_edges_mammals: .: (0.000445)
test_out_edges_nonexistent: .: (0.000208)
test_out_edges_primates: .: (0.000682)
test_out_edges_rodents: .: (0.000373)
test_parent: .: (0.000268)
test_path: .: (0.000255)
test_remove_edge: .: (0.000257)
test_remove_edge_if: .: (0.000271)
test_remove_edge_if_nothing_removed: .: (0.000568)
test_remove_edge_nonexistent: .: (0.000246)
test_remove_node: .: (0.000306)
test_remove_node_if: .: (0.000238)
test_remove_node_if_false: .: (0.000400)
test_remove_node_nonexistent: .: (0.000245)
test_remove_nonsense_nodes: .: (0.000267)
test_subtree: .: (0.000326)
test_subtree_with_all_paths: .: (0.000494)
test_total_distance: .: (0.000220)
Bio::TestTreeEdge:
test_distance: .: (0.000248)
test_distance=: .: (0.000173)
test_distance_string: .: (0.000327)
test_distance_string=: .: (0.000168)
test_initialize: .: (0.000157)
test_inspect: .: (0.000115)
test_to_s: .: (0.000113)
Bio::TestTreeNode:
test_bootstrap: .: (0.000257)
test_bootstrap=: .: (0.000166)
test_bootstrap_string: .: (0.000104)
test_bootstrap_string=: .: (0.000198)
test_initialize: .: (0.000141)
test_inspect: .: (0.000145)
test_name: .: (0.000122)
test_to_s: .: (0.000106)
Bio::TestUniProt:
test_gene_name: .: (0.007634)
Bio::TestUniProtKB:
test_ac: .: (0.007251)
test_accession: .: (0.007365)
test_cc: .: (0.009625)
test_cc_alternative_products: .: (0.016113)
test_cc_database: .: (0.010118)
test_cc_mass_spectrometry: .: (0.009667)
test_de: .: (0.007297)
test_dr: .: (0.009616)
test_dr_with_key: .: (0.010480)
test_dr_with_key_empty: .: (0.009285)
test_dt: .: (0.007416)
test_dt_annotation: .: (0.006979)
test_dt_created: .: (0.007184)
test_dt_sequence: .: (0.010515)
test_entry: .: (0.027125)
test_ft: .: (0.064608)
test_gene_name: .: (0.007540)
test_gene_names: .: (0.007278)
test_gn: .: (0.006946)
test_gn_old_parser: .: (0.006976)
test_gn_uniprot_parser: .: (0.006707)
test_id_line: .: (0.006855)
test_id_line_data_class: .: (0.007102)
test_id_line_entry_name: .: (0.007118)
test_id_line_molecule_type: .: (0.007021)
test_id_line_sequence_length: .: (0.007188)
test_kw: .: (0.006829)
test_molecule: .: (0.007098)
test_oc: .: (0.007002)
test_og_1: .: (0.007892)
test_og_2: .: (0.009824)
test_og_3: .: (0.007521)
test_og_4: .: (0.007099)
test_og_5: .: (0.007043)
test_og_6: .: (0.006760)
test_os: .: (0.006998)
test_os_access: .: (0.006884)
test_os_access2: .: (0.006755)
test_ox: .: (0.007126)
test_protein_name: .: (0.007132)
test_ref: .: (0.016464)
test_seq: .: (0.007101)
test_sequence_length: .: (0.006923)
test_sq: .: (0.006999)
test_sq_crc64: .: (0.008223)
test_sq_len: .: (0.007385)
test_sq_mw: .: (0.007416)
test_synonyms: .: (0.007012)
Bio::TestUniProtKB_CC:
test_allergen: .: (0.000417)
test_alternative_products_access_as_hash: .: (0.000518)
test_alternative_products_ai: .: (0.000432)
test_alternative_products_apu: .: (0.000795)
test_alternative_products_as: .: (0.000413)
test_alternative_products_rf: .: (0.000122)
test_biophysicochemical_properties: .: (0.000603)
test_biotechnology: .: (0.000573)
test_catalytic_activity: .: (0.000265)
test_caution: .: (0.000289)
test_cofactor: .: (0.000264)
test_developmental_stage: .: (0.000288)
test_disease: .: (0.000508)
test_domain: .: (0.000500)
test_enzyme_regulation: .: (0.000267)
test_function: .: (0.000305)
test_induction: .: (0.000444)
test_interaction: .: (0.000343)
test_mass_spectrometry: .: (0.000387)
test_miscellaneous: .: (0.000245)
test_pathway: .: (0.000291)
test_pharmaceutical: .: (0.000303)
test_polymorphism: .: (0.000536)
test_ptm: .: (0.000250)
test_rna_editing: .: (0.000586)
test_similarity: .: (0.000243)
test_subcellular_location: .: (0.000303)
test_subunit: .: (0.000207)
test_tissue_specificity: .: (0.000280)
test_toxic_dose: .: (0.000215)
test_web_resource: .: (0.000392)
Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2:
test_cc_web_resource: .: (0.000520)
Bio::TestUniProtKB_DE_since_rel14_0:
test_private_parse_DE_line_rel14: .: (0.000961)
test_protein_name: .: (0.000484)
test_synonyms: .: (0.000596)
Bio::TestUniProtKB_ID_since_rel9_0:
test_aalen: .: (0.000274)
test_entry: .: (0.000146)
test_entry_id: .: (0.000312)
test_entry_name: .: (0.000150)
test_id_line: .: (0.000144)
test_molecule: .: (0.000145)
test_sequence_length: .: (0.000265)
Bio::TestUniProtKB_P28907:
test_ac: .: (0.002695)
test_accession: .: (0.002582)
test_cc: .: (0.003656)
test_cc_alternative_products: .: (0.003503)
test_cc_database: .: (0.003611)
test_cc_mass_spectrometry: .: (0.003464)
test_de: .: (0.002685)
test_dr: .: (0.006576)
test_dr_with_key: .: (0.006571)
test_dr_with_key_empty: .: (0.006491)
test_dt: .: (0.002925)
test_dt_annotation: .: (0.002714)
test_dt_created: .: (0.002676)
test_dt_sequence: .: (0.002760)
test_entry: .: (0.002711)
test_ft: .: (0.005188)
test_gene_name: .: (0.002759)
test_gene_names: .: (0.002610)
test_gn: .: (0.002685)
test_gn_old_parser: .: (0.002926)
test_gn_uniprot_parser: .: (0.002564)
test_id_line: .: (0.002645)
test_id_line_data_class: .: (0.004945)
test_id_line_entry_name: .: (0.002749)
test_id_line_sequence_length: .: (0.002662)
test_kw: .: (0.003182)
test_oc: .: (0.002734)
test_os: .: (0.002746)
test_os_access: .: (0.002727)
test_os_access2: .: (0.002556)
test_ox: .: (0.002928)
test_protein_name: .: (0.002832)
test_protein_name_after_calling_de: .: (0.002997)
test_ref: .: (0.004834)
test_seq: .: (0.003558)
test_sequence_length: .: (0.002724)
test_sq: .: (0.002721)
test_sq_crc64: .: (0.002597)
test_sq_len: .: (0.002568)
test_sq_mw: .: (0.002691)
test_synonyms: .: (0.003137)
test_synonyms_after_calling_de: .: (0.002811)
Bio::TestUniProtKB_Ref:
test_RA: .: (0.000828)
test_RC: .: (0.000367)
test_RG: .: (0.000358)
test_RL: .: (0.000359)
test_RN: .: (0.000356)
test_RP: .: (0.000657)
test_RT: .: (0.000457)
test_RX: .: (0.000367)
test_ref: .: (0.000375)
Bio::TestUniProtKB_SwissProtRel41_0:
test_multiple_RP_lines: .: (0.000327)
Bio::TestUniProtKB_SwissProtRel41_1:
test_alternative_products: .: (0.000663)
test_alternative_products_with_ft: .: (0.001340)
Bio::TestUniProtKB_SwissProtRel41_10:
test_RC_lines: .: (0.000459)
Bio::TestUniProtKB_SwissProtRel41_20:
test_CC_allergen: .: (0.000385)
test_RL_lines: .: (0.000170)
Bio::TestUniProtKB_SwissProtRel42_6:
test_CC_rna_editing: .: (0.001089)
Bio::TestUniProtKB_UniProtRel1_12:
test_DOI_in_RX_line: .: (0.000310)
test_RG_line: .: (0.000191)
Bio::TestUniProtKB_UniProtRel2_0:
test_GN_line: .: (0.000769)
Bio::TestUniProtKB_UniProtRel2_1:
test_CC_mass_spectrometry: .: (0.000388)
Bio::TestUniProtKB_UniProtRel2_3:
test_DR_PDB: .: (0.000621)
test_RL_line: .: (0.000170)
Bio::TestUniProtKB_UniProtRel3_4:
test_CC_biophysiochemical_properties: .: (0.001027)
test_RP_line: .: (0.000319)
Bio::TestUniProtKB_UniProtRel3_5:
test_entry_name_format: .: (0.000198)
Bio::TestUniProtKB_UniProtRel4_0:
test_CC_interaction: .: (0.000456)
test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000289)
test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000593)
test_CC_interaction_isoform: .: (0.000251)
test_CC_interaction_no_gene_name: .: (0.000241)
test_CC_interaction_self_association: .: (0.000273)
Bio::TestUniProtKB_UniProtRel5_0:
test_DR_line: .: (0.000332)
Bio::TestUniProtKB_UniProtRel5_4:
test_multiple_cofactors: .: (0.000394)
Bio::TestUniProtKB_UniProtRel6_0:
test_OG_line: .: (0.000972)
Bio::TestUniProtKB_UniProtRel6_1:
test_FT_metal: .: (0.000413)
Bio::TestUniProtKB_UniProtRel6_5:
test_HI_line: .: (0.000372)
Bio::TestUniProtKB_UniProtRel7_0:
test_CC_copyright_statement: .: (0.000326)
test_DT_line: .: (0.000217)
Bio::TestUniProtKB_UniProtRel7_6:
test_10000aa: .: (0.006646)
Bio::TestUniProtKB_UniProtRel8_0:
test_CC_alternative_products: .: (0.000841)
test_CC_web_resource: .: (0.000107)
test_FT_VER_SEQ: .: (0.000237)
test_OH_line_exception: .: (0.000266)
test_OH_lines: .: (0.000784)
Bio::TestUtils:
test_centreOfGravity: .: (0.001083)
test_dihedral_angle: .: (0.000580)
test_distance: .: (0.000822)
test_geometricCentre: .: (0.000437)
test_rad2deg: .: (0.000265)
Bio::TestWeightedGraph:
test_bellman_ford_on_negative_weighted_graph: .: (0.000380)
test_dijkstra_on_weighted_graph: .: (0.000263)
Finished in 23.267657006 seconds.
-------------------------------------------------------------------------------
3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications
100% passed
-------------------------------------------------------------------------------
165.77 tests/s, 923.43 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_i386.buildinfo
dpkg-genchanges --build=binary -O../ruby-bio_2.0.4-1_i386.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/24953/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/24953/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/24953 and its subdirectories
I: Current time: Tue May 23 09:17:06 +14 2023
I: pbuilder-time-stamp: 1684783026