sbuild (Debian sbuild) 0.89.3+deb13u1 (16 August 2025) on +==============================================================================+ | ruby-bio 2.0.6-1+rebuild1766571925 (amd64) Wed, 24 Dec 2025 10:25:26 +0000 | +==============================================================================+ Package: ruby-bio Version: 2.0.6-1+rebuild1766571925 Source Version: 2.0.6-1+rebuild1766571925 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: No tarballs found in /home/admin/.cache/sbuild I: Creating chroot on-demand by running: mmdebstrap --variant=buildd --arch=amd64 --skip=output/mknod --format=tar unstable - I: Unpacking tarball from STDIN to /tmp/tmp.sbuild.oERJJC8ZLx... I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: finding correct signed-by value... I: using /tmp/mmdebstrap.iZLjzp4by9 as tempdir I: skipping output/mknod as requested for ./dev/console I: skipping output/mknod as requested for ./dev/full I: skipping output/mknod as requested for ./dev/null I: skipping output/mknod as requested for ./dev/ptmx I: skipping output/mknod as requested for ./dev/random I: skipping output/mknod as requested for ./dev/tty I: skipping output/mknod as requested for ./dev/urandom I: skipping output/mknod as requested for ./dev/zero I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: installing remaining packages inside the chroot... I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.iZLjzp4by9... I: success in 12.1415 seconds I: The chroot directory at /tmp/tmp.sbuild.oERJJC8ZLx will be removed at the end of the build I: To avoid creating a new chroot from scratch every time, either: I: - place a chroot tarball at /home/admin/.cache/sbuild/unstable-amd64.tar and update it manually, for example by running: mmdebstrap --variant=buildd --arch=amd64 --skip=output/mknod --format=tar unstable /home/admin/.cache/sbuild/unstable-amd64.tar I: - or let sbuild take care of this via the setting UNSHARE_MMDEBSTRAP_KEEP_TARBALL by adding '$unshare_mmdebstrap_keep_tarball = 1;' to your ~/.config/sbuild/config.pl. I: - or completely disable this behaviour via the setting UNSHARE_MMDEBSTRAP_AUTO_CREATE by adding '$unshare_mmdebstrap_auto_create = 0;' to your ~/.config/sbuild/config.pl. I: Refer to UNSHARE_MMDEBSTRAP_KEEP_TARBALL in sbuild.conf(5) for more information I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 24 Dec 2025 10:25:41 +0000 | +------------------------------------------------------------------------------+ Ign:1 file:/mass-rebuild ./ InRelease Get:2 file:/mass-rebuild ./ Release [1617 B] Get:2 file:/mass-rebuild ./ Release [1617 B] Ign:3 file:/mass-rebuild ./ Release.gpg Get:4 file:/mass-rebuild ./ Packages [70.4 kB] Get:5 http://deb.debian.org/debian unstable InRelease [187 kB] Get:6 http://deb.debian.org/debian experimental InRelease [90.7 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages [10.2 MB] Get:8 http://deb.debian.org/debian experimental/main amd64 Packages [429 kB] Get:9 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [48.9 kB] Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [105 kB] Fetched 11.1 MB in 1s (8482 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libselinux1 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/85.8 kB of archives. After this operation, 1024 B disk space will be freed. Get:1 file:/mass-rebuild ./ libselinux1 3.9-4+rebuild1766544377 [85.8 kB] (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11800 files and directories currently installed.) Preparing to unpack .../libselinux1_3.9-4+rebuild1766544377_amd64.deb ... Unpacking libselinux1:amd64 (3.9-4+rebuild1766544377) over (3.9-4+b1) ... Setting up libselinux1:amd64 (3.9-4+rebuild1766544377) ... Processing triggers for libc-bin (2.42-6) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 24 Dec 2025 10:25:44 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /home/admin/mass-rebuild/builds/3/ruby-bio/ruby-bio_2.0.6-1+rebuild1766571925.dsc exists in /home/admin/mass-rebuild/builds/3/ruby-bio; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 24 Dec 2025 10:25:45 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, build-essential, docbook-to-man, rdtool Filtered Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, build-essential, docbook-to-man, rdtool dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-jBWYTK/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Sources [682 B] Get:5 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Packages [701 B] Fetched 1992 B in 0s (0 B/s) Reading package lists... Ign:1 file:/mass-rebuild ./ InRelease Get:2 file:/mass-rebuild ./ Release [1617 B] Get:2 file:/mass-rebuild ./ Release [1617 B] Ign:3 file:/mass-rebuild ./ Release.gpg Hit:4 http://deb.debian.org/debian experimental InRelease Hit:5 http://incoming.debian.org/debian-buildd buildd-unstable InRelease Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz file gem2deb gem2deb-test-runner gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libffi8 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libmagic-mgc libmagic1t64 libosp5 libpipeline1 libruby libruby3.3 libtool libuchardet0 libunistring5 libxml2-16 libyaml-0-2 m4 man-db opensp openssl po-debconf rake rdtool ruby ruby-all-dev ruby-csv ruby-did-you-mean ruby-libxml ruby-minitest ruby-net-telnet ruby-power-assert ruby-rd ruby-ruby2-keywords ruby-rubygems ruby-test-unit ruby-webrick ruby-xmlrpc ruby3.3 ruby3.3-dev rubygems-integration sensible-utils sgml-base sgml-data xml-core Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml git-buildpackage pristine-tar gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff gmp-doc libgmp10-doc libmpfr-dev libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser doc-base libmail-box-perl ri ruby-dev bundler sgml-base-doc perlsgml w3-recs libxml2-utils Recommended packages: apt-file debian-policy devscripts python3-debian curl | wget | lynx libarchive-cpio-perl ruby-sdbm libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery ruby3.3-doc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz file gem2deb gem2deb-test-runner gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libffi8 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libmagic-mgc libmagic1t64 libosp5 libpipeline1 libruby libruby3.3 libtool libuchardet0 libunistring5 libxml2-16 libyaml-0-2 m4 man-db opensp openssl po-debconf rake rdtool ruby ruby-all-dev ruby-csv ruby-did-you-mean ruby-libxml ruby-minitest ruby-net-telnet ruby-power-assert ruby-rd ruby-ruby2-keywords ruby-rubygems ruby-test-unit ruby-webrick ruby-xmlrpc ruby3.3 ruby3.3-dev rubygems-integration sbuild-build-depends-main-dummy sensible-utils sgml-base sgml-data xml-core 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 24.9 MB/25.1 MB of archives. After this operation, 95.5 MB of additional disk space will be used. Get:1 file:/mass-rebuild ./ ruby-libxml 5.0.5-2+rebuild1766548530 [108 kB] Get:2 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [892 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-2 [98.9 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.29 [92.6 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.29 [943 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15.2 [972 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15.2 [448 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-50 [74.5 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get:42 http://deb.debian.org/debian unstable/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get:46 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3 [26.1 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2+b1 [53.8 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get:53 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get:55 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 ruby-minitest all 5.26.1-1 [67.3 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 ruby-power-assert all 2.0.5-1 [11.7 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 gem2deb-test-runner amd64 2.2.6 [18.4 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 ruby3.3-dev amd64 3.3.8-2 [1045 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 ruby-all-dev amd64 1:3.3+b1 [6496 B] Get:64 http://deb.debian.org/debian unstable/main amd64 gem2deb amd64 2.2.6 [48.3 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 ruby-rd all 0.6.38-5 [62.0 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 rdtool all 0.6.38-5 [42.5 kB] Preconfiguring packages ... Fetched 24.9 MB in 0s (102 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 11799 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.5.4-1_amd64.deb ... Unpacking openssl (3.5.4-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.46-5_amd64.deb ... 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Preparing to unpack .../37-docbook-to-man_1%3a2.0.0-50_amd64.deb ... Unpacking docbook-to-man (1:2.0.0-50) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../38-rubygems-integration_1.19_all.deb ... Unpacking rubygems-integration (1.19) ... Selecting previously unselected package ruby-csv. Preparing to unpack .../39-ruby-csv_3.3.4-1_all.deb ... Unpacking ruby-csv (3.3.4-1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../40-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../41-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-ruby2-keywords. Preparing to unpack .../42-ruby-ruby2-keywords_0.0.5-1_all.deb ... Unpacking ruby-ruby2-keywords (0.0.5-1) ... Selecting previously unselected package ruby-webrick. 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Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../50-ruby-rubygems_3.6.7-2_all.deb ... Unpacking ruby-rubygems (3.6.7-2) ... Selecting previously unselected package ruby. Preparing to unpack .../51-ruby_1%3a3.3+b1_amd64.deb ... Unpacking ruby (1:3.3+b1) ... Selecting previously unselected package rake. Preparing to unpack .../52-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../53-ruby-minitest_5.26.1-1_all.deb ... Unpacking ruby-minitest (5.26.1-1) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../54-ruby-power-assert_2.0.5-1_all.deb ... Unpacking ruby-power-assert (2.0.5-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../55-ruby-test-unit_3.6.2-1_all.deb ... Unpacking ruby-test-unit (3.6.2-1) ... Selecting previously unselected package gem2deb-test-runner. Preparing to unpack .../56-gem2deb-test-runner_2.2.6_amd64.deb ... Unpacking gem2deb-test-runner (2.2.6) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../57-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../58-libgmp-dev_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package ruby3.3-dev:amd64. Preparing to unpack .../59-ruby3.3-dev_3.3.8-2_amd64.deb ... Unpacking ruby3.3-dev:amd64 (3.3.8-2) ... Selecting previously unselected package ruby-all-dev:amd64. Preparing to unpack .../60-ruby-all-dev_1%3a3.3+b1_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:3.3+b1) ... Selecting previously unselected package gem2deb. Preparing to unpack .../61-gem2deb_2.2.6_amd64.deb ... Unpacking gem2deb (2.2.6) ... Selecting previously unselected package ruby-rd. Preparing to unpack .../62-ruby-rd_0.6.38-5_all.deb ... Unpacking ruby-rd (0.6.38-5) ... Selecting previously unselected package rdtool. Preparing to unpack .../63-rdtool_0.6.38-5_all.deb ... Unpacking rdtool (0.6.38-5) ... Selecting previously unselected package ruby-libxml:amd64. Preparing to unpack .../64-ruby-libxml_5.0.5-2+rebuild1766548530_amd64.deb ... Unpacking ruby-libxml:amd64 (5.0.5-2+rebuild1766548530) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../65-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-2) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up bsdextrautils (2.41.3-2) ... Setting up ruby-power-assert (2.0.5-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2+b1) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Setting up libdebhelper-perl (13.29) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.2-1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.194-1) ... Setting up libosp5 (1.5.2-15.2) ... Setting up ruby-minitest (5.26.1-1) ... Setting up autotools-dev (20240727.1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up ruby-csv (3.3.4-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.2-1) ... Setting up autoconf (2.72-3.1) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.5.2-3) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up sgml-base (1.31+nmu1) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up openssl (3.5.4-1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up ruby-rd (0.6.38-5) ... Setting up automake (1:1.18.1-3) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up libtool (2.5.4-9) ... Setting up opensp (1.5.2-15.2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up xml-core (0.19) ... Setting up po-debconf (1.0.22) ... Setting up rubygems-integration (1.19) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.29) ... Setting up rake (13.2.1-1) ... Setting up libruby3.3:amd64 (3.3.8-2) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby3.3-dev:amd64 (3.3.8-2) ... Setting up ruby3.3 (3.3.8-2) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby-all-dev:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up rdtool (0.6.38-5) ... Setting up ruby-libxml:amd64 (5.0.5-2+rebuild1766548530) ... Setting up gem2deb-test-runner (2.2.6) ... Setting up gem2deb (2.2.6) ... Processing triggers for libc-bin (2.42-6) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-to-man (1:2.0.0-50) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Wed, 24 Dec 2025 10:25:53 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Wed, 24 Dec 2025 10:25:53 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) amd64 (x86_64) Toolchain package versions: binutils_2.45.50.20251209-1 dpkg-dev_1.23.3 g++-15_15.2.0-12 gcc-15_15.2.0-12 libc6-dev_2.42-6 libstdc++-15-dev_15.2.0-12 libstdc++6_15.2.0-12 linux-libc-dev_6.17.13-1 Package versions: apt_3.1.12 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45.50.20251209-1 binutils-common_2.45.50.20251209-1 binutils-x86-64-linux-gnu_2.45.50.20251209-1 bsdextrautils_2.41.3-2 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20250419 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-12 cpp-15-x86-64-linux-gnu_15.2.0-12 cpp-x86-64-linux-gnu_4:15.2.0-4 dash_0.5.12-12 debconf_1.5.91 debhelper_13.29 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 docbook_4.5-11 docbook-to-man_1:2.0.0-50 dpkg_1.23.3 dpkg-dev_1.23.3 dwz_0.16-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-12 g++-15-x86-64-linux-gnu_15.2.0-12 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-12 gcc-15-base_15.2.0-12 gcc-15-x86-64-linux-gnu_15.2.0-12 gcc-x86-64-linux-gnu_4:15.2.0-4 gem2deb_2.2.6 gem2deb-test-runner_2.2.6 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.12 libarchive-zip-perl_1.68-1 libasan8_15.2.0-12 libatomic1_15.2.0-12 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.45.50.20251209-1 libblkid1_2.41.3-2 libbz2-1.0_1.0.8-6 libc-bin_2.42-6 libc-dev-bin_2.42-6 libc-gconv-modules-extra_2.42-6 libc6_2.42-6 libc6-dev_2.42-6 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-12 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45.50.20251209-1 libctf0_2.45.50.20251209-1 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.29 libdpkg-perl_1.23.3 libelf1t64_0.194-1 libffi8_3.5.2-3 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-12 libgcc-s1_15.2.0-12 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp-dev_2:6.3.0+dfsg-5 libgmp10_2:6.3.0+dfsg-5 libgmpxx4ldbl_2:6.3.0+dfsg-5 libgomp1_15.2.0-12 libgprofng0_2.45.50.20251209-1 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-12 libisl23_0.27-1 libitm1_15.2.0-12 libjansson4_2.14-2+b4 liblsan0_15.2.0-12 liblz4-1_1.10.0-6 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.3-2 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libnettle8t64_3.10.2-1 libosp5_1.5.2-15.2 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libquadmath0_15.2.0-12 libruby_1:3.3+b1 libruby3.3_3.3.8-2 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+rebuild1766544377 libsframe2_2.45.50.20251209-1 libsmartcols1_2.41.3-2 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-12 libstdc++6_15.2.0-12 libsystemd0_259-1 libtinfo6_6.5+20251123-1 libtool_2.5.4-9 libtsan2_15.2.0-12 libubsan1_15.2.0-12 libuchardet0_0.0.8-2 libudev1_259-1 libunistring5_1.3-2 libuuid1_2.41.3-2 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2 libyaml-0-2_0.2.5-2+b1 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.13-1 m4_1.4.20-2 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20250131-2 ncurses-base_6.5+20251123-1 ncurses-bin_6.5+20251123-1 opensp_1.5.2-15.2 openssl_3.5.4-1 openssl-provider-legacy_3.5.4-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 rake_13.2.1-1 rdtool_0.6.38-5 rpcsvc-proto_1.4.3-1 ruby_1:3.3+b1 ruby-all-dev_1:3.3+b1 ruby-csv_3.3.4-1 ruby-did-you-mean_1.6.3-2 ruby-libxml_5.0.5-2+rebuild1766548530 ruby-minitest_5.26.1-1 ruby-net-telnet_0.2.0-1 ruby-power-assert_2.0.5-1 ruby-rd_0.6.38-5 ruby-ruby2-keywords_0.0.5-1 ruby-rubygems_3.6.7-2 ruby-test-unit_3.6.2-1 ruby-webrick_1.9.1-1 ruby-xmlrpc_0.3.3-2 ruby3.3_3.3.8-2 ruby3.3-dev_3.3.8-2 rubygems-integration_1.19 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sgml-data_2.0.11+nmu1 sqv_1.3.0-5 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 util-linux_2.41.3-2 xml-core_0.19 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b2 +------------------------------------------------------------------------------+ | Build Wed, 24 Dec 2025 10:25:53 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- Format: 3.0 (quilt) Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1+rebuild1766571925 Maintainer: Debian Ruby Team Uploaders: Lucas Nussbaum , Cédric Boutillier , Homepage: https://bioruby.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-bio Vcs-Git: https://salsa.debian.org/ruby-team/ruby-bio.git Testsuite: autopkgtest-pkg-ruby Build-Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit Build-Depends-Indep: docbook-to-man, rdtool Package-List: ruby-bio deb ruby optional arch=all Checksums-Sha1: a0cd4e46dd790e55ce38de08e2991a0a9b2fc4d1 1452516 ruby-bio_2.0.6.orig.tar.gz 43f3917eb9eecf863b3994609c0ad3d0446d80e7 14624 ruby-bio_2.0.6-1+rebuild1766571925.debian.tar.xz Checksums-Sha256: c96e0c54dcd9b9d413afad6b8702e4b1be290631b459402024c446ef922605b3 1452516 ruby-bio_2.0.6.orig.tar.gz f11a5b50064a29b4f4776f01dc0b32099b9f96c1c7649e6eb5915f791a89d5e7 14624 ruby-bio_2.0.6-1+rebuild1766571925.debian.tar.xz Files: 9c4372512937a004ed39a200510677fd 1452516 ruby-bio_2.0.6.orig.tar.gz 3e9688712e33b35cc33ad6904a56514c 14624 ruby-bio_2.0.6-1+rebuild1766571925.debian.tar.xz Ruby-Versions: all dpkg-source: warning: extracting unsigned source package (ruby-bio_2.0.6-1+rebuild1766571925.dsc) dpkg-source: info: extracting ruby-bio in /build/reproducible-path/ruby-bio-2.0.6 dpkg-source: info: unpacking ruby-bio_2.0.6.orig.tar.gz dpkg-source: info: unpacking ruby-bio_2.0.6-1+rebuild1766571925.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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 24 Dec 2025 10:25:54 +0000 | +------------------------------------------------------------------------------+ apt-get update -q && apt-get install -t experimental -qy ruby-all-dev --------------------------------------------------------------------- Ign:1 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ InRelease Ign:2 file:/mass-rebuild ./ InRelease Get:3 file:/mass-rebuild ./ Release [1617 B] Get:4 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Release [609 B] Ign:5 copy:/build/reproducible-path/resolver-jBWYTK/apt_archive ./ Release.gpg Get:3 file:/mass-rebuild ./ Release [1617 B] Ign:6 file:/mass-rebuild ./ Release.gpg Hit:7 http://deb.debian.org/debian unstable InRelease Hit:8 http://deb.debian.org/debian experimental InRelease Hit:9 http://incoming.debian.org/debian-buildd buildd-unstable InRelease Fetched 609 B in 0s (1907 B/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: libruby3.4 ruby3.4 ruby3.4-dev Recommended packages: ruby-sdbm fonts-lato libjs-jquery ruby3.4-doc The following NEW packages will be installed: libruby3.4 ruby3.4 ruby3.4-dev The following packages will be upgraded: ruby-all-dev 1 upgraded, 3 newly installed, 0 to remove and 26 not upgraded. Need to get 8784 kB of archives. After this operation, 36.3 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian experimental/main amd64 libruby3.4 amd64 3.4.5-1~exp1 [6731 kB] Get:2 http://deb.debian.org/debian experimental/main amd64 ruby3.4 amd64 3.4.5-1~exp1 [920 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 ruby3.4-dev amd64 3.4.5-1~exp1 [1127 kB] Get:4 http://deb.debian.org/debian experimental/main amd64 ruby-all-dev amd64 1:3.3+support3.4~0 [6292 B] debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline Fetched 8784 kB in 0s (88.0 MB/s) Selecting previously unselected package libruby3.4:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18833 files and directories currently installed.) Preparing to unpack .../libruby3.4_3.4.5-1~exp1_amd64.deb ... Unpacking libruby3.4:amd64 (3.4.5-1~exp1) ... Selecting previously unselected package ruby3.4. Preparing to unpack .../ruby3.4_3.4.5-1~exp1_amd64.deb ... Unpacking ruby3.4 (3.4.5-1~exp1) ... Selecting previously unselected package ruby3.4-dev:amd64. Preparing to unpack .../ruby3.4-dev_3.4.5-1~exp1_amd64.deb ... Unpacking ruby3.4-dev:amd64 (3.4.5-1~exp1) ... Preparing to unpack .../ruby-all-dev_1%3a3.3+support3.4~0_amd64.deb ... Unpacking ruby-all-dev:amd64 (1:3.3+support3.4~0) over (1:3.3+b1) ... Setting up libruby3.4:amd64 (3.4.5-1~exp1) ... Setting up ruby3.4 (3.4.5-1~exp1) ... Setting up ruby3.4-dev:amd64 (3.4.5-1~exp1) ... Setting up ruby-all-dev:amd64 (1:3.3+support3.4~0) ... Processing triggers for man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.42-6) ... I: Finished running 'apt-get update -q && apt-get install -t experimental -qy ruby-all-dev'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ADDRESS=pt_BR.UTF-8 LC_ALL=C.UTF-8 LC_IDENTIFICATION=pt_BR.UTF-8 LC_MEASUREMENT=pt_BR.UTF-8 LC_MONETARY=pt_BR.UTF-8 LC_NAME=pt_BR.UTF-8 LC_NUMERIC=pt_BR.UTF-8 LC_PAPER=pt_BR.UTF-8 LC_TELEPHONE=pt_BR.UTF-8 LC_TIME=pt_BR.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mAutomated rebuild -b dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.6-1+rebuild1766571925 dpkg-buildpackage: info: source distribution UNRELEASED dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=ruby --with ruby debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ruby-bio-2.0.6' 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/reproducible-path/ruby-bio-2.0.6' 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/reproducible-path/ruby-bio-2.0.6' dh_auto_install dh_ruby --install /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install files │ └──────────────────────────────────────────────────────────────────────────────┘ install -d /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/bl2seq/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format0.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/format8.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/genomenet.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/ncbioptions.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/remote.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rexml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/rpsblast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast/wublast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/blat/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/clustalw.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/emboss.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta/format10.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/msf.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/gcg/seq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/genscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/hmmer.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/iprscan/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/mafft.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/mast.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/meme/motif.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/muscle.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/baseml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/rates.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/codeml.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/common_report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/paml/yn00.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/alignment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/phylip/distance_matrix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/probcons.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/psort.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/pts1.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sim4/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sim4.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/sosui/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/spidey/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/targetp/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tcoffee.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/appl/tmhmm/report.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/command.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/features.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/compat/references.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/aa.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/codontable.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/data/na.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/aaindex.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/format_embl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/sptr.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/swissprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/trembl.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprot.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/uniprotkb.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprotkb.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fantom.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/defline.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/fasta_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/format_qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta/qual_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fasta.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/fastq_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq/format_fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/fastq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/common.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/ddbj.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/format_genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genbank_to_biosequence.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/genpept.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/genbank/refseq.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/gff.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/go.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/kegg/brite.rb 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/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/helix.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/hydropathy.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/nucleotide.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/taylor.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/turn.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme/zappo.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/color_scheme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/contingency_table.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/analysis_basic.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/cut_symbol.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/dense_int_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/dense_int_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/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/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/double_stranded.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/enzymes.yaml /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/sorted_num_array.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/sorted_num_array.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme/string_formatting.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/restriction_enzyme.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/util/sirna.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio/version.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 /build/reproducible-path/ruby-bio-2.0.6/lib/bio.rb /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb ┌──────────────────────────────────────────────────────────────────────────────┐ │ ruby-bio: Install Rubygems integration metadata │ └──────────────────────────────────────────────────────────────────────────────┘ generating gemspec at /build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all/specifications/bio-2.0.6.gemspec /usr/bin/ruby3.3 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.3 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.6/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.3.0:/var/lib/gems/3.3.0:/usr/local/lib/ruby/gems/3.3.0:/usr/lib/ruby/gems/3.3.0:/usr/lib/x86_64-linux-gnu/ruby/gems/3.3.0:/usr/share/rubygems-integration/3.3.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-linux-gnu/rubygems-integration/3.3.0 ruby3.3 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.3 -w -I"test" /usr/share/rubygems-integration/all/gems/rake-13.2.1/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_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.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 Bio::UniProt is an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::UniProt may be deprecated in the future. Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000239) test_dbs: .: (0.000094) test_go_ids: .: (0.000084) test_go_terms: .: (0.000081) test_parser: .: (0.000187) test_set_date: .: (0.000087) test_set_desc: .: (0.000083) test_to_str: .: (0.000091) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000344) test_mktmpdir_without_block: .: (0.000242) test_remove_entry_secure: .: (0.000178) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.001678) test_call_command_fork: .: (0.000115) test_call_command_open3: .: (0.001343) test_call_command_popen: .: (0.001343) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.001294) test_call_command_fork: .: (0.000051) test_call_command_open3: .: (0.001280) test_call_command_popen: .: (0.001273) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.001288) test_call_command_fork: .: (0.000052) test_call_command_open3: .: (0.001263) test_call_command_popen: .: (0.001375) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.001156) test_call_command_fork_chdir: .: (0.000110) test_call_command_popen_chdir: .: (0.001005) test_query_command_chdir: .: (0.001032) test_query_command_fork_chdir: .: (0.000101) test_query_command_popen_chdir: .: (0.000989) Bio::FuncTestCommandQuery: test_query_command: .: (0.002185) test_query_command_fork: .: (0.000679) test_query_command_open3: .: (0.002262) test_query_command_popen: .: (0.002264) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000324) test_initialize: .: (0.000134) test_path: .: (0.000089) test_path_after_close: .: (0.000178) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.007936) test_output_fasta: .: (0.006648) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000505) test_accession: .: (0.000071) test_accessions: .: (0.000497) test_comment: .: (0.000058) test_common_name: .: (0.000816) test_definition: .: (0.000082) test_features: .: (0.001663) test_gi: .: (0.000091) test_keywords: .: (0.000788) test_locus: .: (0.000046) test_nid: .: (0.000062) test_organism: .: (0.000096) test_origin: .: (0.000061) test_references: .: (0.001799) test_segment: .: (0.000522) test_source: .: (0.000442) test_taxonomy: .: (0.001304) test_version: .: (0.000077) test_versions: .: (0.000801) Bio::TestAA: test_13: .: (0.000703) test_1n: .: (0.000041) test_name2one: .: (0.000063) test_name2three: .: (0.000787) test_one2name: .: (0.000043) test_one2three: .: (0.000035) test_three2name: .: (0.000032) test_three2one: .: (0.001531) test_to_1_1: .: (0.000049) test_to_1_3: .: (0.000067) test_to_1_name: .: (0.000343) test_to_3_1: .: (0.000040) test_to_3_3: .: (0.000032) test_to_3_name: .: (0.000043) test_to_re: .: (0.000864) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000085) Bio::TestAAindex: test_api: .: (0.000061) test_auto_aax1: .: (0.000113) test_auto_aax2: .: (0.000094) Bio::TestAAindex1: test_author: .: (0.000139) test_comment: .: (0.000089) test_correlation_coefficient: .: (0.000177) test_dblinks: .: (0.000089) test_definition: .: (0.000086) test_entry_id: .: (0.000080) test_index: .: (0.000512) test_journal: .: (0.000117) test_title: .: (0.000094) Bio::TestAAindex2: test_access_A_R: .: (0.000349) test_access_R_A: .: (0.000298) test_author: .: (0.000097) test_cols: .: (0.000082) test_comment: .: (0.000083) test_dblinks: .: (0.000178) test_definition: .: (0.000098) test_entry_id: .: (0.000081) test_journal: .: (0.000093) test_matrix: .: (0.000398) test_matrix_1_2: .: (0.000270) test_matrix_2_2: .: (0.000255) test_matrix_A_R: .: (0.000341) test_matrix_R_A: .: (0.000260) test_matrix_determinant: .: (0.001012) test_matrix_rank: .: (0.001032) test_matrix_transpose: .: (0.000324) test_rows: .: (0.000089) test_title: .: (0.000089) Bio::TestAAindexConstant: test_delimiter: .: (0.000085) test_tagsize: .: (0.000034) Bio::TestAbif: test_complement: .: (0.006091) test_seq: .: (0.005825) test_to_biosequence: .: (0.006209) Bio::TestActsLikeMap: test_mixin: .: (0.000152) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000134) Bio::TestActsLikeMarker: test_mixin: .: (0.000088) Bio::TestAlignment: test_add_seq_no_key: .: (0.000132) test_add_seq_using_seq_with_aaseq_method: .: (0.000074) test_add_seq_using_seq_with_definition_method: .: (0.000044) test_add_seq_using_seq_with_entry_id_method: .: (0.000104) test_add_seq_using_seq_with_naseq_method: .: (0.000054) test_add_seq_using_seq_with_seq_method: .: (0.000049) test_consensus_iupac_gap_modes: .: (0.000186) test_consensus_iupac_missing_char: .: (0.000076) test_consensus_iupac_missing_char_option: .: (0.000084) test_consensus_iupac_no_gaps: .: (0.000156) test_consensus_iupac_of_ambiguous_bases: .: (0.000152) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002117) test_consensus_opt_gap_mode: .: (0.000249) test_consensus_opt_missing_char: .: (0.000097) test_consensus_string_no_gaps: .: (0.000096) test_consensus_threshold_four_sequences: .: (0.000131) test_consensus_threshold_two_sequences: .: (0.000149) test_convert_match: .: (0.000142) test_convert_unmatch: .: (0.000065) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000061) test_convert_unmatch_different_match_char: .: (0.000055) test_convert_unmatch_multiple_sequences: .: (0.000079) test_default_gap_char: .: (0.000081) test_default_gap_regexp_matches_default_gap_char: .: (0.000038) test_default_missing_char: .: (0.000083) test_each_site_equal_length: .: (0.000069) test_each_site_unequal_length: .: (0.000067) test_equals: .: (0.000080) test_match_line_protein: .: (0.000193) test_normalizebang_extends_sequences_with_gaps: .: (0.000061) test_seq_length_is_max_seq_length: .: (0.000042) test_seq_length_when_one_sequence: .: (0.000037) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000092) test_seqclass_when_seqclass_set: .: (0.000039) test_seqclass_when_sequence_used: .: (0.000037) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000038) test_set_and_get_gap_char: .: (0.000034) test_store_cannot_override_key: .: (0.000040) test_store_with_default_keys_and_user_defined_keys: .: (0.000044) test_store_with_nil_key_uses_next_number_for_key: .: (0.000039) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000103) test_alignment_concat: .: (0.000063) test_alignment_length: .: (0.000034) test_alignment_lstrip!: .: (0.000067) test_alignment_lstrip_nil: .: (0.000101) test_alignment_normalize!: .: (0.000083) test_alignment_rstrip!: .: (0.000073) test_alignment_rstrip_nil: .: (0.000044) test_alignment_site: .: (0.000041) test_alignment_slice: .: (0.000038) test_alignment_strip!: .: (0.000078) test_alignment_strip_nil: .: (0.000047) test_alignment_subseq: .: (0.000060) test_alignment_window: .: (0.000038) test_collect_each_site: .: (0.000057) test_consensus_each_site_default: .: (0.000115) test_consensus_each_site_gap_mode_1: .: (0.000081) test_consensus_each_site_gap_mode_minus1: .: (0.000067) test_consensus_iupac: .: (0.000154) test_consensus_string_default: .: (0.000062) test_consensus_string_half: .: (0.000059) test_convert_match: .: (0.000050) test_convert_unmatch: .: (0.000044) test_each_seq: .: (0.000047) test_each_site: .: (0.000078) test_each_site_step: .: (0.000053) test_each_window: .: (0.000072) test_match_line: .: (0.000441) test_match_line_amino: .: (0.000651) test_match_line_nuc: .: (0.000073) test_private_alignment_site: .: (0.000042) test_remove_all_gaps!: .: (0.000059) test_seqclass: .: (0.000041) test_seqclass=: .: (0.000050) test_seqclass_default: .: (0.000031) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.005226) test_determine_seq_method: .: (0.000748) test_entries: .: (0.000547) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000223) test_avoid_same_name_numbering: .: (0.000062) test_clustal_have_same_name_true: .: (0.000046) test_have_same_name_false: .: (0.000044) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000085) test_gap_char_default: .: (0.000037) test_gap_char_never_nil: .: (0.000034) test_gap_regexp: .: (0.000034) test_gap_regexp=: .: (0.000035) test_gap_regexp_never_nil: .: (0.000034) test_get_all_property_default: .: (0.000034) test_get_all_property_nodefault: .: (0.000042) test_is_gap_default_false: .: (0.000038) test_is_gap_default_true: .: (0.000037) test_is_gap_nodefault_false: .: (0.000037) test_is_gap_nodefault_true: .: (0.000036) test_missing_char=: .: (0.000035) test_missing_char_default: .: (0.000033) test_missing_char_never_nil: .: (0.000033) test_seqclass=: .: (0.000041) test_seqclass_default: .: (0.000033) test_seqclass_never_nil: .: (0.000033) test_set_all_property: .: (0.000039) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000234) test_consensus_string_50percent: .: (0.000043) test_consensus_string_50percent_nil: .: (0.000040) test_consensus_string_default: .: (0.000034) test_consensus_string_default_nil: .: (0.000034) test_has_gap_false: .: (0.000037) test_has_gap_true: .: (0.000035) test_match_line_amino_100percent: .: (0.000046) test_match_line_amino_missing: .: (0.000069) test_match_line_amino_strong: .: (0.000047) test_match_line_amino_weak: .: (0.000058) test_match_line_nuc_100percent: .: (0.000042) test_match_line_nuc_missing: .: (0.000043) test_remove_gaps!: .: (0.000146) test_remove_gaps_bang_not_removed: .: (0.000050) Bio::TestAtomFinder: test_atoms: .: (0.009681) test_each_atom: .: (0.000099) test_find_atom: .: (0.000074) Bio::TestBioFastaDefline: test_acc_version: .: (0.000222) test_accession: .: (0.000186) test_accessions: .: (0.000151) test_description: .: (0.000129) test_descriptions: .: (0.000126) test_entry_id: .: (0.000118) test_get: .: (0.000148) test_get_all_by_type: .: (0.000116) test_get_by_type: .: (0.000125) test_gi: .: (0.000113) test_id_strings: .: (0.000274) test_locus: .: (0.003140) test_method_missing: .: (0.000246) test_to_s: .: (0.000151) test_words: .: (0.000333) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000639) test_goid2term: .: (0.000177) test_parse_goids: .: (0.000159) Bio::TestBioGenBank: test_basecount: .: (0.000177) test_circular: .: (0.000115) test_classification: .: (0.000140) test_date: .: (0.000103) test_date_modified: .: (0.000414) test_division: .: (0.000121) test_each_cds_feature: .: (0.000415) test_each_cds_qualifiers: .: (0.000334) test_each_gene: .: (0.000326) test_entry_id: .: (0.000108) test_length: .: (0.000102) test_locus_circular: .: (0.000117) test_locus_class: .: (0.000198) test_locus_date: .: (0.000152) test_locus_division: .: (0.000114) test_locus_entry_id: .: (0.000111) test_locus_length: .: (0.000109) test_locus_natype: .: (0.000108) test_locus_strand: .: (0.000137) test_natype: .: (0.000127) test_seq: .: (0.000165) test_seq_len: .: (0.000162) test_strand: .: (0.000113) test_strandedness: .: (0.000102) test_to_biosequence: .: (0.001329) Bio::TestBioGenPept: test_circular: .: (0.000168) test_date: .: (0.000086) test_dbsource: .: (0.000079) test_division: .: (0.000080) test_entry_id: .: (0.000078) test_length: .: (0.000078) test_locus: .: (0.000080) test_seq: .: (0.000092) test_seq_len: .: (0.000084) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000219) test_aaseq: .: (0.000127) test_chromosome: .: (0.000099) test_codon_usage: .: (0.000148) test_cu_list: .: (0.000091) test_dblinks_as_hash: .: (0.000112) test_dblinks_as_strings: .: (0.000088) test_definition: .: (0.000105) test_division: .: (0.000092) test_eclinks: .: (0.000109) test_entry: .: (0.000086) test_entry_id: .: (0.000088) test_gbposition: .: (0.000096) test_gene: .: (0.000104) test_genes: .: (0.000095) test_keggclass: .: (0.000111) test_keggclasses: .: (0.000118) test_locations: .: (0.000163) test_motifs_as_hash: .: (0.000128) test_motifs_as_strings: .: (0.000089) test_name: .: (0.000097) test_names_as_array: .: (0.000103) test_new: .: (0.000096) test_ntlen: .: (0.000142) test_ntseq: .: (0.000168) test_organism: .: (0.000091) test_orthologs_as_hash: .: (0.000108) test_orthologs_as_strings: .: (0.000220) test_pathway: .: (0.000118) test_pathway_after_pathways_as_strings: .: (0.000133) test_pathway_before_pathways_as_strings: .: (0.000131) test_pathways_as_hash: .: (0.000105) test_pathways_as_strings: .: (0.000092) test_position: .: (0.000097) test_structure: .: (0.000102) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.000821) test_comment: .: (0.000165) test_data_source: .: (0.000149) test_definition: .: (0.000143) test_disease: .: (0.000151) test_entry_id: .: (0.000151) test_lineage: .: (0.000184) test_nalen: .: (0.000148) test_name: .: (0.000146) test_new: .: (0.000254) test_num_gene: .: (0.000152) test_num_rna: .: (0.000137) test_original_databases: .: (0.000306) test_original_db: .: (0.000156) test_plasmids: .: (0.000218) test_references: .: (0.005727) test_statistics: .: (0.000864) test_taxid: .: (0.000897) test_taxonomy: .: (0.000854) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.001480) test_comment: .: (0.000784) test_data_source: .: (0.000748) test_definition: .: (0.000110) test_disease: .: (0.000849) test_entry_id: .: (0.000785) test_lineage: .: (0.000467) test_nalen: .: (0.000407) test_name: .: (0.000131) test_new: .: (0.001217) test_num_gene: .: (0.000410) test_num_rna: .: (0.000104) test_original_databases: .: (0.000391) test_original_db: .: (0.001192) test_plasmids: .: (0.000732) test_references: .: (0.000756) test_statistics: .: (0.001480) test_taxid: .: (0.000754) test_taxonomy: .: (0.000637) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000190) test_compounds_as_strings: .: (0.000209) test_dblinks_as_hash: .: (0.000083) test_dblinks_as_strings: .: (0.000073) test_description: .: (0.000087) test_diseases_as_hash: .: (0.000074) test_diseases_as_strings: .: (0.000069) test_entry_id: .: (0.000082) test_enzymes_as_strings: .: (0.000082) test_genes_as_hash: .: (0.000071) test_genes_as_strings: .: (0.000069) test_keggclass: .: (0.000082) test_ko_pathway: .: (0.000080) test_modules_as_hash: .: (0.000098) test_modules_as_strings: .: (0.000077) test_name: .: (0.000085) test_new: .: (0.000081) test_organism: .: (0.000080) test_orthologs_as_hash: .: (0.000184) test_orthologs_as_strings: .: (0.000079) test_pathways_as_hash: .: (0.000082) test_pathways_as_strings: .: (0.000073) test_reactions_as_hash: .: (0.000072) test_reactions_as_strings: .: (0.000069) test_references: .: (0.000070) test_rel_pathways_as_hash: .: (0.000087) test_rel_pathways_as_strings: .: (0.000077) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000224) test_compounds_as_strings: .: (0.000121) test_dblinks_as_hash: .: (0.000092) test_dblinks_as_strings: .: (0.000084) test_description: .: (0.000109) test_diseases_as_hash: .: (0.000095) test_diseases_as_strings: .: (0.000085) test_entry_id: .: (0.000093) test_enzymes_as_strings: .: (0.000081) test_genes_as_hash: .: (0.000114) test_genes_as_strings: .: (0.000097) test_keggclass: .: (0.000095) test_ko_pathway: .: (0.000091) test_modules_as_hash: .: (0.000089) test_modules_as_strings: .: (0.000084) test_name: .: (0.000093) test_new: .: (0.000086) test_organism: .: (0.000091) test_orthologs_as_hash: .: (0.000099) test_orthologs_as_strings: .: (0.000178) test_pathways_as_hash: .: (0.000100) test_pathways_as_strings: .: (0.000085) test_reactions_as_hash: .: (0.000081) test_reactions_as_strings: .: (0.000084) test_references: .: (0.000080) test_rel_pathways_as_hash: .: (0.000095) test_rel_pathways_as_strings: .: (0.000087) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000140) test_compounds_as_strings: .: (0.000076) test_dblinks_as_hash: .: (0.000069) test_dblinks_as_strings: .: (0.000068) test_description: .: (0.000079) test_diseases_as_hash: .: (0.000069) test_diseases_as_strings: .: (0.000067) test_entry_id: .: (0.000154) test_enzymes_as_strings: .: (0.000074) test_genes_as_hash: .: (0.000068) test_genes_as_strings: .: (0.000067) test_keggclass: .: (0.000081) test_ko_pathway: .: (0.000077) test_modules_as_hash: .: (0.000069) test_modules_as_strings: .: (0.000067) test_name: .: (0.000077) test_new: .: (0.000073) test_organism: .: (0.000076) test_orthologs_as_hash: .: (0.000096) test_orthologs_as_strings: .: (0.000078) test_pathways_as_hash: .: (0.000073) test_pathways_as_strings: .: (0.000070) test_reactions_as_hash: .: (0.000067) test_reactions_as_strings: .: (0.000065) test_references: .: (0.000117) test_rel_pathways_as_hash: .: (0.000080) test_rel_pathways_as_strings: .: (0.000071) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000142) test_compounds_as_strings: .: (0.000084) test_dblinks_as_hash: .: (0.000107) test_dblinks_as_strings: .: (0.000084) test_description: .: (0.000201) test_diseases_as_hash: .: (0.000098) test_diseases_as_strings: .: (0.000084) test_entry_id: .: (0.000094) test_enzymes_as_strings: .: (0.000081) test_genes_as_hash: .: (0.000079) test_genes_as_strings: .: (0.000079) test_keggclass: .: (0.000092) test_ko_pathway: .: (0.000089) test_modules_as_hash: .: (0.000120) test_modules_as_strings: .: (0.000091) test_name: .: (0.000093) test_new: .: (0.000088) test_organism: .: (0.000089) test_orthologs_as_hash: .: (0.000083) test_orthologs_as_strings: .: (0.000079) test_pathways_as_hash: .: (0.000086) test_pathways_as_strings: .: (0.000081) test_reactions_as_hash: .: (0.000078) test_reactions_as_strings: .: (0.000077) test_references: .: (0.000309) test_rel_pathways_as_hash: .: (0.000117) test_rel_pathways_as_strings: .: (0.000090) Bio::TestBioKeggDRUG: test_activity: .: (0.000172) test_comment: .: (0.000101) test_dblinks_as_hash: .: (0.000131) test_dblinks_as_strings: .: (0.000099) test_entry_id: .: (0.000100) test_formula: .: (0.000117) test_kcf: .: (0.000089) test_mass: .: (0.000099) test_name: .: (0.000110) test_names: .: (0.000107) test_pathways_as_hash: .: (0.000113) test_pathways_as_strings: .: (0.000093) test_products: .: (0.000103) test_remark: .: (0.000104) Bio::TestBioKeggGLYCAN: test_comment: .: (0.001935) test_composition: .: (0.000117) test_compounds: .: (0.000095) test_dblinks_as_hash: .: (0.000178) test_dblinks_as_strings: .: (0.000112) test_entry_id: .: (0.000094) test_enzymes: .: (0.000099) test_kcf: .: (0.000080) test_keggclass: .: (0.000106) test_mass: .: (0.000096) test_name: .: (0.000089) test_orthologs_as_hash: .: (0.000121) test_orthologs_as_strings: .: (0.000101) test_pathways_as_hash: .: (0.000174) test_pathways_as_strings: .: (0.000090) test_reactions: .: (0.000097) test_references: .: (0.000110) test_remark: .: (0.000094) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000308) test_composition: .: (0.000097) test_compounds: .: (0.000079) test_dblinks_as_hash: .: (0.000094) test_dblinks_as_strings: .: (0.000074) test_entry_id: .: (0.000079) test_enzymes: .: (0.000076) test_kcf: .: (0.000065) test_keggclass: .: (0.000076) test_mass: .: (0.000230) test_name: .: (0.000085) test_orthologs_as_hash: .: (0.000075) test_orthologs_as_strings: .: (0.000068) test_pathways_as_hash: .: (0.000070) test_pathways_as_strings: .: (0.000065) test_reactions: .: (0.000073) test_references: .: (0.000069) test_remark: .: (0.000225) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000223) test_compounds_as_strings: .: (0.000149) test_dblinks_as_hash: .: (0.000102) test_dblinks_as_strings: .: (0.000092) test_description: .: (0.000100) test_diseases_as_hash: .: (0.000101) test_diseases_as_strings: .: (0.000102) test_entry_id: .: (0.000102) test_enzymes_as_strings: .: (0.000088) test_genes_as_hash: .: (0.000085) test_genes_as_strings: .: (0.000084) test_keggclass: .: (0.000098) test_ko_pathway: .: (0.000422) test_modules_as_hash: .: (0.000136) test_modules_as_strings: .: (0.000107) test_name: .: (0.000102) test_new: .: (0.000094) test_organism: .: (0.000098) test_orthologs_as_hash: .: (0.000088) test_orthologs_as_strings: .: (0.000085) test_pathways_as_hash: .: (0.000094) test_pathways_as_strings: .: (0.000089) test_reactions_as_hash: .: (0.000193) test_reactions_as_strings: .: (0.000140) test_references: .: (0.000219) test_rel_pathways_as_hash: .: (0.000151) test_rel_pathways_as_strings: .: (0.000115) Bio::TestBioLITDB: test_author: .: (0.000153) test_entry_id: .: (0.000081) test_field: .: (0.000094) test_journal: .: (0.000077) test_keyword: .: (0.000092) test_reference: .: (0.000148) test_title: .: (0.000092) test_volume: .: (0.000084) Bio::TestBioNBRF: test_aalen: .: (0.000136) test_aaseq: .: (0.000066) test_entry: .: (0.000061) test_length: .: (0.000061) test_nalen: .: (0.000091) test_naseq: .: (0.000075) test_seq: .: (0.000063) test_seq_class: .: (0.000058) test_to_nbrf: .: (0.000073) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000136) test_to_newick_format_leaf: .: (0.000118) test_to_newick_format_leaf_NHX: .: (0.000077) Bio::TestBl2seqReport: test_db_len: .: (0.000356) test_db_num: .: (0.000237) test_new: .: (0.000150) test_undefed_methods: .: (0.002051) test_undefed_methods_for_iteration: .: (0.000499) Bio::TestBl2seqReportConstants: test_rs: .: (0.000089) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000198) test_hits: .: (0.000150) Bio::TestBlast: test_blast_reports_format0: .: (0.003264) test_blast_reports_format0_with_block: .: (0.000402) test_blast_reports_format7: .: (0.005769) test_blast_reports_format7_with_block: .: (0.004974) test_blast_reports_format7_with_parser: .: (0.006671) test_blast_reports_format7_with_parser_with_block: .: (0.004912) test_blast_reports_format8: .: (0.000296) test_blast_reports_format8_with_block: .: (0.000235) test_blast_reports_format8_with_parser: .: (0.000121) test_blast_reports_format8_with_parser_with_block: .: (0.000099) test_blast_reports_xml: .: (0.006263) test_blast_reports_xml_with_block: .: (0.004958) test_blastll: .: (0.000077) test_db: .: (0.000059) test_exec_genomenet: .: (0.000050) test_exec_local: .: (0.000049) test_exec_ncbi: .: (0.000047) test_filter: .: (0.000067) test_format: .: (0.000059) test_make_command_line: .: (0.000177) test_make_command_line_2: .: (0.000148) test_matrix: .: (0.000057) test_new: .: (0.000094) test_new_opt_string: .: (0.000096) test_option: .: (0.000066) test_option_set: .: (0.000100) test_option_set_m0: .: (0.000086) test_options: .: (0.000056) test_output: .: (0.000055) test_parse_result: .: (0.005907) test_parser: .: (0.000078) test_program: .: (0.000066) test_query: .: (0.000076) test_self_local: .: (0.000160) test_self_remote: .: (0.000939) test_server: .: (0.000077) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000164) test_delete: .: (0.000137) test_equal_equal: .: (0.000135) test_get: .: (0.000128) test_make_command_line_options: .: (0.000118) test_normalize!: .: (0.000155) test_parse: .: (0.000095) test_set: .: (0.000174) Bio::TestBlastReport: test_db: .: (0.004756) test_db_len: .: (0.005647) test_db_num: .: (0.004849) test_each_hit: .: (0.005394) test_each_iteration: .: (0.004764) test_eff_space: .: (0.005349) test_entrez_query: .: (0.004736) test_entropy: .: (0.005236) test_expect: .: (0.004777) test_filter: .: (0.005217) test_gap_extend: .: (0.004756) test_gap_open: .: (0.005247) test_hits: .: (0.004816) test_hsp_len: .: (0.005225) test_inclusion: .: (0.004755) test_iterations: .: (0.005324) test_kappa: .: (0.004816) test_lambda: .: (0.005327) test_matrix: .: (0.004822) test_message: .: (0.005319) test_parameters: .: (0.004802) test_pattern: .: (0.005260) test_program: .: (0.004741) test_query_def: .: (0.005239) test_query_id: .: (0.004766) test_query_len: .: (0.005244) test_reference: .: (0.004785) test_sc_match: .: (0.005346) test_sc_mismatch: .: (0.004828) test_statistics: .: (0.005256) test_version: .: (0.004776) Bio::TestBlastReportDefault: test_db: .: (0.000327) test_db_len: .: (0.000284) test_db_num: .: (0.000228) test_each_hit: .: (0.000242) test_each_iteration: .: (0.000207) test_eff_space: .: (0.000257) test_entropy: .: (0.000246) test_expect: .: (0.000250) test_gap_extend: .: (0.000241) test_gap_open: .: (0.000243) test_gapped_entropy: .: (0.000222) test_gapped_kappa: .: (0.000212) test_gapped_lambda: .: (0.000214) test_hits: .: (0.000214) test_iterations: .: (0.000200) test_kappa: .: (0.000215) test_lambda: .: (0.000217) test_matrix: .: (0.000275) test_message: .: (0.000206) test_pattern: .: (0.000200) test_program: .: (0.000215) test_query_def: .: (0.000218) test_query_len: .: (0.000206) test_reference: .: (0.000216) test_sc_match: .: (0.000243) test_sc_mismatch: .: (0.000238) test_version: .: (0.000205) Bio::TestBlastReportHit: test_Hit_accession: .: (0.005716) test_Hit_bit_score: .: (0.004885) test_Hit_definition: .: (0.005483) test_Hit_evalue: .: (0.004719) test_Hit_hit_id: .: (0.005595) test_Hit_hsps: .: (0.004710) test_Hit_identity: .: (0.005391) test_Hit_lap_at: .: (0.004787) test_Hit_len: .: (0.005355) test_Hit_midline: .: (0.004690) test_Hit_num: .: (0.005297) test_Hit_overlap: .: (0.004720) test_Hit_query_def: .: (0.005334) test_Hit_query_end: .: (0.004723) test_Hit_query_id: .: (0.005269) test_Hit_query_len: .: (0.004708) test_Hit_query_seq: .: (0.005284) test_Hit_query_start: .: (0.004696) test_Hit_taeget_def: .: (0.005263) test_Hit_target_end: .: (0.004712) test_Hit_target_id: .: (0.005309) test_Hit_target_len: .: (0.004715) test_Hit_target_seq: .: (0.005281) test_Hit_target_start: .: (0.004744) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000357) test_Hit_definition: .: (0.000247) test_Hit_evalue: .: (0.000237) test_Hit_hsps: .: (0.000214) test_Hit_identity: .: (0.000229) test_Hit_lap_at: .: (0.000980) test_Hit_len: .: (0.000330) test_Hit_midline: .: (0.000306) test_Hit_overlap: .: (0.000397) test_Hit_query_end: .: (0.000318) test_Hit_query_seq: .: (0.000299) test_Hit_query_start: .: (0.000292) test_Hit_taeget_def: .: (0.000221) test_Hit_target_end: .: (0.000280) test_Hit_target_id: .: (0.000342) test_Hit_target_len: .: (0.000234) test_Hit_target_seq: .: (0.000289) test_Hit_target_start: .: (0.000281) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.034583) test_Hit_bit_score: .: (0.014717) test_Hit_definition: .: (0.014361) test_Hit_evalue: .: (0.014121) test_Hit_hit_id: .: (0.014047) test_Hit_hsps: .: (0.014052) test_Hit_identity: .: (0.014333) test_Hit_lap_at: .: (0.014279) test_Hit_len: .: (0.014019) test_Hit_midline: .: (0.014416) test_Hit_num: .: (0.014211) test_Hit_overlap: .: (0.014205) test_Hit_query_def: .: (0.014011) test_Hit_query_end: .: (0.014029) test_Hit_query_id: .: (0.014449) test_Hit_query_len: .: (0.014211) test_Hit_query_seq: .: (0.014373) test_Hit_query_start: .: (0.014239) test_Hit_taeget_def: .: (0.014085) test_Hit_target_end: .: (0.014461) test_Hit_target_id: .: (0.014291) test_Hit_target_len: .: (0.014206) test_Hit_target_seq: .: (0.014116) test_Hit_target_start: .: (0.014504) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.014261) test_Hit_bit_score: .: (0.014328) test_Hit_definition: .: (0.014010) test_Hit_evalue: .: (0.014584) test_Hit_hit_id: .: (0.014166) test_Hit_hsps: .: (0.014234) test_Hit_identity: .: (0.014113) test_Hit_lap_at: .: (0.014632) test_Hit_len: .: (0.014232) test_Hit_midline: .: (0.014242) test_Hit_num: .: (0.014001) test_Hit_overlap: .: (0.014545) test_Hit_query_def: .: (0.014123) test_Hit_query_end: .: (0.014172) test_Hit_query_id: .: (0.014036) test_Hit_query_len: .: (0.014576) test_Hit_query_seq: .: (0.014162) test_Hit_query_start: .: (0.014185) test_Hit_taeget_def: .: (0.014020) test_Hit_target_end: .: (0.014487) test_Hit_target_id: .: (0.014217) test_Hit_target_len: .: (0.014158) test_Hit_target_seq: .: (0.014132) test_Hit_target_start: .: (0.014408) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.004945) test_Hit_bit_score: .: (0.004726) test_Hit_definition: .: (0.005337) test_Hit_evalue: .: (0.004869) test_Hit_hit_id: .: (0.004961) test_Hit_hsps: .: (0.004909) test_Hit_identity: .: (0.004714) test_Hit_lap_at: .: (0.005291) test_Hit_len: .: (0.004894) test_Hit_midline: .: (0.004396) test_Hit_num: .: (0.005457) test_Hit_overlap: .: (0.004737) test_Hit_query_def: .: (0.005304) test_Hit_query_end: .: (0.004887) test_Hit_query_id: .: (0.004421) test_Hit_query_len: .: (0.005438) test_Hit_query_seq: .: (0.004842) test_Hit_query_start: .: (0.005240) test_Hit_taeget_def: .: (0.004712) test_Hit_target_end: .: (0.004534) test_Hit_target_id: .: (0.005431) test_Hit_target_len: .: (0.004868) test_Hit_target_seq: .: (0.004978) test_Hit_target_start: .: (0.004919) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000224) test_Hit_bit_score: .: (0.000080) test_Hit_definition: .: (0.000064) test_Hit_evalue: .: (0.000061) test_Hit_hit_id: .: (0.000072) test_Hit_hsps: .: (0.000059) test_Hit_identity: .: (0.000058) test_Hit_lap_at: .: (0.000063) test_Hit_len: .: (0.000057) test_Hit_midline: .: (0.000057) test_Hit_num: .: (0.000058) test_Hit_overlap: .: (0.000059) test_Hit_query_def: .: (0.000059) test_Hit_query_end: .: (0.000059) test_Hit_query_id: .: (0.000057) test_Hit_query_len: .: (0.000056) test_Hit_query_seq: .: (0.000057) test_Hit_query_start: .: (0.000057) test_Hit_taeget_def: .: (0.000057) test_Hit_target_end: .: (0.000057) test_Hit_target_id: .: (0.000056) test_Hit_target_len: .: (0.000057) test_Hit_target_seq: .: (0.000067) test_Hit_target_start: .: (0.000059) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.004624) test_Hsp_bit_score: .: (0.005412) test_Hsp_density: .: (0.004949) test_Hsp_evalue: .: (0.005346) test_Hsp_gaps: .: (0.004767) test_Hsp_hit_frame: .: (0.004429) test_Hsp_hit_from: .: (0.005428) test_Hsp_hit_to: .: (0.004902) test_Hsp_hseq: .: (0.005329) test_Hsp_identity: .: (0.004788) test_Hsp_midline: .: (0.004438) test_Hsp_mismatch_count: .: (0.005320) test_Hsp_num: .: (0.004903) test_Hsp_pattern_from: .: (0.005333) test_Hsp_pattern_to: .: (0.004691) test_Hsp_percent_identity: .: (0.004505) test_Hsp_positive: .: (0.005406) test_Hsp_qseq: .: (0.004809) test_Hsp_query_frame: .: (0.005331) test_Hsp_query_from: .: (0.004779) test_Hsp_query_to: .: (0.004423) test_Hsp_score: .: (0.005326) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000478) test_Hsp_bit_score: .: (0.000248) test_Hsp_evalue: .: (0.000227) test_Hsp_gaps: .: (0.000224) test_Hsp_hit_frame: .: (0.000222) test_Hsp_hit_from: .: (0.000287) test_Hsp_hit_to: .: (0.000282) test_Hsp_hseq: .: (0.000284) test_Hsp_identity: .: (0.000223) test_Hsp_midline: .: (0.000287) test_Hsp_percent_identity: .: (0.000222) test_Hsp_positive: .: (0.000304) test_Hsp_qseq: .: (0.000305) test_Hsp_query_frame: .: (0.000251) test_Hsp_query_from: .: (0.000290) test_Hsp_query_to: .: (0.000296) test_Hsp_score: .: (0.000225) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.014263) test_Hsp_bit_score: .: (0.014795) test_Hsp_density: .: (0.014376) test_Hsp_evalue: .: (0.014138) test_Hsp_gaps: .: (0.014695) test_Hsp_hit_frame: .: (0.014134) test_Hsp_hit_from: .: (0.014071) test_Hsp_hit_to: .: (0.014691) test_Hsp_hseq: .: (0.014161) test_Hsp_identity: .: (0.014090) test_Hsp_midline: .: (0.014631) test_Hsp_mismatch_count: .: (0.014232) test_Hsp_num: .: (0.014717) test_Hsp_pattern_from: .: (0.014345) test_Hsp_pattern_to: .: (0.013965) test_Hsp_percent_identity: .: (0.014623) test_Hsp_positive: .: (0.014118) test_Hsp_qseq: .: (0.014020) test_Hsp_query_frame: .: (0.014638) test_Hsp_query_from: .: (0.014295) test_Hsp_query_to: .: (0.014224) test_Hsp_score: .: (0.014873) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.014800) test_Hsp_bit_score: .: (0.015342) test_Hsp_density: .: (0.015708) test_Hsp_evalue: .: (0.014797) test_Hsp_gaps: .: (0.014658) test_Hsp_hit_frame: .: (0.015519) test_Hsp_hit_from: .: (0.015041) test_Hsp_hit_to: .: (0.015974) test_Hsp_hseq: .: (0.015170) test_Hsp_identity: .: (0.015005) test_Hsp_midline: .: (0.015717) test_Hsp_mismatch_count: .: (0.015078) test_Hsp_num: .: (0.037424) test_Hsp_pattern_from: .: (0.015880) test_Hsp_pattern_to: .: (0.015139) test_Hsp_percent_identity: .: (0.015096) test_Hsp_positive: .: (0.014894) test_Hsp_qseq: .: (0.014712) test_Hsp_query_frame: .: (0.015454) test_Hsp_query_from: .: (0.015201) test_Hsp_query_to: .: (0.014849) test_Hsp_score: .: (0.014910) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.006051) test_Hsp_bit_score: .: (0.005006) test_Hsp_density: .: (0.005371) test_Hsp_evalue: .: (0.005220) test_Hsp_gaps: .: (0.004862) test_Hsp_hit_frame: .: (0.005737) test_Hsp_hit_from: .: (0.005028) test_Hsp_hit_to: .: (0.004516) test_Hsp_hseq: .: (0.005923) test_Hsp_identity: .: (0.004986) test_Hsp_midline: .: (0.005609) test_Hsp_mismatch_count: .: (0.005270) test_Hsp_num: .: (0.004921) test_Hsp_pattern_from: .: (0.005956) test_Hsp_pattern_to: .: (0.005039) test_Hsp_percent_identity: .: (0.004555) test_Hsp_positive: .: (0.006101) test_Hsp_qseq: .: (0.005066) test_Hsp_query_frame: .: (0.005426) test_Hsp_query_from: .: (0.005155) test_Hsp_query_to: .: (0.004835) test_Hsp_score: .: (0.005720) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000247) test_Hsp_bit_score: .: (0.000071) test_Hsp_density: .: (0.000067) test_Hsp_evalue: .: (0.000072) test_Hsp_gaps: .: (0.000071) test_Hsp_hit_frame: .: (0.000063) test_Hsp_hit_from: .: (0.000061) test_Hsp_hit_to: .: (0.000059) test_Hsp_hseq: .: (0.000059) test_Hsp_identity: .: (0.000057) test_Hsp_midline: .: (0.000057) test_Hsp_mismatch_count: .: (0.000059) test_Hsp_num: .: (0.000059) test_Hsp_pattern_from: .: (0.000058) test_Hsp_pattern_to: .: (0.000056) test_Hsp_percent_identity: .: (0.000057) test_Hsp_positive: .: (0.000057) test_Hsp_qseq: .: (0.000057) test_Hsp_query_frame: .: (0.000058) test_Hsp_query_from: .: (0.000060) test_Hsp_query_to: .: (0.000057) test_Hsp_score: .: (0.000057) Bio::TestBlastReportIteration: test_hits: .: (0.004966) test_message: .: (0.005433) test_num: .: (0.005187) test_statistics: .: (0.004900) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000331) test_message: .: (0.000215) test_num: .: (0.000208) Bio::TestBlastReportIterationMulti: test_each: .: (0.015157) test_hits: .: (0.016408) test_message: .: (0.015147) test_num: .: (0.014557) test_query_def: .: (0.014989) test_query_id: .: (0.014658) test_query_len: .: (0.037176) test_statistics: .: (0.015515) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.014877) test_hits: .: (0.014585) test_message: .: (0.014266) test_num: .: (0.015026) test_query_def: .: (0.014695) test_query_id: .: (0.014231) test_query_len: .: (0.014839) test_statistics: .: (0.014223) Bio::TestBlastReportIterationREXML: test_hits: .: (0.005096) test_message: .: (0.005112) test_num: .: (0.005063) test_statistics: .: (0.004750) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000163) test_message: .: (0.000070) test_num: .: (0.000062) test_statistics: .: (0.000060) Bio::TestBlastReportMulti: test_db: .: (0.014838) test_db_len: .: (0.014463) test_db_num: .: (0.014469) test_each_hit: .: (0.014322) test_each_iteration: .: (0.015240) test_eff_space: .: (0.014508) test_entropy: .: (0.014334) test_expect: .: (0.014972) test_filter: .: (0.014320) test_gap_extend: .: (0.014982) test_gap_open: .: (0.014600) test_hits: .: (0.014188) test_hsp_len: .: (0.014818) test_iterations: .: (0.014271) test_kappa: .: (0.014948) test_lambda: .: (0.014667) test_matrix: .: (0.036182) test_message: .: (0.014620) test_parameters: .: (0.013853) test_pattern: .: (0.015152) test_program: .: (0.014340) test_query_def: .: (0.013845) test_query_id: .: (0.014535) test_query_len: .: (0.013140) test_reference: .: (0.014951) test_reports: .: (0.014728) test_statistics: .: (0.013086) test_version: .: (0.015138) Bio::TestBlastReportMultiREXML: test_db: .: (0.014662) test_db_len: .: (0.013704) test_db_num: .: (0.014768) test_each_hit: .: (0.014481) test_each_iteration: .: (0.013875) test_eff_space: .: (0.014491) test_entropy: .: (0.013988) test_expect: .: (0.014186) test_filter: .: (0.014665) test_gap_extend: .: (0.013108) test_gap_open: .: (0.015155) test_hits: .: (0.014916) test_hsp_len: .: (0.013032) test_iterations: .: (0.015060) test_kappa: .: (0.014824) test_lambda: .: (0.013022) test_matrix: .: (0.014903) test_message: .: (0.014671) test_parameters: .: (0.012987) test_pattern: .: (0.014860) test_program: .: (0.014699) test_query_def: .: (0.013174) test_query_id: .: (0.015454) test_query_len: .: (0.014780) test_reference: .: (0.013904) test_reports: .: (0.014036) test_statistics: .: (0.014104) test_version: .: (0.014056) Bio::TestBlastReportREXML: test_db: .: (0.004942) test_db_len: .: (0.004739) test_db_num: .: (0.004802) test_each_hit: .: (0.004453) test_each_iteration: .: (0.005922) test_eff_space: .: (0.004757) test_entrez_query: .: (0.004694) test_entropy: .: (0.004690) test_expect: .: (0.005875) test_filter: .: (0.004727) test_gap_extend: .: (0.004738) test_gap_open: .: (0.004713) test_hits: .: (0.004417) test_hsp_len: .: (0.005807) test_inclusion: .: (0.004754) test_iterations: .: (0.004794) test_kappa: .: (0.004730) test_lambda: .: (0.005189) test_matrix: .: (0.005145) test_message: .: (0.004748) test_parameters: .: (0.004851) test_pattern: .: (0.004416) test_program: .: (0.005819) test_query_def: .: (0.004744) test_query_id: .: (0.004745) test_query_len: .: (0.004754) test_reference: .: (0.005206) test_sc_match: .: (0.005241) test_sc_mismatch: .: (0.004729) test_statistics: .: (0.004893) test_version: .: (0.004408) Bio::TestBlastReportTabular: test_db: .: (0.000161) test_db_len: .: (0.000067) test_db_num: .: (0.000061) test_each_hit: .: (0.000063) test_each_iteration: .: (0.000059) test_eff_space: .: (0.000058) test_entrez_query: .: (0.000062) test_entropy: .: (0.000058) test_expect: .: (0.000057) test_filter: .: (0.000056) test_gap_extend: .: (0.000056) test_gap_open: .: (0.000056) test_hits: .: (0.000061) test_hsp_len: .: (0.000076) test_inclusion: .: (0.000061) test_iterations: .: (0.000058) test_kappa: .: (0.000057) test_lambda: .: (0.000056) test_matrix: .: (0.000056) test_message: .: (0.000059) test_parameters: .: (0.000060) test_pattern: .: (0.000066) test_program: .: (0.000058) test_query_def: .: (0.000059) test_query_id: .: (0.000058) test_query_len: .: (0.000058) test_reference: .: (0.000057) test_sc_match: .: (0.000058) test_sc_mismatch: .: (0.000056) test_statistics: .: (0.000059) test_version: .: (0.000056) Bio::TestChain: test_aaseq: .: (0.000180) test_addLigand: .: (0.000046) test_addResidue: .: (0.000043) test_atom_seq: .: (0.000047) test_comp: .: (0.000062) test_each: .: (0.000046) test_each_heterogen: .: (0.000046) test_each_residue: .: (0.000047) test_get_heterogen_by_id: .: (0.000042) test_get_residue_by_id: .: (0.000042) test_inspect: .: (0.000825) test_rehash: .: (0.000062) test_rehash_heterogens: .: (0.000040) test_rehash_residues: .: (0.000039) test_square_brace: .: (0.000046) test_to_s: .: (0.000053) Bio::TestChainFinder: test_chains: .: (0.000154) test_each_chain: .: (0.000054) test_find_chain: .: (0.000046) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.004020) test_header: .: (0.000291) test_match_line: .: (0.000371) test_sequence0: .: (0.000259) test_sequence1: .: (0.000352) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.003575) test_header: .: (0.000526) test_match_line: .: (0.000351) test_sequence0: .: (0.000664) test_sequence1: .: (0.000352) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.004112) test_header: .: (0.000251) test_match_line: .: (0.000239) test_sequence0: .: (0.000241) test_sequence1: .: (0.000240) Bio::TestCodonTable: test_Tables: .: (0.000104) test_accessor: .: (0.000053) test_definition: .: (0.000034) test_each: .: (0.000044) test_revtrans: .: (0.000068) test_self_accessor: .: (0.000036) test_self_copy: .: (0.000370) test_set_accessor: .: (0.037078) test_start: .: (0.000053) test_start_codon?: .: (0.000045) test_stop: .: (0.000034) test_stop_codon?: .: (0.000039) test_table: .: (0.000034) Bio::TestCodonTableConstants: test_Definitions: .: (0.000105) test_Starts: .: (0.000043) test_Tables: .: (0.000035) test_stops: .: (0.000041) Bio::TestColorScheme: test_buried: .: (0.001587) Bio::TestCommand: test_command_constants: .: (0.000103) test_escape_shell: .: (0.000065) test_escape_shell_unix: .: (0.000045) test_escape_shell_windows: .: (0.000057) test_make_cgi_params_by_array_of_array: .: (0.000150) test_make_cgi_params_by_array_of_hash: .: (0.000129) test_make_cgi_params_by_array_of_string: .: (0.000064) test_make_cgi_params_by_hash_in_string: .: (0.000193) test_make_cgi_params_by_hash_in_symbol: .: (0.000737) test_make_cgi_params_by_string: .: (0.000149) test_make_command_line: .: (0.000057) test_make_command_line_unix: .: (0.000044) test_make_command_line_windows: .: (0.000045) test_safe_command_line_array: .: (0.000049) test_safe_command_line_array_passthrough: .: (0.000045) Bio::TestContingencyTable: test_lite_example: .: (0.063250) Bio::TestDB: test_entry_id: .: (0.000318) test_exists: .: (0.000048) test_fetch: .: (0.000074) test_get: .: (0.000036) test_open: .: (0.000035) test_tags: .: (0.000036) Bio::TestDataType: test_const_like_method: .: (0.000260) test_pdb_achar: .: (0.000095) test_pdb_atom: .: (0.000080) test_pdb_character: .: (0.000077) test_pdb_date: .: (0.000077) test_pdb_idcode: .: (0.000076) test_pdb_integer: .: (0.000039) test_pdb_list: .: (0.000042) test_pdb_lstring: .: (0.000073) test_pdb_real: .: (0.000061) test_pdb_resudue_name: .: (0.000078) test_pdb_slist: .: (0.000039) test_pdb_string: .: (0.000117) test_pdb_stringrj: .: (0.000041) test_pdb_symop: .: (0.000083) test_specification_list: .: (0.000048) Bio::TestEMBL: test_ac: .: (0.000248) test_accession: .: (0.000152) test_cc: .: (0.000120) test_de: .: (0.000138) test_division: .: (0.000251) test_dr: .: (0.000134) test_dt: .: (0.000127) test_dt_created: .: (0.000120) test_dt_iterator: .: (0.000114) test_dt_updated: .: (0.000115) test_each_cds: .: (0.000212) test_each_gene: .: (0.000181) test_entry: .: (0.000271) test_fh: .: (0.000134) test_ft: .: (0.000194) test_ft_accessor: .: (0.000187) test_ft_iterator: .: (0.000196) test_id_line: .: (0.000140) test_id_line_data_class: .: (0.000246) test_id_line_division: .: (0.000154) test_id_line_entry_name: .: (0.000137) test_id_line_iterator: .: (0.000132) test_id_line_molecule_type: .: (0.000133) test_id_line_sequence_length: .: (0.000145) test_kw: .: (0.000137) test_molecule: .: (0.000150) test_oc: .: (0.000287) test_og: .: (0.000123) test_os: .: (0.000152) test_ref: .: (0.000182) test_references: .: (0.000247) test_seq: .: (0.000380) test_sequence_length: .: (0.000161) test_sq: .: (0.000140) test_sq_get: .: (0.000131) test_sv: .: (0.000125) test_version: .: (0.000128) Bio::TestEMBL89: test_ac: .: (0.000197) test_accession: .: (0.000128) test_cc: .: (0.000113) test_de: .: (0.000130) test_division: .: (0.000160) test_dr: .: (0.000226) test_dt: .: (0.000124) test_dt_created: .: (0.000127) test_dt_iterator: .: (0.000114) test_dt_updated: .: (0.000114) test_each_cds: .: (0.000381) test_each_gene: .: (0.000184) test_entry: .: (0.000153) test_fh: .: (0.000122) test_ft: .: (0.000179) test_ft_accessor: .: (0.000174) test_ft_iterator: .: (0.000180) test_id_line: .: (0.000319) test_id_line_data_class: .: (0.000146) test_id_line_division: .: (0.000133) test_id_line_entry_name: .: (0.000131) test_id_line_iterator: .: (0.000129) test_id_line_molecule_type: .: (0.000128) test_id_line_sequence_length: .: (0.000127) test_id_line_sequence_version: .: (0.000129) test_kw: .: (0.000125) test_molecule: .: (0.000158) test_oc: .: (0.000346) test_og: .: (0.000129) test_os: .: (0.000141) test_ref: .: (0.000165) test_references: .: (0.000218) test_seq: .: (0.000244) test_sequence_length: .: (0.000141) test_sq: .: (0.000129) test_sq_get: .: (0.000304) test_sv: .: (0.000157) test_version: .: (0.000142) Bio::TestEMBLAPI: test_ac: .: (0.000127) test_accessions: .: (0.000063) Bio::TestEMBLCommon: test_ac: .: (0.000091) test_accession: .: (0.000038) test_accessions: .: (0.000036) test_de: .: (0.000034) test_definition: .: (0.000034) test_description: .: (0.000035) test_dr: .: (0.000035) test_keywords: .: (0.000035) test_kw: .: (0.000035) test_oc: .: (0.000034) test_og: .: (0.000034) test_os: .: (0.000036) test_ref: .: (0.000034) test_references: .: (0.000035) Bio::TestEMBLDB: test_fetch: .: (0.000117) test_p_entry2hash: .: (0.000034) Bio::TestEMBLToBioSequence: test_classification: .: (0.001689) test_date_created: .: (0.000264) test_date_modified: .: (0.000196) test_definition: .: (0.000159) test_division: .: (0.000156) test_entry_id: .: (0.000152) test_entry_version: .: (0.000147) test_features: .: (0.000207) test_keywords: .: (0.000144) test_molecule_type: .: (0.000154) test_primary_accession: .: (0.000144) test_references: .: (0.000250) test_release_created: .: (0.000150) test_release_modified: .: (0.000157) test_secondary_accessions: .: (0.000149) test_sequence_version: .: (0.000162) test_species: .: (0.000139) test_topology: .: (0.000160) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.001328) test_date_created: .: (0.001194) test_date_modified: .: (0.001239) test_definition: .: (0.001199) test_division: .: (0.001200) test_entry_id: .: (0.001252) test_entry_version: .: (0.003623) test_features: .: (0.001838) test_keywords: .: (0.001687) test_molecule_type: .: (0.001508) test_primary_accession: .: (0.001244) test_references: .: (0.001330) test_release_created: .: (0.001267) test_release_modified: .: (0.001225) test_secondary_accessions: .: (0.001217) test_sequence_version: .: (0.001289) test_species: .: (0.001226) test_topology: .: (0.001307) Bio::TestFasta: test_db: .: (0.000109) test_format: .: (0.000037) test_format_arg_integer: .: (0.000046) test_format_arg_str: .: (0.000041) test_ktup: .: (0.000040) test_matrix: .: (0.000039) test_option: .: (0.000061) test_options: .: (0.000168) test_output: .: (0.000036) test_program: .: (0.000038) test_server: .: (0.000037) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000112) test_accession: .: (0.000049) test_accessions: .: (0.000051) test_description: .: (0.000046) test_descriptions: .: (0.000044) test_entry_id: .: (0.000042) test_get_all_by_type: .: (0.000043) test_gi: .: (0.000044) test_id_strings: .: (0.000073) test_list_ids: .: (0.000046) test_locus: .: (0.000044) test_words: .: (0.000065) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000103) test_accession: .: (0.000053) test_accessions: .: (0.000052) test_description: .: (0.000046) test_descriptions: .: (0.000046) test_emb: .: (0.000053) test_entry_id: .: (0.000045) test_get_all_by_type: .: (0.000047) test_get_emb: .: (0.000048) test_gi: .: (0.000046) test_id_strings: .: (0.000068) test_list_ids: .: (0.000048) test_locus: .: (0.000047) test_words: .: (0.000065) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000090) test_accession: .: (0.000050) test_accessions: .: (0.000046) test_description: .: (0.000042) test_descriptions: .: (0.000041) test_entry_id: .: (0.000042) test_get_all_by_type: .: (0.000041) test_gi: .: (0.000042) test_id_strings: .: (0.000060) test_list_ids: .: (0.000043) test_locus: .: (0.000042) test_sp: .: (0.000049) test_words: .: (0.000057) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000108) test_accession: .: (0.000064) test_accessions: .: (0.000068) test_description: .: (0.000058) test_descriptions: .: (0.000059) test_entry_id: .: (0.000057) test_get_all_by_type: .: (0.000059) test_gi: .: (0.000058) test_id_strings: .: (0.000114) test_list_ids: .: (0.000084) test_locus: .: (0.000064) test_words: .: (0.000118) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000109) test_accession: .: (0.000058) test_accessions: .: (0.000054) test_description: .: (0.000062) test_descriptions: .: (0.000053) test_entry_id: .: (0.000051) test_get_all_by_type: .: (0.000052) test_gi: .: (0.000051) test_id_strings: .: (0.000091) test_list_ids: .: (0.000054) test_locus: .: (0.000052) test_words: .: (0.000089) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000087) test_accession: .: (0.000041) test_accessions: .: (0.000039) test_description: .: (0.000037) test_descriptions: .: (0.000038) test_entry_id: .: (0.000036) test_get_all_by_type: .: (0.000039) test_gi: .: (0.000036) test_id_strings: .: (0.000049) test_list_ids: .: (0.000038) test_locus: .: (0.000037) test_words: .: (0.000046) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000088) test_accession: .: (0.000047) test_accessions: .: (0.000044) test_description: .: (0.000041) test_descriptions: .: (0.000041) test_entry_id: .: (0.000039) test_get: .: (0.000046) test_get_all_by_type: .: (0.000043) test_id_strings: .: (0.000073) test_list_ids: .: (0.000041) test_locus: .: (0.000040) test_sp: .: (0.000046) test_words: .: (0.000074) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000089) test_accession: .: (0.000046) test_accessions: .: (0.000043) test_description: .: (0.000041) test_descriptions: .: (0.000041) test_entry_id: .: (0.000040) test_get: .: (0.000045) test_get_all_by_type: .: (0.000041) test_id_strings: .: (0.000084) test_list_ids: .: (0.000042) test_locus: .: (0.000040) test_tr: .: (0.000046) test_words: .: (0.000089) Bio::TestFastaFirstName: test_first_name1: .: (0.000091) test_first_name_multi_identifier: .: (0.000045) test_first_name_single_worded_defintion: .: (0.000038) test_no_definition: .: (0.000037) test_space_before_first_name: .: (0.000037) test_tabbed_defintion: .: (0.000037) Bio::TestFastaFormat: test_aalen: .: (0.000103) test_aaseq: .: (0.000050) test_acc_version: .: (0.000068) test_accession: .: (0.000070) test_accessions: .: (0.000063) test_data: .: (0.000043) test_definition: .: (0.000040) test_entry: .: (0.000042) test_entry_id: .: (0.000053) test_entry_overrun: .: (0.000041) test_first_name: .: (0.000042) test_gi: .: (0.000056) test_identifiers: .: (0.000058) test_length: .: (0.000048) test_query: .: (0.000053) test_seq: .: (0.000046) Bio::TestFastaFormatConst: test_delimiter: .: (0.000084) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000119) test_data: .: (0.000046) test_definition: .: (0.000043) test_entry: .: (0.000043) test_entry_id: .: (0.000063) test_first_name: .: (0.000046) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000088) test_naseq: .: (0.000042) test_naseq_class: .: (0.000042) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000094) Bio::TestFastaInitialize: test_new_1: .: (0.000235) test_option: .: (0.000040) test_option_backward_compatibility: .: (0.000058) Bio::TestFastaNumericFormat: test_arg: .: (0.000111) test_data: .: (0.000061) test_definition: .: (0.000040) test_each: .: (0.000057) test_entry: .: (0.000039) test_entry_id: .: (0.000048) test_length: .: (0.000056) test_to_biosequence: .: (0.000397) Bio::TestFastaQuery: test_query: .: (0.000094) test_self_local: .: (0.000029) test_self_parser: .: (0.000027) test_self_remote: .: (0.000025) Bio::TestFastacmd: test_database: .: (0.000088) test_fastacmd: .: (0.000034) test_methods: .: (0.000047) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.000302) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000227) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000218) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.000759) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.000240) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000210) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000191) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.000572) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.000328) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.000201) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000195) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000193) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.000481) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.000549) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.000560) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.000210) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000188) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000185) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.001289) test_error_probabilities_as_sanger: .: (0.001083) test_error_probabilities_as_solexa: .: (0.001130) test_quality_scores_as_illumina: .: (0.000155) test_quality_scores_as_sanger: .: (0.000130) test_quality_scores_as_solexa: .: (0.000141) test_validate_format: .: (0.000249) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000492) test_entry_id: .: (0.000373) test_error_probabilities: .: (0.032247) test_nalen: .: (0.000417) test_naseq: .: (0.000703) test_quality_scores: .: (0.000764) test_quality_string: .: (0.000311) test_roundtrip: .: (0.033200) test_seq: .: (0.000374) test_sequence_string: .: (0.000310) test_to_biosequence: .: (0.028980) test_to_biosequence_and_output: .: (0.001830) test_to_s: .: (0.000935) test_validate_format: .: (0.000387) test_validate_format_with_array: .: (0.000687) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000281) test_mask_20_with_empty_string: .: (0.000161) test_mask_20_with_longer_string: .: (0.000157) test_mask_20_with_x: .: (0.000150) test_mask_60: .: (0.000183) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.001707) test_error_probabilities_as_sanger: .: (0.001454) test_error_probabilities_as_solexa: .: (0.001765) test_quality_scores_as_illumina: .: (0.000175) test_quality_scores_as_sanger: .: (0.000133) test_quality_scores_as_solexa: .: (0.000159) test_validate_format: .: (0.000253) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.001110) test_error_probabilities_as_sanger: .: (0.001033) test_error_probabilities_as_solexa: .: (0.001664) test_quality_scores_as_illumina: .: (0.000184) test_quality_scores_as_sanger: .: (0.000172) test_quality_scores_as_solexa: .: (0.000122) test_validate_format: .: (0.000252) Bio::TestFeature: test_append: .: (0.000114) test_append_nil: .: (0.000042) test_assoc: .: (0.000048) test_each: .: (0.000036) test_feature: .: (0.000034) test_locations: .: (0.000365) test_new: .: (0.000050) test_position: .: (0.000035) test_qualifiers: .: (0.000033) Bio::TestFeatures: test_append: .: (0.000119) test_arg: .: (0.000041) test_each: .: (0.000038) test_features: .: (0.000040) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000478) test_aaindex2: .: (0.000136) test_blast: .: (0.000101) test_blastxml: .: (0.000450) test_embl: .: (0.000143) test_embl_oldrelease: .: (0.000132) test_fastaformat: .: (0.000397) test_fastanumericformat: .: (0.000068) test_fastq: .: (0.000100) test_genbank: .: (0.000115) test_genpept: .: (0.000125) test_hmmer: .: (0.000106) test_maxml_cluster: .: (0.001656) test_maxml_sequence: .: (0.000061) test_medline: .: (0.000074) test_prosite: .: (0.002848) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002107) test_transfac: .: (0.000806) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000126) test_auto_1arg_filename: .: (0.000184) test_auto_1arg_io: .: (0.000169) test_auto_1arg_io_with_block: .: (0.000286) test_auto_1arg_with_block: .: (0.000260) test_auto_2arg_filename_mode: .: (0.000151) test_auto_2arg_filename_mode_with_block: .: (0.000256) test_auto_3arg: .: (0.000143) test_auto_3arg_with_block: .: (0.000370) test_foreach: .: (0.000228) test_new_2arg_class: .: (0.000079) test_new_2arg_nil: .: (0.000127) test_open_0arg: .: (0.000055) test_open_1arg_class: .: (0.000049) test_open_1arg_filename: .: (0.000138) test_open_1arg_io: .: (0.000134) test_open_1arg_io_with_block: .: (0.000261) test_open_1arg_nil: .: (0.000052) test_open_1arg_with_block: .: (0.000377) test_open_2arg_autodetect: .: (0.000153) test_open_2arg_autodetect_io: .: (0.000140) test_open_2arg_autodetect_io_with_block: .: (0.000277) test_open_2arg_autodetect_with_block: .: (0.000256) test_open_2arg_class: .: (0.000077) test_open_2arg_class_io: .: (0.000072) test_open_2arg_class_io_with_block: .: (0.000195) test_open_2arg_class_with_block: .: (0.000256) test_open_2arg_filename_mode: .: (0.000154) test_open_2arg_filename_mode_with_block: .: (0.000253) test_open_3arg: .: (0.000277) test_open_3arg_with_block: .: (0.000680) test_open_4arg: .: (0.000539) test_to_a: .: (0.000233) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000220) test_close: .: (0.000070) test_dbclass: .: (0.000065) test_dbclass_eq: .: (0.000072) test_dbclass_nil: .: (0.000091) test_each: .: (0.000153) test_each_entry: .: (0.000173) test_ended_pos: .: (0.000115) test_entry_pos_flag: .: (0.000069) test_entry_raw: .: (0.000141) test_eof?: .: (0.000120) test_next_entry: .: (0.000148) test_path: .: (0.000060) test_pos: .: (0.000108) test_raw: .: (0.000224) test_rewind: .: (0.000110) test_start_pos: .: (0.000109) test_start_pos_ended_pos_not_recorded: .: (0.000109) test_to_io: .: (0.000066) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000139) test_simpleformat2: .: (0.000084) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000095) test_eof_false_after_prefetch: .: (0.000080) test_eof_false_first: .: (0.000044) test_eof_true: .: (0.000068) test_getc: .: (0.000048) test_getc_after_prefetch: .: (0.000046) test_gets: .: (0.000045) test_gets_equal_prefetch_gets: .: (0.000049) test_gets_paragraph_mode: .: (0.000158) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000166) test_gets_paragraph_mode_within_buffer: .: (0.000183) test_gets_rs: .: (0.000072) test_gets_rs_equal_prefetch_gets: .: (0.000072) test_gets_rs_within_buffer: .: (0.000124) test_pos: .: (0.000050) test_pos=: .: (0.000056) test_prefetch_buffer: .: (0.000046) test_prefetch_gets: .: (0.000058) test_prefetch_gets_with_arg: .: (0.000061) test_rewind: .: (0.000046) test_skip_spaces: .: (0.000052) test_to_io: .: (0.000051) test_ungetc: .: (0.000050) test_ungetc_after_prefetch: .: (0.000052) test_ungets: .: (0.000059) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000121) test_self_open_file: .: (0.014761) test_self_open_file_with_block: .: (0.000070) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000103) test_parse_file_open_arg_int_perm: .: (0.000038) test_parse_file_open_arg_int_perm_opt: .: (0.000037) test_parse_file_open_arg_integer: .: (0.000034) test_parse_file_open_arg_nil: .: (0.000033) test_parse_file_open_arg_opt: .: (0.000049) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000044) test_parse_file_open_arg_str: .: (0.000040) test_parse_file_open_arg_str_opt: .: (0.000043) test_parse_file_open_arg_str_perm: .: (0.000040) test_parse_file_open_arg_str_perm_opt: .: (0.000041) test_parse_file_open_arg_str_with_enc: .: (0.000042) test_parse_file_open_arg_str_with_ext_enc: .: (0.000041) test_parse_file_open_mode_integer: .: (0.000033) test_parse_file_open_mode_nil: .: (0.000038) test_parse_file_open_mode_str: .: (0.000038) test_parse_file_open_mode_str_with_enc: .: (0.000038) test_parse_file_open_mode_str_with_ext_enc: .: (0.000038) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000096) test_entry: .: (0.000044) test_entry_ended_pos: .: (0.000041) test_entry_pos_flag: .: (0.000046) test_entry_start_pos: .: (0.000038) test_get_entry: .: (0.000058) test_rewind: .: (0.000046) test_skip_leader: .: (0.000047) test_stream: .: (0.000036) test_stream_pos: .: (0.000046) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000093) test_delimiter_overrun: .: (0.000038) test_entry: .: (0.000057) test_entry_ended_pos: .: (0.000047) test_entry_ended_pos_default_nil: .: (0.000046) test_entry_start_pos: .: (0.000046) test_entry_start_pos_default_nil: .: (0.000043) test_get_entry: .: (0.000084) test_get_parsed_entry: .: (0.000093) test_header: .: (0.000038) test_skip_leader: .: (0.000054) test_skip_leader_without_header: .: (0.000054) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000135) test_entry_ended_pos: .: (0.000095) test_entry_start_pos: .: (0.000084) test_flag_to_fetch_header: .: (0.000080) test_get_entry: .: (0.000110) test_get_parsed_entry: .: (0.000117) test_rewind: .: (0.000087) test_skip_leader: .: (0.000054) Bio::TestGCGMsf: test_alignment: .: (0.000499) test_checksum: .: (0.000101) test_compcheck: .: (0.000099) test_date: .: (0.000089) test_description: .: (0.000085) test_entry_id: .: (0.000084) test_gap_length_weight: .: (0.000088) test_gap_weight: .: (0.000088) test_heading: .: (0.000093) test_length: .: (0.000089) test_seq_type: .: (0.000089) test_symbol_comparison_table: .: (0.000092) test_validate_checksum: .: (0.000576) Bio::TestGFF: test_record_class: .: (0.000237) test_records: .: (0.000142) Bio::TestGFF2: test_const_version: .: (0.000261) test_gff_version: .: (0.000187) test_metadata: .: (0.000190) test_metadata_size: .: (0.000204) test_records_size: .: (0.002003) test_to_s: .: (0.000321) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000119) test_attributes_case2: .: (0.000521) test_attributes_incompatible_backslash_semicolon: .: (0.000111) Bio::TestGFF2MetaData: test_data: .: (0.000087) test_directive: .: (0.000034) test_parse: .: (0.000039) Bio::TestGFF2Record: test_attribute: .: (0.000207) test_attribute_nonexistent: .: (0.000117) test_attributes: .: (0.000405) test_attributes_to_hash: .: (0.000153) test_comment_only?: .: (0.000116) test_delete_attribute: .: (0.000127) test_delete_attribute_multiple: .: (0.000384) test_delete_attribute_multiple2: .: (0.000155) test_delete_attribute_multiple_nil: .: (0.000129) test_delete_attribute_nil: .: (0.000123) test_delete_attribute_nonexistent: .: (0.000121) test_delete_attributes: .: (0.000305) test_delete_attributes_multiple: .: (0.000131) test_delete_attributes_nonexistent: .: (0.000120) test_end: .: (0.000111) test_eqeq: .: (0.000291) test_eqeq_false: .: (0.000442) test_feature: .: (0.000121) test_frame: .: (0.000108) test_get_attribute: .: (0.000151) test_get_attribute_nonexistent: .: (0.000253) test_get_attributes: .: (0.000156) test_get_attributes_nonexistent: .: (0.000111) test_replace_attributes: .: (0.000146) test_replace_attributes_multiple_multiple_over: .: (0.000340) test_replace_attributes_multiple_multiple_same: .: (0.000135) test_replace_attributes_multiple_multiple_two: .: (0.000136) test_replace_attributes_multiple_single: .: (0.000127) test_replace_attributes_nonexistent: .: (0.000122) test_replace_attributes_nonexistent_multiple: .: (0.000125) test_replace_attributes_single_multiple: .: (0.000230) test_score: .: (0.000111) test_self_parse: .: (0.000289) test_seqname: .: (0.000221) test_set_attribute: .: (0.000129) test_set_attribute_multiple: .: (0.000126) test_set_attribute_nonexistent: .: (0.000122) test_sort_attributes_by_tag!: .: (0.000200) test_sort_attributes_by_tag_bang_test2: .: (0.000154) test_sort_attributes_by_tag_bang_with_block: .: (0.000143) test_source: .: (0.000111) test_start: .: (0.000107) test_strand: .: (0.000107) test_to_s: .: (0.000175) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000103) test_comment_eq: .: (0.000040) test_comment_only?: .: (0.000038) test_comment_only_false: .: (0.000037) test_to_s: .: (0.000041) test_to_s_not_empty: .: (0.000086) Bio::TestGFF3: test_const_version: .: (0.000324) test_gff_version: .: (0.000210) test_records: .: (0.000268) test_sequence_regions: .: (0.000204) test_sequences: .: (0.000237) test_to_s: .: (0.000406) Bio::TestGFF3MetaData: test_data: .: (0.000087) test_directive: .: (0.000034) test_parse: .: (0.000041) Bio::TestGFF3Record: test_attributes: .: (0.000158) test_end: .: (0.000092) test_feature: .: (0.000089) test_frame: .: (0.000088) test_id: .: (0.000088) test_score: .: (0.000087) test_seqname: .: (0.000087) test_source: .: (0.000086) test_start: .: (0.000087) test_strand: .: (0.000085) test_to_s: .: (0.000156) test_to_s_attr_order_changed: .: (0.000182) Bio::TestGFF3RecordEscape: test_escape: .: (0.000104) test_escape_attribute: .: (0.000054) test_escape_seqid: .: (0.000053) test_unescape: .: (0.000070) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000158) test_eqeq: .: (0.001823) test_new_from_sequences_na: .: (0.000095) test_new_from_sequences_na_aa: .: (0.000136) test_new_from_sequences_na_aa_boundary_gap: .: (0.000182) test_new_from_sequences_na_aa_example: .: (0.000137) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000376) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000125) test_process_sequences_na: .: (0.000087) test_process_sequences_na_aa: .: (0.000081) test_process_sequences_na_aa_reverse_frameshift: .: (0.000075) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000080) test_process_sequences_na_aa_tooshort: .: (0.000127) test_process_sequences_na_tooshort: .: (0.000103) test_to_s: .: (0.000263) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000123) test_attributes_one: .: (0.000050) test_attributes_with_escaping: .: (0.000059) test_id_multiple: .: (0.000108) test_id_multiple2: .: (0.000089) test_id_replace: .: (0.000058) test_id_set: .: (0.000068) test_initialize_9: .: (0.000035) test_phase: .: (0.000058) test_score: .: (0.000247) test_to_s_void: .: (0.000054) Bio::TestGFF3RecordTarget: test_end: .: (0.000124) test_parse: .: (0.000074) test_start: .: (0.000040) test_strand: .: (0.000038) test_target_id: .: (0.000040) test_to_s: .: (0.000069) Bio::TestGFF3SequenceRegion: test_end: .: (0.000089) test_parse: .: (0.000076) test_seqid: .: (0.000043) test_start: .: (0.000038) test_to_s: .: (0.000184) Bio::TestGFFRecord: test_attributes: .: (0.000109) test_comment: .: (0.000050) test_end: .: (0.000048) test_feature: .: (0.000047) test_frame: .: (0.000047) test_score: .: (0.000046) test_seqname: .: (0.000048) test_source: .: (0.000046) test_start: .: (0.000046) test_strand: .: (0.000046) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000083) Bio::TestGeneAssociation: test_aspect: .: (0.000103) test_assigned_by: .: (0.000046) test_date: .: (0.000044) test_db: .: (0.000044) test_db_object_id: .: (0.000043) test_db_object_name: .: (0.000043) test_db_object_symbol: .: (0.000043) test_db_object_synonym: .: (0.000059) test_db_object_type: .: (0.000044) test_db_reference: .: (0.000044) test_evidence: .: (0.000044) test_goid: .: (0.000050) test_parser: .: (0.000208) test_qualifier: .: (0.000046) test_taxon: .: (0.000050) test_to_str: .: (0.000055) test_with: .: (0.000045) Bio::TestGenscanReport: test_date_run: .: (0.000454) test_gccontent: .: (0.000316) test_genscan_version: .: (0.000307) test_isochore: .: (0.000299) test_length: .: (0.000427) test_matrix: .: (0.000306) test_predictions_size: .: (0.000299) test_query_name: .: (0.000302) test_time: .: (0.000321) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000499) test_donor_score: .: (0.000317) test_exon_type: .: (0.000305) test_exon_type_long: .: (0.000390) test_first: .: (0.000305) test_initiation_score: .: (0.001339) test_last: .: (0.001693) test_number: .: (0.002955) test_p_value: .: (0.002851) test_phase: .: (0.001968) test_range: .: (0.002485) test_score: .: (0.002127) test_strand: .: (0.001570) test_t_score: .: (0.001917) test_termination_score: .: (0.001652) Bio::TestGenscanReportGene: test_aaseq: .: (0.002656) test_naseq: .: (0.001610) test_number: .: (0.000348) test_polyA: .: (0.000334) test_promoter: .: (0.000322) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000612) test_reports_ary_contents: .: (0.000383) Bio::TestHMMERReportConstants: test_rs: .: (0.000087) Bio::TestHMMERReportHit: test_accession: .: (0.000423) test_append_hsp: .: (0.000388) test_bit_score: .: (0.000961) test_definition: .: (0.000535) test_description: .: (0.000371) test_each: .: (0.000382) test_each_hsp: .: (0.000373) test_entry_id: .: (0.000359) test_evalue: .: (0.000356) test_hit: .: (0.000795) test_hit_id: .: (0.000496) test_hsps: .: (0.000366) test_num: .: (0.000361) test_score: .: (0.000353) test_target_def: .: (0.000353) test_target_id: .: (0.000354) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000418) test_each: .: (0.000365) test_each_hit: .: (0.000630) test_histogram: .: (0.000436) test_hits: .: (0.000361) test_hsps: .: (0.000364) test_parameter: .: (0.000371) test_program: .: (0.000377) test_query_info: .: (0.000370) test_statistical_detail: .: (0.000500) test_total_seq_searched: .: (0.000372) test_whole_seq_top_hits: .: (0.000376) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000527) test_histogram: .: (0.000432) test_statistical_detail: .: (0.000443) test_total_seq_searched: .: (0.000415) test_whole_seq_top_hit: .: (0.000630) Bio::TestHMMERReportHsp: test_accession: .: (0.000428) test_bit_score: .: (0.000368) test_csline: .: (0.000629) test_domain: .: (0.000381) test_evalue: .: (0.000364) test_flatseq: .: (0.000358) test_hmm_f: .: (0.000353) test_hmm_t: .: (0.022863) test_hmmseq: .: (0.000378) test_hsp: .: (0.000366) test_midline: .: (0.000363) test_query_frame: .: (0.000361) test_query_from: .: (0.000592) test_query_seq: .: (0.000374) test_query_to: .: (0.000364) test_rfline: .: (0.000360) test_score: .: (0.000384) test_seq_f: .: (0.000647) test_seq_ft: .: (0.000375) test_seq_t: .: (0.000361) test_set_alignment: .: (0.000355) test_targat_to: .: (0.000361) test_target_frame: .: (0.000615) test_target_from: .: (0.000376) test_target_seq: .: (0.000360) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000418) test_find_hetatm: .: (0.000104) test_hetatms: .: (0.000131) Bio::TestHeterogen: test_addAtom: .: (0.000156) test_each: .: (0.000091) test_each_hetatm: .: (0.000078) test_get_residue_id_from_atom: .: (0.000070) test_het_atom: .: (0.000061) test_iCode: .: (0.000061) test_inspect: .: (0.000071) test_resSeq: .: (0.000062) test_sort: .: (0.000081) test_square_bracket: .: (0.000074) test_to_s: .: (0.000107) test_update_resudue_id: .: (0.000063) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000114) test_find_heterogen: .: (0.000053) test_heterogens: .: (0.000060) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000129) test_match_description: .: (0.000063) test_match_evalue: .: (0.000058) test_match_ipr_description: .: (0.000058) test_match_ipr_id: .: (0.000057) test_match_match_end: .: (0.000058) test_match_match_start: .: (0.000058) test_match_method: .: (0.000058) test_matches_size: .: (0.000056) test_query_id: .: (0.000058) test_query_length: .: (0.000056) Bio::TestIprscanRawReport: test_entry_id: .: (0.000913) test_match_accession: .: (0.000808) test_match_crc64: .: (0.000780) test_match_date: .: (0.000785) test_match_description: .: (0.000774) test_match_evalue: .: (0.000805) test_match_go_terms: .: (0.003909) test_match_ipr_description: .: (0.001495) test_match_ipr_id: .: (0.001431) test_match_match_end: .: (0.000951) test_match_match_start: .: (0.001120) test_match_method: .: (0.000901) test_match_query_id: .: (0.000926) test_match_query_length: .: (0.001021) test_match_status: .: (0.000842) test_obj: .: (0.000764) test_query_id: .: (0.000755) test_query_length: .: (0.000756) test_self_reports_in_raw: .: (0.003427) Bio::TestIprscanReport: test_output_raw: .: (0.000340) test_to_raw: .: (0.000217) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000262) test_match_accession: .: (0.000224) test_match_date: .: (0.000203) test_match_description: .: (0.000509) test_match_evalue: .: (0.000258) test_match_go_terms: .: (0.000205) test_match_ipr_description: .: (0.000196) test_match_ipr_id: .: (0.000194) test_match_match_end: .: (0.000196) test_match_match_start: .: (0.000196) test_match_method: .: (0.000187) test_match_status: .: (0.000190) test_matches_size: .: (0.000187) test_query_id: .: (0.000584) test_query_length: .: (0.000299) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000307) test_to_hash_match?: .: (0.000277) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.000580) Bio::TestKeggCompound: test_comment: .: (0.000213) test_dblinks_as_hash: .: (0.000223) test_dblinks_as_strings: .: (0.000124) test_entry_id: .: (0.000121) test_enzymes: .: (0.000257) test_formula: .: (0.000118) test_kcf: .: (0.000105) test_mass: .: (0.000113) test_name: .: (0.000122) test_names: .: (0.000122) test_pathways_as_hash: .: (0.000195) test_pathways_as_strings: .: (0.000280) test_reactions: .: (0.000284) test_remark: .: (0.000119) test_rpairs: .: (0.000138) Bio::TestKeggEnzyme: test_all_reac: .: (0.000327) test_classes: .: (0.000252) test_cofactors: .: (0.000241) test_comment: .: (0.000250) test_dblinks_as_hash: .: (0.000283) test_dblinks_as_strings: .: (0.000267) test_diseases: .: (0.000288) test_entry: .: (0.000462) test_entry_id: .: (0.000325) test_genes: .: (0.007741) test_genes_as_hash: .: (0.006501) test_genes_as_strings: .: (0.001264) test_inhibitors: .: (0.000241) test_iubmb_reactions: .: (0.000240) test_kegg_reactions: .: (0.000236) test_motifs: .: (0.000202) test_name: .: (0.000254) test_names: .: (0.000274) test_obsolete?: .: (0.000220) test_orthologs_as_hash: .: (0.000256) test_orthologs_as_strings: .: (0.000292) test_pathways_as_hash: .: (0.000356) test_pathways_as_strings: .: (0.000327) test_products: .: (0.000335) test_reaction: .: (0.000329) test_structures: .: (0.000430) test_substrates: .: (0.000331) test_sysname: .: (0.002408) Bio::TestKeggGenesDblinks: test_data: .: (0.000142) test_dblinks_0: .: (0.000059) test_dblinks_1: .: (0.000048) test_dblinks_2: .: (0.000048) Bio::TestKeggGenesStructure: test_data: .: (0.000101) test_ids: .: (0.000070) test_ids_in_array: .: (0.000060) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004074) test_graphics__size: .: (0.003382) test_id: .: (0.003123) test_link: .: (0.002829) test_name: .: (0.004743) test_reaction: .: (0.003492) test_type: .: (0.003208) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.003756) test_graphics__size: .: (0.016182) test_id: .: (0.012177) test_link: .: (0.003836) test_name: .: (0.003321) test_reaction: .: (0.003262) test_type: .: (0.003104) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.002924) test_category: .: (0.002812) test_entry_id: .: (0.003934) test_fgcolor=: .: (0.003537) test_height=: .: (0.003282) test_label=: .: (0.003044) test_shape=: .: (0.003148) test_width=: .: (0.002865) test_x=: .: (0.002891) test_y=: .: (0.003652) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.003666) test_graphics__size: .: (0.003252) test_id: .: (0.003073) test_link: .: (0.003106) test_name: .: (0.002879) test_reaction: .: (0.002842) test_type: .: (0.002856) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000159) test_graphics=: .: (0.000047) test_id=: .: (0.000049) test_link=: .: (0.000047) test_name=: .: (0.000047) test_reaction=: .: (0.000043) test_type=: .: (0.000044) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000111) test_category=: .: (0.000058) test_entry_id=: .: (0.000055) test_fgcolor=: .: (0.000056) test_height=: .: (0.000054) test_label=: .: (0.000290) test_pathway=: .: (0.000054) test_shape=: .: (0.000059) test_width=: .: (0.000056) test_x=: .: (0.000053) test_y=: .: (0.000053) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.003588) test_coords: .: (0.003249) test_fgcolor: .: (0.002955) test_height: .: (0.003109) test_name: .: (0.002894) test_type: .: (0.002852) test_width: .: (0.003598) test_x: .: (0.003752) test_y: .: (0.003124) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.003170) test_coords: .: (0.003106) test_fgcolor: .: (0.002870) test_height: .: (0.002809) test_name: .: (0.003592) test_type: .: (0.003609) test_width: .: (0.003296) test_x: .: (0.003091) test_y: .: (0.003005) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000126) test_coords=: .: (0.000050) test_fgcolor=: .: (0.000044) test_height=: .: (0.000044) test_name=: .: (0.000137) test_type=: .: (0.000046) test_width=: .: (0.000043) test_x=: .: (0.000041) test_y=: .: (0.000041) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.002871) test_entries__size: .: (0.002829) test_image: .: (0.003564) test_link: .: (0.003605) test_name: .: (0.003283) test_number: .: (0.003108) test_org: .: (0.003001) test_reactions=: .: (0.002916) test_reactions__size: .: (0.002866) test_relations=: .: (0.002875) test_relations__size: .: (0.004323) test_title: .: (0.003255) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.006182) test_name: .: (0.005654) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000115) test_initialize_0: .: (0.000036) test_initialize_1: .: (0.000059) test_initialize_2: .: (0.000039) test_name=: .: (0.000046) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.002890) test_name: .: (0.003646) test_products: .: (0.003265) test_substrates: .: (0.003137) test_type: .: (0.003068) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000111) test_name=: .: (0.000051) test_products=: .: (0.000047) test_substraces=: .: (0.000106) test_type=: .: (0.000046) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000102) test_entry_id=: .: (0.000056) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.002880) test_entry2: .: (0.002818) test_name: .: (0.003688) test_type: .: (0.003647) test_value: .: (0.003208) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000096) test_node1=: .: (0.000060) test_node2=: .: (0.000054) test_rel=: .: (0.000056) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000091) test_entry2=: .: (0.000046) test_name=: .: (0.000049) test_type=: .: (0.000143) test_value=: .: (0.000049) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.006141) test_name: .: (0.005578) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000123) test_initialize_0: .: (0.000036) test_initialize_1: .: (0.000035) test_initialize_2: .: (0.000036) test_name=: .: (0.000046) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000090) test_initialize_0: .: (0.000034) test_initialize_1: .: (0.000034) test_initialize_2: .: (0.000035) test_name=: .: (0.000046) Bio::TestKeggModule: test_compounds: .: (0.000215) test_compounds_as_hash: .: (0.000121) test_compounds_as_strings: .: (0.000101) test_definition: .: (0.000105) test_entry_id: .: (0.000090) test_keggclass: .: (0.000088) test_name: .: (0.000087) test_new: .: (0.000097) test_orthologs: .: (0.000125) test_orthologs_as_array: .: (0.000128) test_orthologs_as_hash: .: (0.000114) test_orthologs_as_strings: .: (0.000097) test_pathways: .: (0.000086) test_pathways_as_hash: .: (0.000082) test_pathways_as_strings: .: (0.000079) test_reactions: .: (0.000123) test_reactions_as_hash: .: (0.000119) test_reactions_as_strings: .: (0.000156) Bio::TestKeggOrthology: test_dblinks: .: (0.000315) test_dblinks_as_hash: .: (0.000224) test_dblinks_as_strings: .: (0.000205) test_definition: .: (0.000216) test_entry_id: .: (0.000235) test_genes_as_hash: .: (0.005422) test_genes_as_strings: .: (0.001794) test_keggclass: .: (0.000282) test_keggclasses: .: (0.000280) test_modules: .: (0.000213) test_modules_as_hash: .: (0.000199) test_modules_as_strings: .: (0.000204) test_name: .: (0.000208) test_names: .: (0.000205) test_pathways_as_strings: .: (0.000201) test_pathways_in_keggclass: .: (0.000260) test_references: .: (0.000284) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000168) test_compounds_as_strings: .: (0.000091) test_dblinks_as_hash: .: (0.000088) test_dblinks_as_strings: .: (0.000083) test_description: .: (0.000098) test_diseases_as_hash: .: (0.000087) test_diseases_as_strings: .: (0.000084) test_entry_id: .: (0.000096) test_enzymes_as_strings: .: (0.000084) test_genes_as_hash: .: (0.000083) test_genes_as_strings: .: (0.000083) test_keggclass: .: (0.000096) test_ko_pathway: .: (0.000091) test_modules_as_hash: .: (0.000115) test_modules_as_strings: .: (0.000094) test_name: .: (0.000097) test_organism: .: (0.000094) test_orthologs_as_hash: .: (0.000110) test_orthologs_as_strings: .: (0.000085) test_pathways_as_hash: .: (0.000092) test_pathways_as_strings: .: (0.000085) test_reactions_as_hash: .: (0.000083) test_reactions_as_strings: .: (0.000081) test_references: .: (0.000093) test_rel_pathways_as_hash: .: (0.000106) test_rel_pathways_as_strings: .: (0.000091) Bio::TestKeggReaction: test_definition: .: (0.000180) test_entry_id: .: (0.000108) test_enzymes: .: (0.000105) test_equation: .: (0.000102) test_name: .: (0.000106) test_orthologs_as_hash: .: (0.000115) test_orthologs_as_strings: .: (0.000098) test_pathways_as_hash: .: (0.000102) test_pathways_as_strings: .: (0.000089) test_rpairs_as_hash: .: (0.000116) test_rpairs_as_strings: .: (0.000093) test_rpairs_as_tokens: .: (0.000119) Bio::TestLasergene: test_methods: .: (0.003860) Bio::TestLocations: test_complement: .: (0.000134) test_hat: .: (0.000417) test_normal: .: (0.000070) test_replace_single_base: .: (0.000050) test_should_not_modify_argument: .: (0.000047) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.002061) test_locations_to_s: .: (0.000871) Bio::TestMEDLINE: test_authors: .: (0.000407) test_authors_with_last_name_all_caps: .: (0.000049) test_authors_with_suffix: .: (0.000045) Bio::TestMEDLINE_20146148: test_ab: .: (0.000222) test_ad: .: (0.000140) test_au: .: (0.000129) test_authors: .: (0.000223) test_doi: .: (0.000138) test_dp: .: (0.000166) test_ip: .: (0.000126) test_mh: .: (0.000136) test_pages: .: (0.000129) test_pg: .: (0.000126) test_pii: .: (0.000127) test_pmid: .: (0.000199) test_pt: .: (0.000135) test_reference: .: (0.000241) test_self_new: .: (0.000143) test_so: .: (0.000128) test_ta: .: (0.000126) test_ti: .: (0.000130) test_ui: .: (0.000122) test_vi: .: (0.000165) test_year: .: (0.000128) Bio::TestMapSimple: test_attributes: .: (0.000132) Bio::TestMapping: test_add_mapping_as_map: .: (0.000137) test_add_mapping_as_marker: .: (0.000069) test_contains_marker?: .: (0.000055) test_mapped_to?: .: (0.000048) test_mapping_location_comparison: .: (0.000137) test_mappings_as_map_each: .: (0.000050) test_mappings_as_marker_each: .: (0.000070) test_mappings_on: .: (0.000071) test_multiple_mappings_between_same_marker_and_map: .: (0.000235) test_positions_on: .: (0.000078) test_raise_error_kind_of: .: (0.000172) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000173) test_check_options_with_invalid_opts: .: (0.000088) test_check_options_with_valid_opts: .: (0.000077) test_command_to_be_run: .: (0.000090) test_config_defaults: .: (0.000061) test_minimal_config: .: (0.000066) test_more_config: .: (0.000169) test_run: .: (0.000047) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000209) test_report_has_motifs: .: (0.000106) Bio::TestModel: test_addChain: .: (0.000099) test_comp: .: (0.000055) test_each: .: (0.000053) test_each_chain: .: (0.000044) test_inspect: .: (0.000042) test_rehash: .: (0.000037) test_square_brace: .: (0.000040) test_to_s: .: (0.000043) Bio::TestModelFinder: test_find_model: .: (0.000103) Bio::TestMotif: test_creation_and_attributes: .: (0.000104) test_length: .: (0.000036) Bio::TestMyGraph: test_cliquishness: .: (0.000309) Bio::TestNA: test_accessor: .: (0.000082) test_na: .: (0.000038) test_name: .: (0.000036) test_names: .: (0.000033) test_to_re: .: (0.000099) test_weight: .: (0.000044) test_weight_rna: .: (0.000037) Bio::TestNAConstants: test_NAMES: .: (0.000076) test_NAMES_1_to_name: .: (0.000034) test_WEIGHT: .: (0.000038) Bio::TestNATranslate: test_translate: .: (0.000164) test_translate_1: .: (0.000065) test_translate_2: .: (0.000041) test_translate_3: .: (0.000039) test_translate_4: .: (0.000085) test_translate_5: .: (0.000043) test_translate_6: .: (0.000144) Bio::TestNCBIDB: test_fetch: .: (0.000107) test_p_entry2hash: .: (0.000032) test_p_subtag2array: .: (0.000030) test_p_toptag2array: .: (0.000030) Bio::TestNewick: test_reparse: .: (0.000638) test_reparse_before_lazy_parsing: .: (0.000194) test_string_tree: .: (0.000354) Bio::TestNewick2: test_string_tree: .: (0.000316) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000093) test_parse_newick_leaf: .: (0.000086) test_parse_newick_tokenize: .: (0.000149) Bio::TestNexus: test_nexus: .: (0.004062) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000127) test_uncapitalized_letter_Q32725_9POAL: .: (0.000056) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000104) test_load_parameters: .: (0.000052) test_parameters: .: (0.000036) test_set_default_parameters: .: (0.000047) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000330) test_expected_parameters_set_in_control_file: .: (0.000312) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000104) test_new_with_parameters: .: (0.000051) test_new_with_two_argument: .: (0.000049) test_new_without_argument: .: (0.000043) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.000544) test_rates_hundred_and_fiftieth_position: .: (0.002739) test_rates_last_position: .: (0.000600) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.000456) test_tree: .: (0.000362) test_tree_length: .: (0.000352) test_tree_log_likelihood: .: (0.000350) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000638) test_parameters_should_be_loaded_from_control: .: (0.000227) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.000611) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000146) test_dN_dS: .: (0.000097) test_kappa: .: (0.000075) test_lnL: .: (0.000071) test_m3_classes: .: (0.000120) test_m3_lnL: .: (0.000068) test_m3_to_s: .: (0.000458) test_m3_tree: .: (0.000211) test_omega: .: (0.000075) test_to_s: .: (0.000068) test_tree: .: (0.000107) test_tree_length: .: (0.000072) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000247) test_p: .: (0.000168) test_position: .: (0.000162) test_probability: .: (0.000518) test_w: .: (0.000182) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000256) test_graph_omega: .: (0.000201) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000272) test_footer: .: (0.000074) test_header: .: (0.000086) test_initialize: .: (0.000077) test_models: .: (0.000077) test_nb_sites: .: (0.000262) test_num_codons: .: (0.000097) test_num_sequences: .: (0.000079) test_significant: .: (0.000083) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000145) test_nb_sites: .: (0.000120) test_significant: .: (0.000082) test_sites: .: (0.000465) Bio::TestPDB: test_accession: .: (0.000661) test_addModel: .: (0.000338) test_authors: .: (0.000315) test_bracket: .: (0.000423) test_classification: .: (0.000354) test_dbref: .: (0.000366) test_definition: .: (0.000464) test_each: .: (0.000349) test_each_model: .: (0.000335) test_entry_id: .: (0.000422) test_helix: .: (0.000354) test_inspect: .: (0.000326) test_jrnl: .: (0.000432) test_keywords: .: (0.000332) test_record: .: (0.000336) test_remark: .: (0.000424) test_seqres: .: (0.000490) test_sheet: .: (0.000450) test_ssbond: .: (0.000336) test_to_s: .: (0.000424) test_turn: .: (0.000329) test_version: .: (0.000328) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000122) test_U12: .: (0.000055) test_U13: .: (0.000053) test_U22: .: (0.000051) test_U23: .: (0.000050) test_U33: .: (0.000052) test_altLoc: .: (0.000052) test_chainID: .: (0.000050) test_charge: .: (0.000052) test_element: .: (0.000051) test_iCode: .: (0.000050) test_name: .: (0.000050) test_resName: .: (0.000049) test_resSeq: .: (0.000066) test_segID: .: (0.000052) test_serial: .: (0.000050) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000094) test_anisou: .: (0.000042) test_chainID: .: (0.000039) test_charge: .: (0.000038) test_comparable: .: (0.000052) test_do_parse: .: (0.000040) test_element: .: (0.000039) test_iCode: .: (0.000038) test_name: .: (0.000037) test_occupancy: .: (0.000054) test_original_data: .: (0.000043) test_record_name: .: (0.000040) test_resName: .: (0.000037) test_resSeq: .: (0.000038) test_residue: .: (0.000038) test_segID: .: (0.000039) test_serial: .: (0.000037) test_sigatm: .: (0.000037) test_tempFactor: .: (0.000044) test_ter: .: (0.000039) test_to_a: .: (0.000042) test_to_s: .: (0.000054) test_x: .: (0.000045) test_xyz: .: (0.000056) test_y: .: (0.000044) test_z: .: (0.000043) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000101) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000089) test_idcode: .: (0.000041) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000104) test_chainID2: .: (0.000053) test_icode1: .: (0.000048) test_icode2: .: (0.000048) test_measure: .: (0.000048) test_modNum: .: (0.000047) test_pep1: .: (0.000048) test_pep2: .: (0.000048) test_seqNum1: .: (0.000047) test_seqNum2: .: (0.000045) test_serNum: .: (0.000046) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000096) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000088) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000095) test_alpha: .: (0.000045) test_b: .: (0.000042) test_beta: .: (0.000042) test_c: .: (0.000040) test_gamma: .: (0.000040) test_sGroup: .: (0.000042) test_z: .: (0.000041) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000106) test_database: .: (0.000059) test_dbAccession: .: (0.000069) test_dbIdCode: .: (0.000057) test_dbseqBegin: .: (0.000055) test_dbseqEnd: .: (0.000055) test_idCode: .: (0.000054) test_idbnsBeg: .: (0.000053) test_insertBegin: .: (0.000055) test_insertEnd: .: (0.000054) test_seqBegin: .: (0.000063) test_seqEnd: .: (0.000055) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000100) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000092) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000165) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000088) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000089) test_depDate: .: (0.000048) test_idCode: .: (0.000042) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000102) test_hetID: .: (0.000048) test_iCode: .: (0.000046) test_numHetAtoms: .: (0.000045) test_seqNum: .: (0.000045) test_text: .: (0.000044) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000092) test_anisou: .: (0.000370) test_chainID: .: (0.000056) test_charge: .: (0.000039) test_comparable: .: (0.000053) test_do_parse: .: (0.000039) test_element: .: (0.000037) test_iCode: .: (0.000037) test_name: .: (0.000037) test_occupancy: .: (0.000052) test_original_data: .: (0.000040) test_record_name: .: (0.000039) test_resName: .: (0.000036) test_resSeq: .: (0.000037) test_residue: .: (0.000037) test_segID: .: (0.000038) test_serial: .: (0.000036) test_sigatm: .: (0.000038) test_tempFactor: .: (0.000043) test_ter: .: (0.000038) test_to_a: .: (0.000041) test_to_s: .: (0.000359) test_x: .: (0.000054) test_xyz: .: (0.000051) test_y: .: (0.000043) test_z: .: (0.000041) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000216) test_ChainH: .: (0.000065) test_ICode1: .: (0.000060) test_altLoc1: .: (0.000059) test_altLoc2: .: (0.000080) test_altLocH: .: (0.000060) test_chainID2: .: (0.000058) test_iCode2: .: (0.000058) test_iCodeH: .: (0.000059) test_name1: .: (0.000058) test_name2: .: (0.000057) test_nameH: .: (0.000286) test_resName1: .: (0.000072) test_resName2: .: (0.000062) test_resSeq1: .: (0.000061) test_resSeq2: .: (0.000060) test_resSeqH: .: (0.000060) test_sym1: .: (0.000060) test_sym2: .: (0.000059) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000100) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000107) test_altLoc2: .: (0.000058) test_chainID1: .: (0.000054) test_chainID2: .: (0.000053) test_iCode1: .: (0.000055) test_iCode2: .: (0.000053) test_name1: .: (0.000053) test_name2: .: (0.000053) test_resName1: .: (0.000052) test_resName2: .: (0.000209) test_resSeq1: .: (0.000057) test_resSeq2: .: (0.000052) test_sym1: .: (0.000052) test_sym2: .: (0.000051) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000101) test_numCoord: .: (0.000044) test_numHelix: .: (0.000042) test_numHet: .: (0.000042) test_numRemark: .: (0.000041) test_numSeq: .: (0.000040) test_numSheet: .: (0.000041) test_numSite: .: (0.000039) test_numTer: .: (0.000040) test_numTurn: .: (0.000040) test_numXform: .: (0.000040) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000084) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000235) test_comment: .: (0.000050) test_iCode: .: (0.000064) test_idCode: .: (0.000049) test_resName: .: (0.000047) test_seqNum: .: (0.000048) test_stdRes: .: (0.000047) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000101) test_Mn2: .: (0.000042) test_Mn3: .: (0.000039) test_Vn: .: (0.000038) test_iGiven: .: (0.000042) test_serial: .: (0.000038) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000089) test_Mn2: .: (0.000041) test_Mn3: .: (0.000038) test_Vn: .: (0.000038) test_iGiven: .: (0.000038) test_serial: .: (0.000038) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000085) test_Mn2: .: (0.000039) test_Mn3: .: (0.000044) test_Vn: .: (0.000039) test_iGiven: .: (0.000038) test_serial: .: (0.000038) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000097) test_rIdCode: .: (0.000046) test_repDate: .: (0.000043) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000090) test_On2: .: (0.000040) test_On3: .: (0.000037) test_Tn: .: (0.000036) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000090) test_modId: .: (0.000046) test_modNum: .: (0.000044) test_modType: .: (0.000044) test_record: .: (0.000044) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000197) test_text: .: (0.000044) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000097) test_Sn2: .: (0.000040) test_Sn3: .: (0.000038) test_Un: .: (0.000038) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000085) test_Sn2: .: (0.000039) test_Sn3: .: (0.000037) test_Un: .: (0.000037) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000082) test_Sn2: .: (0.000039) test_Sn3: .: (0.000037) test_Un: .: (0.000037) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000101) test_conflict: .: (0.000054) test_database: .: (0.000051) test_dbIdCode: .: (0.000050) test_dbRes: .: (0.000135) test_dbSeq: .: (0.000052) test_iCode: .: (0.000050) test_idCode: .: (0.000049) test_resName: .: (0.000057) test_seqNum: .: (0.000049) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000105) test_numRes: .: (0.000053) test_resName: .: (0.000053) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000112) test_curChainId: .: (0.000701) test_curICode: .: (0.000072) test_curResName: .: (0.000084) test_curResSeq: .: (0.000065) test_endChainID: .: (0.000812) test_endICode: .: (0.000084) test_endResName: .: (0.000064) test_endSeqNum: .: (0.000730) test_initChainID: .: (0.000066) test_initICode: .: (0.000708) test_initResName: .: (0.000066) test_initSeqNum: .: (0.000462) test_numStrands: .: (0.000067) test_prevAtom: .: (0.000591) test_prevChainId: .: (0.000083) test_prevICode: .: (0.000784) test_prevResName: .: (0.000072) test_prevResSeq: .: (0.000459) test_sense: .: (0.000078) test_sheetID: .: (0.000493) test_strand: .: (0.000071) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000142) test_chainID: .: (0.000058) test_charge: .: (0.000673) test_element: .: (0.000056) test_iCode: .: (0.000055) test_name: .: (0.000795) test_resName: .: (0.000072) test_resSeq: .: (0.000055) test_segID: .: (0.000632) test_serial: .: (0.000070) test_sigOcc: .: (0.000055) test_sigTemp: .: (0.000715) test_sigX: .: (0.000509) test_sigY: .: (0.000065) test_sigZ: .: (0.000053) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000711) test_SigmaU12: .: (0.000058) test_SigmaU13: .: (0.000654) test_SigmaU22: .: (0.000075) test_SigmaU23: .: (0.000054) test_SigmaU33: .: (0.001089) test_altLoc: .: (0.000074) test_chainID: .: (0.000055) test_charge: .: (0.001212) test_element: .: (0.000070) test_iCode: .: (0.000054) test_name: .: (0.000707) test_resName: .: (0.000070) test_resSeq: .: (0.001294) test_segID: .: (0.000059) test_serial: .: (0.000054) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000148) test_chainID2: .: (0.000391) test_chainID3: .: (0.000066) test_chainID4: .: (0.000058) test_iCode1: .: (0.000825) test_iCode2: .: (0.000065) test_iCode3: .: (0.000074) test_iCode4: .: (0.000086) test_numRes: .: (0.000079) test_resName1: .: (0.000062) test_resName2: .: (0.000602) test_resName3: .: (0.000074) test_resName4: .: (0.000060) test_seq1: .: (0.000630) test_seq2: .: (0.000631) test_seq3: .: (0.000080) test_seq4: .: (0.000060) test_seqNum: .: (0.000643) test_siteID: .: (0.000731) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000468) test_altLoc2: .: (0.000057) test_atom1: .: (0.000292) test_atom2: .: (0.000054) test_chainID1: .: (0.000292) test_chainID2: .: (0.000051) test_iCode1: .: (0.000050) test_iCode2: .: (0.000793) test_resName1: .: (0.000056) test_resName2: .: (0.000051) test_resSeq1: .: (0.000064) test_resSeq2: .: (0.000049) test_sym1: .: (0.000049) test_sym2: .: (0.000048) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000140) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000107) test_sIdCode: .: (0.000050) test_sprsdeDate: .: (0.000044) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000096) test_iCode: .: (0.000045) test_resName: .: (0.000043) test_resSeq: .: (0.000042) test_serial: .: (0.000514) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000106) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000099) test_t1: .: (0.000046) test_t2: .: (0.000043) test_t3: .: (0.000042) test_text: .: (0.000043) Bio::TestPROSITE: test_ac: .: (0.000692) test_cc: .: (0.000677) test_de: .: (0.000542) test_division: .: (0.000599) test_dr: .: (0.008199) test_dt: .: (0.000554) test_false_neg: .: (0.000565) test_false_pos: .: (0.000527) test_false_positive_sequences: .: (0.000550) test_list_falsenegative: .: (0.010608) test_list_falsepositive: .: (0.009994) test_list_potentialhit: .: (0.007430) test_list_truepositive: .: (0.009408) test_list_unknown: .: (0.008456) test_list_xref: .: (0.007370) test_ma: .: (0.000518) test_max_repeat: .: (0.000500) test_name: .: (0.000490) test_nr: .: (0.000531) test_pa: .: (0.000527) test_pa2re: .: (0.000525) test_partial: .: (0.000642) test_pdb_xref: .: (0.000641) test_pdoc_xref: .: (0.000642) test_positive: .: (0.000662) test_positive_hits: .: (0.000688) test_positive_sequences: .: (0.000698) test_release: .: (0.000778) test_ru: .: (0.000644) test_self_pa2re: .: (0.000697) test_site: .: (0.000729) test_skip_flag: .: (0.000659) test_swissprot_release_number: .: (0.000731) test_swissprot_release_sequences: .: (0.000675) test_taxon_range: .: (0.002146) test_total: .: (0.000637) test_total_hits: .: (0.000980) test_total_sequences: .: (0.000758) test_unknown: .: (0.000620) test_unknown_hits: .: (0.001105) test_unknown_sequences: .: (0.000525) Bio::TestPROSITEConst: test_delimiter: .: (0.000115) test_tagsize: .: (0.000035) Bio::TestPTS1: test_function_set: .: (0.000093) test_function_set_number_1: .: (0.000416) test_function_set_number_2: .: (0.000046) test_function_set_number_3: .: (0.000038) test_function_show: .: (0.000035) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000104) Bio::TestPTS1New: test_fungi: .: (0.000080) test_general: .: (0.000039) test_metazoa: .: (0.000038) Bio::TestQualifier: test_qualifier: .: (0.000076) test_value: .: (0.000033) Bio::TestREBASE: test_methods: .: (0.000661) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.000495) test_bit_score: .: (0.000325) test_evalue: .: (0.000306) test_gaps: .: (0.000300) test_hit_from: .: (0.000312) test_hit_to: .: (0.000304) test_hseq: .: (0.000403) test_identity: .: (0.000305) test_midline: .: (0.000303) test_percent_identity: .: (0.000284) test_positive: .: (0.000284) test_qseq: .: (0.000295) test_query_from: .: (0.000315) test_query_to: .: (0.000302) test_score: .: (0.000296) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000331) test_hits_size: .: (0.000654) test_iterations_size: .: (0.000636) test_program: .: (0.000261) test_query_def: .: (0.000610) test_query_len: .: (0.000607) test_version: .: (0.000280) test_version_date: .: (0.000254) test_version_number: .: (0.000253) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000377) test_definition: .: (0.000313) test_evalue: .: (0.000304) test_hsps_size: .: (0.000278) test_identity: .: (0.000303) test_lap_at: .: (0.000331) test_len: .: (0.000306) test_midline: .: (0.000326) test_overlap: .: (0.000302) test_query_end: .: (0.000343) test_query_seq: .: (0.000322) test_query_start: .: (0.000324) test_target_def: .: (0.000304) test_target_end: .: (0.000317) test_target_len: .: (0.000301) test_target_seq: .: (0.000317) test_target_start: .: (0.000311) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000222) test_get_entry: .: (0.000196) test_rewind: .: (0.000051) test_skip_leader: .: (0.000082) Bio::TestReference: test_abstract: .: (0.000095) test_affiliations: .: (0.000040) test_authors: .: (0.000037) test_format_bibitem: .: (0.000069) test_format_bibtex: .: (0.000106) test_format_bibtex_with_arguments: .: (0.000093) test_format_cell: .: (0.000053) test_format_current: .: (0.000127) test_format_endnote: .: (0.000062) test_format_general: .: (0.000055) test_format_genome_biol: .: (0.000049) test_format_genome_res: .: (0.000048) test_format_nar: .: (0.000047) test_format_nature: .: (0.000054) test_format_rd: .: (0.000050) test_format_science: .: (0.000066) test_format_trends: .: (0.000048) test_issue: .: (0.000091) test_journal: .: (0.000035) test_mesh: .: (0.000036) test_pages: .: (0.000034) test_pubmed: .: (0.000034) test_pubmed_url: .: (0.000036) test_url: .: (0.000034) test_volume: .: (0.000035) test_year: .: (0.000033) Bio::TestReference_noURL: test_format_endnote: .: (0.000106) test_url: .: (0.000036) Bio::TestReferences: test_append: .: (0.000168) test_each: .: (0.000046) Bio::TestRelation: test_comparison_operator: .: (0.000104) test_uniq: .: (0.000055) Bio::TestResidue: test_addAtom: .: (0.000153) test_each: .: (0.000086) test_each_atom: .: (0.000080) test_get_residue_id_from_atom: .: (0.000069) test_het_atom: .: (0.000062) test_iCode: .: (0.000061) test_inspect: .: (0.000068) test_resSeq: .: (0.000059) test_sort: .: (0.000139) test_square_bracket: .: (0.000074) test_to_s: .: (0.000097) test_update_resudue_id: .: (0.000065) Bio::TestResidueFinder: test_each_residue: .: (0.000110) test_find_residue: .: (0.000051) test_residues: .: (0.000059) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.085879) test_cut_from_bio_sequence_na: .: (0.013378) test_cut_without_permutations: .: (0.009114) test_view_ranges: .: (0.012958) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000679) test_cuts_after_remove_incomplete_cuts: .: (0.000305) test_strands_for_display: .: (0.001298) test_strands_for_display_current: .: (0.000293) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000260) test_fragments_for_display_1: .: (0.000337) test_fragments_for_display_10: .: (0.000520) test_fragments_for_display_2: .: (0.000341) test_fragments_for_display_3: .: (0.000463) test_fragments_for_display_4: .: (0.000386) test_fragments_for_display_5: .: (0.000392) test_fragments_for_display_6: .: (0.000262) test_fragments_for_display_7: .: (0.000257) test_fragments_for_display_8: .: (0.000234) test_fragments_for_display_9: .: (0.000247) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000180) test_obj_3: .: (0.000114) test_obj_7: .: (0.000091) test_obj_z: .: (0.000094) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000152) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000120) test_bracket_eq: .: (0.000075) test_concat: .: (0.000054) test_delete: .: (0.000052) test_dup: .: (0.000072) test_each: .: (0.000067) test_eqeq: .: (0.000142) test_eqeq_false: .: (0.000044) test_eqeq_other: .: (0.000037) test_eqeq_self: .: (0.000037) test_include?: .: (0.000043) test_internal_data: .: (0.000041) test_internal_data_eq: .: (0.000048) test_length: .: (0.000040) test_ltlt: .: (0.000045) test_ltlt_larger: .: (0.000046) test_ltlt_middle: .: (0.000046) test_plus: .: (0.000056) test_plus_error: .: (0.000063) test_push: .: (0.000049) test_reverse_each: .: (0.000069) test_self_bracket: .: (0.000041) test_self_new: .: (0.000048) test_size: .: (0.000040) test_sort!: .: (0.000130) test_to_a: .: (0.000041) test_uniq!: .: (0.000037) test_unshift: .: (0.000057) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.002216) test_complement: .: (0.001998) test_complement_with_cut_symbols: .: (0.002048) test_cut_locations: .: (0.001875) test_cut_locations_in_enzyme_notation: .: (0.001795) test_primary: .: (0.001760) test_primary_with_cut_symbols: .: (0.001844) test_to_re: .: (0.001755) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000448) test_align_with_cuts: .: (0.000330) test_argument_error: .: (0.000522) test_ds: .: (0.000358) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000207) test_complement: .: (0.000085) test_contents: .: (0.000081) test_primary: .: (0.000079) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000164) test_complement: .: (0.000079) test_contents: .: (0.000076) test_primary: .: (0.000073) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000119) test_contents: .: (0.000063) test_primary: .: (0.000059) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000121) test_complement_to_array_index: .: (0.000101) test_complement_to_array_index_class: .: (0.000092) test_contents: .: (0.000067) test_primary: .: (0.000063) test_primary_to_array_index: .: (0.000094) test_primary_to_array_index_class: .: (0.000090) test_to_array_index: .: (0.000269) test_to_array_index_class: .: (0.000179) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000223) test_rebase: .: (0.000065) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.003359) test_creation_with_no_cuts: .: (0.000221) test_cut_locations: .: (0.000203) test_cut_locations_in_enzyme_notation: .: (0.000201) test_orientation: .: (0.000434) test_pattern: .: (0.000205) test_pattern_palindromic?: .: (0.000261) test_stripped: .: (0.000404) test_to_re: .: (0.000178) test_with_cut_symbols: .: (0.000195) test_with_spaces: .: (0.000215) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000582) test_creation_with_no_cuts: .: (0.000210) test_cut_locations: .: (0.000379) test_cut_locations_in_enzyme_notation: .: (0.000203) test_orientation: .: (0.000180) test_pattern: .: (0.000196) test_pattern_palindromic?: .: (0.000230) test_stripped: .: (0.000276) test_to_re: .: (0.000163) test_with_cut_symbols: .: (0.000217) test_with_spaces: .: (0.000313) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000231) test_initialize_with_pattern: .: (0.000140) test_max: .: (0.000060) test_min: .: (0.000056) test_to_array_index: .: (0.000067) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000111) test_bracket_eq: .: (0.000058) test_concat: .: (0.000048) test_delete: .: (0.000041) test_dup: .: (0.000060) test_each: .: (0.000066) test_eqeq: .: (0.000132) test_eqeq_false: .: (0.000040) test_eqeq_other: .: (0.000034) test_eqeq_self: .: (0.000034) test_include?: .: (0.000038) test_internal_data_hash: .: (0.000037) test_internal_data_hash_eq: .: (0.000044) test_length: .: (0.000036) test_ltlt: .: (0.000040) test_ltlt_noeffect: .: (0.000040) test_plus: .: (0.000041) test_plus_error: .: (0.000057) test_private_push_element: .: (0.000042) test_private_push_element_intermediate: .: (0.000041) test_private_push_element_last: .: (0.000041) test_private_push_element_noeffect: .: (0.000039) test_private_sorted_keys: .: (0.000036) test_private_unshift_element: .: (0.000039) test_private_unshift_element_first: .: (0.000042) test_private_unshift_element_intermediate: .: (0.000041) test_private_unshift_element_noeffect: .: (0.000142) test_push: .: (0.000043) test_reverse_each: .: (0.000062) test_self_bracket: .: (0.000035) test_self_new: .: (0.000045) test_size: .: (0.000035) test_sort!: .: (0.000035) test_to_a: .: (0.000035) test_uniq!: .: (0.000034) test_unshift: .: (0.000041) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000101) test_left_padding: .: (0.000053) test_right_padding: .: (0.000051) test_strip_padding: .: (0.000050) Bio::TestSOFT: test_dataset: .: (0.003197) test_series: .: (0.003079) Bio::TestSOSUIReport: test_entry_id: .: (0.000137) test_prediction: .: (0.000063) test_tmh: .: (0.000185) test_tmhs: .: (0.000070) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000077) test_rs: .: (0.000032) Bio::TestSOSUITMH: test_grade: .: (0.000102) test_range: .: (0.000063) test_sequence: .: (0.000060) Bio::TestSampleGraph: test_bellman_ford: .: (0.000208) test_bfs_shortest_path: .: (0.000077) test_breadth_first_search: .: (0.000072) test_depth_first_search: .: (0.000339) test_dijkstra: .: (0.000113) test_dump_list: .: (0.000104) test_dump_matrix: .: (0.000152) test_extract_subgraph_by_label: .: (0.000087) test_extract_subgraph_by_list: .: (0.000087) test_extract_subgraph_retains_disconnected_nodes: .: (0.000065) test_small_world_aka_node_degree_histogram: .: (0.000062) test_to_matrix: .: (0.000141) test_to_matrix_fixed_index: .: (0.000291) test_undirected_cliquishness: .: (0.000128) Bio::TestScf_version_2: test_complement: .: (0.003897) test_seq: .: (0.003726) test_to_biosequence: .: (0.003726) Bio::TestScf_version_3: test_complement: .: (0.010440) test_seq: .: (0.010219) test_to_biosequence: .: (0.010197) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000121) test_AA_new_sequence_all_legal_symbols: .: (0.000044) test_AA_new_sequence_removes_whitespace: .: (0.000040) test_AA_new_sequence_upcases_symbols: .: (0.000039) test_DNA_new_blank_sequence: .: (0.000038) test_DNA_new_sequence_downcases_symbols: .: (0.000040) test_DNA_new_sequence_removes_whitespace: .: (0.000038) test_NA_randomize_with_counts: .: (0.000334) test_NA_randomize_with_counts_and_block: .: (0.000365) test_RNA_new_sequence: .: (0.000041) test_ambiguous_dna_sequence_complement: .: (0.000044) test_ambiguous_rna_sequence_complement: .: (0.000039) test_amino_acid_codes: .: (0.000057) test_amino_acid_molecular_weight: .: (0.000086) test_amino_acid_names: .: (0.000054) test_amino_acid_randomize_can_be_chained: .: (0.000445) test_amino_acid_randomize_has_same_composition: .: (0.000229) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000249) test_dna_composition: .: (0.000050) test_dna_gc_percent: .: (0.000056) test_dna_molecular_weight: .: (0.000068) test_dna_pikachu: .: (0.000043) test_dna_sequence_complement: .: (0.000040) test_dna_sequence_translate: .: (0.000166) test_dna_to_re: .: (0.000077) test_element_reference_operator_with_one_argument: .: (0.000040) test_element_reference_operator_with_two_arguments: .: (0.000037) test_invalid_nucleic_acid_illegal_bases: .: (0.000058) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000061) test_nucleic_acid_names: .: (0.000051) test_randomize_dna_can_be_chained: .: (0.000142) test_randomize_dna_retains_composition: .: (0.000105) test_randomize_dna_with_block: .: (0.000132) test_rna_composition: .: (0.000047) test_rna_gc_percent: .: (0.000056) test_rna_molecular_weight: .: (0.000065) test_rna_pikachu: .: (0.000042) test_rna_sequence_complement: .: (0.000039) test_rna_sequence_translate: .: (0.000135) test_rna_to_re: .: (0.000074) test_total: .: (0.000047) test_two_consecutive_dna_randomizations_not_equal: .: (0.000123) test_valid_dna_sequence_illegal_bases: .: (0.000042) Bio::TestSequenceAA: test_codes: .: (0.000106) test_molecular_weight: .: (0.000062) test_names: .: (0.000049) test_to_re: .: (0.000065) test_to_s: .: (0.000036) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000116) Bio::TestSequenceAANew: test_new: .: (0.000076) test_new_n: .: (0.000038) test_new_r: .: (0.000035) test_new_t: .: (0.000034) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000101) test_concat: .: (0.000040) test_push: .: (0.000034) test_seq: .: (0.000033) test_splicing: .: (0.000091) test_sum: .: (0.000039) test_to_s: .: (0.000035) test_to_str: .: (0.000035) test_total: .: (0.000043) test_window_search: .: (0.000138) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.004942) test_normalize_A: .: (0.000057) test_normalize_a: .: (0.000041) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000856) test_randomize_with_block: .: (0.002101) test_randomize_with_hash: .: (0.000549) test_randomize_with_hash_block: .: (0.001999) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:325:in `test_randomize_equiprobability' =============================================================================== : (0.000437) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:331:in `test_randomize_with_hash_equiprobability' =============================================================================== : (0.000317) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000114) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000048) test_subseq_returns_subsequence: .: (0.000038) test_to_s_returns_self_as_string: .: (0.000045) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.000185) test_window_search_with_width_3_step_two_with_residual: .: (0.000043) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000093) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000072) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000108) test_na_self_randomize: .: (0.000066) Bio::TestSequenceDBLink: test_database: .: (0.000076) test_id: .: (0.000034) test_secondary_ids: .: (0.000035) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.000092) test_parse_uniprot_DR_line: .: (0.000069) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.000458) test_output_width_35: .: (0.000141) test_output_width_nil: .: (0.000239) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.000213) test_output_after_adding_sequence: .: (0.000134) test_output_after_truncating_sequence: .: (0.000086) test_output_from_error_probabilities: .: (0.001523) test_output_width45: .: (0.000113) test_output_with_converting_score_phred2solexa: .: (0.000257) test_output_with_converting_score_solexa2phred: .: (0.000136) test_output_with_default_score: .: (0.000100) Bio::TestSequenceMasker: test_mask: .: (0.000126) test_mask_with_enumerator: .: (0.000073) test_mask_with_enumerator_empty_mask_char: .: (0.000066) test_mask_with_enumerator_excess: .: (0.000321) test_mask_with_enumerator_longer_mask_char: .: (0.000064) test_mask_with_enumerator_shorter: .: (0.000081) test_mask_with_error_probability: .: (0.000061) test_mask_with_quality_score: .: (0.000057) Bio::TestSequenceNA: test_at_content: .: (0.000152) test_at_skew: .: (0.000087) test_codon_usage: .: (0.000056) test_complement: .: (0.000046) test_dna: .: (0.000043) test_dna!: .: (0.000039) test_forward_complement: .: (0.000061) test_gc_content: .: (0.000085) test_gc_percent: .: (0.000070) test_gc_skew: .: (0.000118) test_iliegal_bases: .: (0.000042) test_molecular_weight: .: (0.000053) test_names: .: (0.000067) test_reverse_complement: .: (0.000061) test_rna: .: (0.000040) test_rna!: .: (0.000038) test_splicing: .: (0.000071) test_to_re: .: (0.000072) test_to_s: .: (0.000035) Bio::TestSequenceNACommon: test_composition: .: (0.000104) test_concat: .: (0.000038) test_push: .: (0.000035) test_seq: .: (0.000035) test_splicing: .: (0.000068) test_sum: .: (0.000036) test_to_s: .: (0.000039) test_to_str: .: (0.000035) test_total: .: (0.000040) test_window_search: .: (0.000107) Bio::TestSequenceNANew: test_new: .: (0.000082) test_new_n: .: (0.000037) test_new_r: .: (0.000034) test_new_t: .: (0.000034) Bio::TestSequenceNATranslation: test_translate: .: (0.000177) test_translate_0: .: (0.000347) test_translate_1: .: (0.000098) test_translate_2: .: (0.000088) test_translate_3: .: (0.000086) test_translate_4: .: (0.000107) test_translate_5: .: (0.000087) test_translate_6: .: (0.000088) test_translate_7: .: (0.000210) test_translate_given_codon_table: .: (0.022094) test_translate_n1: .: (0.000233) test_translate_n2: .: (0.000186) test_translate_n3: .: (0.000365) test_translate_unknown_o: .: (0.000103) test_translate_unknown_x: .: (0.000095) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000096) test_convert_scores_from_phred_to_solexa: .: 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test_convert_scores_to_phred: .: (0.000065) test_convert_scores_to_solexa: .: (0.000032) test_p2q: .: (0.000083) test_q2p: .: (0.001167) test_quality_score_type: .: (0.000043) test_self_convert_scores_to_phred: .: (0.000074) test_self_p2q: .: (0.000081) test_self_q2p: .: (0.001322) test_solexa_p2q: .: (0.000090) test_solexa_q2p: .: (0.000850) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000109) test_center: .: (0.000046) test_chomp: .: (0.000055) test_chop: .: (0.000052) test_delete: .: (0.000041) test_delete_prefix: .: (0.000042) test_delete_suffix: .: (0.000040) test_downcase: .: (0.000040) test_each_char: .: (0.000073) test_each_char_enum: .: (0.000063) test_each_grapheme_cluster: .: (0.000216) test_each_grapheme_cluster_enum: .: (0.000068) test_each_line: .: (0.000063) test_each_line_enum: .: (0.000055) test_gsub: .: (0.000050) test_gsub_with_block: .: (0.000176) test_ljust: .: (0.000045) test_lstrip: .: (0.000042) test_multiply: .: (0.000040) test_next: .: (0.000041) test_reverse: .: (0.000042) test_rjust: .: (0.000042) test_rstrip: .: (0.000042) test_slice: .: (0.000043) test_slice2: .: (0.000057) test_split: .: (0.000058) test_squeeze: .: (0.000041) test_strip: .: (0.000041) test_sub: .: (0.000047) test_sub_with_block: .: (0.000098) test_succ: .: (0.000043) test_swapcase: .: (0.000042) test_tr: .: (0.000042) test_tr_s: .: (0.000050) test_upcase: .: (0.000042) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000111) test_partition_nomatch: .: (0.000055) test_partition_sep_TSeq: .: (0.000053) test_partition_sep_regexp: .: (0.000057) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000102) test_rpartition_nomatch: .: (0.000054) test_rpartition_sep_TSeq: .: (0.000053) test_rpartition_sep_regexp: .: (0.000054) Bio::TestShRNA: test_blocK_it: .: (0.021338) test_blocK_it_: .: (0.030237) test_blocK_it_BLOCK_IT: .: (0.012416) test_blocK_it_BLOCK_iT: .: (0.010695) test_blocK_it_piGene: .: (0.010696) test_bottom_strand: .: (0.010604) test_bottom_strand_class: .: (0.010598) test_bottom_strand_nil: .: (0.010502) test_design: .: (0.010479) test_design_BLOCK_IT: .: (0.011129) test_report: .: (0.010513) test_report_before_design: .: (0.010716) test_top_strand: .: (0.010488) test_top_strand_class: .: (0.010462) test_top_strand_nil: .: (0.010951) Bio::TestShRNANew: test_new: .: (0.000359) Bio::TestSiRNA: test_antisense_size: .: (0.000097) test_design: .: (0.010865) test_design_reynolds: .: (0.013627) test_design_uitei: .: (0.010574) test_max_gc_percent: .: (0.000051) test_min_gc_percent: .: (0.000040) test_reynolds: .: (0.012987) test_reynolds?: .: (0.000067) test_uitei: .: (0.010380) test_uitei?: .: (0.000061) Bio::TestSiRNANew: test_new: .: (0.000409) Bio::TestSiRNAPair: test_antisense: .: (0.011197) test_gc_percent: .: (0.010736) test_report: .: (0.010987) test_rule: .: (0.010714) test_sense: .: (0.010574) test_start: .: (0.010977) test_stop: .: (0.010557) test_target: .: (0.010556) Bio::TestSiRNAPairNew: test_new: .: (0.000229) Bio::TestSim4Report: test_all_hits: .: (0.000227) test_each: .: (0.000104) test_each_hit: .: (0.000086) test_hits: .: (0.000088) test_num_hits: .: (0.000072) test_query_def: .: (0.000072) test_query_id: .: (0.000072) test_query_len: .: (0.000071) test_seq1: .: (0.000096) Bio::TestSim4Report2: test_all_hits: .: (0.000149) test_each: .: (0.000086) test_each_hit: .: (0.000080) test_hits: .: (0.000082) test_num_hits: .: (0.000071) test_query_def: .: (0.000068) test_query_id: .: (0.000069) test_query_len: .: (0.000069) test_seq1: .: (0.000091) Bio::TestSim4Report4: test_all_hits: .: (0.000151) test_each: .: (0.000093) test_each_hit: .: (0.000088) test_hits: .: (0.000088) test_num_hits: .: (0.000076) test_query_def: .: (0.000078) test_query_id: .: (0.000077) test_query_len: .: (0.000076) test_seq1: .: (0.000101) Bio::TestSim4ReportHit: test_align: .: (0.000204) test_complement?: .: (0.000082) test_definition: .: (0.000078) test_each: .: (0.000171) test_exons: .: (0.000152) test_hit_id: .: (0.000082) test_hsps: .: (0.000137) test_introns: .: (0.000135) test_len: .: (0.000080) test_query_def: .: (0.000076) test_query_id: .: (0.000072) test_query_len: .: (0.000074) test_segmentpairs: .: (0.000144) test_seq1: .: (0.000099) test_seq2: .: (0.000094) test_target_def: .: (0.000072) test_target_id: .: (0.000071) test_target_len: .: (0.000070) Bio::TestSim4ReportHit2: test_align: .: (0.000169) test_complement?: .: (0.000078) test_definition: .: (0.000072) test_each: .: (0.000137) test_exons: .: (0.000136) test_hit_id: .: (0.000075) test_hsps: .: (0.000132) test_introns: .: (0.000125) test_len: .: (0.000938) test_query_def: .: (0.000211) test_query_id: .: (0.000080) test_query_len: .: (0.000072) test_segmentpairs: .: (0.000153) test_seq1: .: (0.000097) test_seq2: .: (0.000091) test_target_def: .: (0.000072) test_target_id: .: (0.000071) test_target_len: .: (0.000070) Bio::TestSim4ReportHit4: test_align: .: (0.000200) test_complement?: .: (0.000444) test_definition: .: (0.000250) test_each: .: (0.000202) test_exons: .: (0.000184) test_hit_id: .: (0.000084) test_hsps: .: (0.000171) test_introns: .: (0.000172) test_len: .: (0.000081) test_query_def: .: (0.000078) test_query_id: .: (0.000228) test_query_len: .: (0.000086) test_segmentpairs: .: (0.000212) test_seq1: .: (0.000108) test_seq2: .: (0.000099) test_target_def: .: (0.000077) test_target_id: .: (0.000081) test_target_len: .: (0.000079) Bio::TestSim4ReportSegment: test_from: .: (0.000088) test_self_new: .: (0.000050) test_seq: .: (0.000035) test_to: .: (0.000031) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000626) test_direction: .: (0.000133) test_hit_from: .: (0.000118) test_hit_to: .: (0.000113) test_hseq: .: (0.000114) test_midline: .: (0.000110) test_percent_identity: .: (0.000112) test_qseq: .: (0.000112) test_query_from: .: (0.000111) test_query_to: .: (0.000110) test_seq1: .: (0.000372) test_seq2: .: (0.000239) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000177) test_direction: .: (0.000118) test_hit_from: .: (0.000132) test_hit_to: .: (0.000115) test_hseq: .: (0.000113) test_midline: .: (0.000111) test_percent_identity: .: (0.000114) test_qseq: .: (0.000285) test_query_from: .: (0.000135) test_query_to: .: (0.000113) test_seq1: .: (0.000133) test_seq2: .: (0.000130) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000210) test_direction: .: (0.000150) test_hit_from: .: (0.000147) test_hit_to: .: (0.000145) test_hseq: .: (0.000233) test_midline: .: (0.000156) test_percent_identity: .: (0.000146) test_qseq: .: (0.000145) test_query_from: .: (0.000143) test_query_to: .: (0.000144) test_seq1: .: (0.000167) test_seq2: .: (0.000214) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000234) test_direction: .: (0.000156) test_hit_from: .: (0.000150) test_hit_to: .: (0.000146) test_hseq: .: (0.000157) test_midline: .: (0.000147) test_percent_identity: .: (0.000144) test_qseq: .: (0.000184) test_query_from: .: (0.000151) test_query_to: .: (0.000144) test_seq1: .: (0.000160) test_seq2: .: (0.000167) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000207) test_direction: .: (0.000152) test_hit_from: .: (0.000183) test_hit_to: .: (0.000154) test_hseq: .: (0.000148) test_midline: .: (0.000146) test_percent_identity: .: (0.000144) test_qseq: .: (0.000144) test_query_from: .: (0.000144) test_query_to: .: (0.000141) test_seq1: .: (0.000204) test_seq2: .: (0.000188) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000177) test_direction: .: (0.000117) test_hit_from: .: (0.000122) test_hit_to: .: (0.000111) test_hseq: .: (0.000111) test_midline: .: (0.000110) test_percent_identity: .: (0.000108) test_qseq: .: (0.000109) test_query_from: .: (0.000108) test_query_to: .: (0.000138) test_seq1: .: (0.000133) test_seq2: .: (0.000126) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000171) test_direction: .: (0.000115) test_hit_from: .: (0.000112) test_hit_to: .: (0.000109) test_hseq: .: (0.000110) test_midline: .: (0.000108) test_percent_identity: .: (0.000108) test_qseq: .: (0.000109) test_query_from: .: (0.000115) test_query_to: .: (0.000111) test_seq1: .: (0.000127) test_seq2: .: (0.000128) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000093) test_entry_id: .: (0.000041) test_filename: .: (0.000039) test_len: .: (0.000038) test_self_new: .: (0.000045) test_self_parse: .: (0.000073) Bio::TestTMHMMReport: test_entry_id: .: (0.000244) test_exp_aas_in_tmhs: .: (0.000147) test_exp_first_60aa: .: (0.000148) test_helix: .: (0.000734) test_predicted_tmhs: .: (0.000156) test_query_len: .: (0.000135) test_tmhs: .: (0.000141) test_to_s: .: (0.000184) test_total_prob_of_N_in: .: (0.000138) Bio::TestTMHMMReport_reports: test_reports: .: (0.000103) Bio::TestTMHMMTMH: test_entry_id: .: (0.000190) test_pos: .: (0.000140) test_range: .: (0.000136) test_status: .: (0.000135) test_version: .: (0.000135) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000160) test_cutoff: .: (0.000095) test_entry_id: .: (0.000089) test_length: .: (0.000088) test_loc: .: (0.000086) test_name: .: (0.000103) test_networks: .: (0.000086) test_prediction: .: (0.000092) test_query_len: .: (0.000085) test_query_sequences: .: (0.000084) test_rc: .: (0.000085) test_version: .: (0.000087) Bio::TestTargetPReportConst: test_delimiter: .: (0.000079) test_rs: .: (0.000034) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000076) test_togows_access_wait: .: (2.000247) Bio::TestTogoWSREST: test_debug: .: (0.000340) test_debug_default: .: (0.000087) test_internal_http: .: (0.000083) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000093) test_entry: .: (0.000038) test_entry_database_list: .: (0.000034) test_new: .: (0.000084) test_new_with_uri_object: .: (0.000097) test_new_with_uri_string: .: (0.000083) test_retrieve: .: (0.000035) test_search: .: (0.000034) test_search_database_list: .: (0.000034) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000158) test_prepare_return_value: .: (0.000103) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000195) Bio::TestTree: test_get_edge_distance: .: (0.000123) test_get_edge_distance_string: .: (0.000065) test_get_node_name: .: (0.000047) test_initialize: .: (0.000051) test_options: .: (0.000043) test_root: .: (0.000033) test_root=: .: (0.000042) Bio::TestTree2: test_add_edge: .: (0.000227) test_add_node: .: (0.000104) test_adjacency_matrix: .: (0.000115) test_adjacency_matrix_with_block: .: (0.000096) test_adjacent_nodes: .: (0.000107) test_adjacent_nodes_nonexistent: .: (0.000068) test_ancestors: .: (0.000086) test_children: .: (0.000072) test_clear: .: (0.000078) test_clear_node: .: (0.000094) test_clear_node_nonexistent: .: (0.000100) test_collect_edge!: .: (0.000124) test_collect_node!: .: (0.000126) test_concat: .: (0.000121) test_descendents: .: (0.000083) test_distance_matrix: .: (0.000229) test_each_edge: .: (0.000099) test_each_node: .: (0.000090) test_each_out_edge: .: (0.000078) test_each_out_edge_chimpanzee: .: (0.000076) test_each_out_edge_human: .: (0.000074) test_each_out_edge_mammals: .: (0.000090) test_each_out_edge_nonexistent: .: (0.000067) test_each_out_edge_primates: .: (0.000098) test_each_out_edge_rat: .: (0.000076) test_each_out_edge_rodents: .: (0.000097) test_edges: .: (0.000072) test_get_edge: .: (0.000152) test_get_edge_indirect: .: (0.000062) test_get_edge_merged: .: (0.000070) test_get_edge_nonexistent: .: (0.000058) test_get_node_bootstrap: .: (0.000064) test_get_node_bootstrap_string=: .: (0.000067) test_get_node_by_name: .: (0.000104) test_get_node_by_name_noexistent: .: (0.000057) test_include?: .: (0.000080) test_include_nonexistent: .: (0.000077) test_insert_node: .: (0.000108) test_leaves: .: (0.000094) test_leaves_noargs: .: (0.000068) test_lowest_common_ancestor: .: (0.000078) test_nodes: .: (0.000064) test_number_of_edges: .: (0.000060) test_number_of_nodes: .: (0.000062) test_out_degree: .: (0.000082) test_out_degree_nonexistent: .: (0.000063) test_out_edges: .: (0.000082) test_out_edges_mammals: .: (0.000092) test_out_edges_nonexistent: .: (0.000063) test_out_edges_primates: .: (0.000103) test_out_edges_rodents: .: (0.000103) test_parent: .: (0.000084) test_path: .: (0.000076) test_remove_edge: .: (0.000076) test_remove_edge_if: .: (0.000083) test_remove_edge_if_nothing_removed: .: (0.000091) test_remove_edge_nonexistent: .: (0.000089) test_remove_node: .: (0.000091) test_remove_node_if: .: (0.000073) test_remove_node_if_false: .: (0.000079) test_remove_node_nonexistent: .: (0.000077) test_remove_nonsense_nodes: .: (0.000084) test_subtree: .: (0.000100) test_subtree_with_all_paths: .: (0.000151) test_total_distance: .: (0.000069) Bio::TestTreeEdge: test_distance: .: (0.000091) test_distance=: .: (0.000057) test_distance_string: .: (0.000036) test_distance_string=: .: (0.000053) test_initialize: .: (0.000052) test_inspect: .: (0.000037) test_to_s: .: (0.000035) Bio::TestTreeNode: test_bootstrap: .: (0.000080) test_bootstrap=: .: (0.000052) test_bootstrap_string: .: (0.000032) test_bootstrap_string=: .: (0.000057) test_initialize: .: (0.000051) test_inspect: .: (0.000048) test_name: .: (0.000037) test_to_s: .: (0.000033) Bio::TestUniProt: test_gene_name: .: (0.004894) Bio::TestUniProtKB: test_ac: .: (0.001983) test_accession: .: (0.002474) test_cc: .: (0.002493) test_cc_alternative_products: .: (0.003467) test_cc_database: .: (0.002181) test_cc_mass_spectrometry: .: (0.002048) test_de: .: (0.003547) test_dr: .: (0.002867) test_dr_with_key: .: (0.002783) test_dr_with_key_empty: .: (0.002608) test_dt: .: (0.001153) test_dt_annotation: .: (0.001152) test_dt_created: .: (0.003720) test_dt_sequence: .: (0.001557) test_entry: .: (0.001816) test_ft: .: (0.004185) test_gene_name: .: (0.001145) test_gene_names: .: (0.001150) test_gn: .: (0.001191) test_gn_old_parser: .: (0.003215) test_gn_uniprot_parser: .: (0.002004) test_id_line: .: (0.001659) test_id_line_data_class: .: (0.001415) test_id_line_entry_name: .: (0.001353) test_id_line_molecule_type: .: (0.001235) test_id_line_sequence_length: .: (0.001723) test_kw: .: (0.001190) test_molecule: .: (0.001151) test_oc: .: (0.001178) test_og_1: .: (0.002316) test_og_2: .: (0.001966) test_og_3: .: (0.001554) test_og_4: .: (0.001386) test_og_5: .: (0.001252) test_og_6: .: (0.001252) test_os: .: (0.001690) test_os_access: .: (0.001137) test_os_access2: .: (0.001136) test_ox: .: (0.001148) test_protein_name: .: (0.002232) test_ref: .: (0.004267) test_seq: .: (0.001433) test_sequence_length: .: (0.001231) test_sq: .: (0.001655) test_sq_crc64: .: (0.001152) test_sq_len: .: (0.001146) test_sq_mw: .: (0.001145) test_synonyms: .: (0.002558) Bio::TestUniProtKB_CC: test_allergen: .: (0.000167) test_alternative_products_access_as_hash: .: (0.000101) test_alternative_products_ai: .: (0.000133) test_alternative_products_apu: .: (0.000214) test_alternative_products_as: .: (0.000131) test_alternative_products_rf: .: (0.000039) test_biophysicochemical_properties: .: (0.000197) test_biotechnology: .: (0.000433) test_catalytic_activity: .: (0.000113) test_caution: .: (0.000099) test_cofactor: .: (0.000084) test_developmental_stage: .: (0.000094) test_disease: .: (0.000256) test_domain: .: (0.000178) test_enzyme_regulation: .: (0.000090) test_function: .: (0.000101) test_induction: .: (0.000075) test_interaction: .: (0.000113) test_mass_spectrometry: .: (0.000133) test_miscellaneous: .: (0.000078) test_pathway: .: (0.000095) test_pharmaceutical: .: (0.000368) test_polymorphism: .: (0.000228) test_ptm: .: (0.000084) test_rna_editing: .: (0.000112) test_similarity: .: (0.000078) test_subcellular_location: .: (0.000097) test_subunit: .: (0.000066) test_tissue_specificity: .: (0.000092) test_toxic_dose: .: (0.000070) test_web_resource: .: (0.000126) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000188) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000213) test_protein_name: .: (0.000331) test_synonyms: .: (0.000166) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000105) test_entry: .: (0.000048) test_entry_id: .: (0.000045) test_entry_name: .: (0.000043) test_id_line: .: (0.000045) test_molecule: .: (0.000043) test_sequence_length: .: (0.000042) Bio::TestUniProtKB_P03589: test_ac: .: (0.000254) test_accession: .: (0.000182) test_cc: .: (0.000448) test_cc_alternative_products: .: (0.000302) test_cc_database: .: (0.000289) test_cc_mass_spectrometry: .: (0.000289) test_de: .: (0.000190) test_dr: .: (0.000299) test_dr_with_key: .: (0.000368) test_dr_with_key_empty: .: (0.000282) test_dt: .: (0.000165) test_dt_annotation: .: (0.000161) test_dt_created: .: (0.000158) test_dt_sequence: .: (0.000242) test_entry: .: (0.000196) test_ft: .: (0.000285) test_gene_name: .: (0.000204) test_gene_names: .: (0.000185) test_gn: .: (0.000180) test_gn_old_parser: .: (0.000249) test_gn_uniprot_parser: .: (0.000195) test_id_line: .: (0.000166) test_id_line_data_class: .: (0.000163) test_id_line_entry_name: .: (0.000159) test_id_line_sequence_length: .: (0.000185) test_kw: .: (0.000202) test_oc: .: (0.000186) test_oh: .: (0.000331) test_os: .: (0.000179) test_os_access: .: (0.000176) test_os_access2: .: (0.000173) test_ox: .: (0.000198) test_protein_name: .: (0.000214) test_protein_name_after_calling_de: .: (0.000613) test_ref: .: (0.000224) test_seq: .: (0.000341) test_sequence_length: .: (0.000173) test_sq: .: (0.000172) test_sq_crc64: .: (0.000174) test_sq_len: .: (0.000181) test_sq_mw: .: (0.000178) test_synonyms: .: (0.000187) Bio::TestUniProtKB_P28907: test_ac: .: (0.000536) test_accession: .: (0.000457) test_cc: .: (0.000788) test_cc_alternative_products: .: (0.000816) test_cc_database: .: (0.000769) test_cc_mass_spectrometry: .: (0.000755) test_de: .: (0.001753) test_dr: .: (0.001907) test_dr_with_key: .: (0.001910) test_dr_with_key_empty: .: (0.002837) test_dt: .: (0.000459) test_dt_annotation: .: (0.000466) test_dt_created: .: (0.000451) test_dt_sequence: .: (0.000439) test_entry: .: (0.000449) test_ft: .: (0.001026) test_gene_name: .: (0.000531) test_gene_names: .: (0.001773) test_gn: .: (0.000535) test_gn_old_parser: .: (0.000891) test_gn_uniprot_parser: .: (0.000871) test_id_line: .: (0.000486) test_id_line_data_class: .: (0.000836) test_id_line_entry_name: .: (0.000585) test_id_line_sequence_length: .: (0.000489) test_kw: .: (0.000633) test_oc: .: (0.000589) test_os: .: (0.000579) test_os_access: .: (0.000537) test_os_access2: .: (0.000556) test_ox: .: (0.000510) test_protein_name: .: (0.000564) test_protein_name_after_calling_de: .: (0.000540) test_ref: .: (0.001251) test_seq: .: (0.000535) test_sequence_length: .: (0.000462) test_sq: .: (0.000504) test_sq_crc64: .: (0.000540) test_sq_len: .: (0.000515) test_sq_mw: .: (0.000510) test_synonyms: .: (0.000555) test_synonyms_after_calling_de: .: (0.000591) Bio::TestUniProtKB_P49144: test_ac: .: (0.000359) test_accession: .: (0.000272) test_cc: .: (0.001788) test_cc_alternative_products: .: (0.000468) test_cc_database: .: (0.000483) test_cc_mass_spectrometry: .: (0.000846) test_de: .: (0.000272) test_dr: .: (0.000495) test_dr_with_key: .: (0.000777) test_dr_with_key_empty: .: (0.000509) test_dt: .: (0.000270) test_dt_annotation: .: (0.000548) test_dt_created: .: (0.000255) test_dt_sequence: .: (0.000269) test_entry: .: (0.000420) test_ft: .: (0.000673) test_gene_name: .: (0.000289) test_gene_names: .: (0.000401) test_gn: .: (0.000265) test_gn_old_parser: .: (0.000288) test_gn_uniprot_parser: .: (0.000364) test_id_line: .: (0.000238) test_id_line_data_class: .: (0.000253) test_id_line_entry_name: .: (0.000249) test_id_line_sequence_length: .: (0.000346) test_kw: .: (0.000285) test_oc: .: (0.000827) test_os: .: (0.000249) test_os_access: .: (0.000242) test_os_access2: .: (0.000241) test_ox: .: (0.000238) test_protein_name: .: (0.000257) test_protein_name_after_calling_de: .: (0.000256) test_ref: .: (0.000319) test_seq: .: (0.000330) test_sequence_length: .: (0.000259) test_sq: .: (0.000278) test_sq_crc64: .: (0.000262) test_sq_len: .: (0.000285) test_sq_mw: .: (0.000274) test_synonyms: .: (0.000289) test_synonyms_after_calling_de: .: (0.000290) Bio::TestUniProtKB_Ref: test_RA: .: (0.000173) test_RC: .: (0.000117) test_RG: .: (0.000104) test_RL: .: (0.000099) test_RN: .: (0.000101) test_RP: .: (0.000101) test_RT: .: (0.000102) test_RX: .: (0.000100) test_ref: .: (0.000107) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000116) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000230) test_alternative_products_with_ft: .: (0.000323) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000156) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000161) test_RL_lines: .: (0.000058) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000257) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000110) test_RG_line: .: (0.000060) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.001682) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000140) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000092) test_RL_line: .: (0.000059) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000326) test_RP_line: .: (0.000103) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000068) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000455) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000120) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000085) test_CC_interaction_isoform: .: (0.000079) test_CC_interaction_no_gene_name: .: (0.000077) test_CC_interaction_self_association: .: (0.000089) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000124) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000130) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000168) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000441) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000142) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000113) test_DT_line: .: (0.000068) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.001828) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000311) test_CC_web_resource: .: (0.000037) test_FT_VER_SEQ: .: (0.000082) test_OH_line_exception: .: (0.000336) test_OH_lines: .: (0.000170) Bio::TestUtils: test_centreOfGravity: .: (0.000223) test_dihedral_angle: .: (0.000161) test_distance: .: (0.000145) test_geometricCentre: .: (0.000109) test_rad2deg: .: (0.000070) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000153) test_dijkstra_on_weighted_graph: .: (0.000059) Finished in 7.452714709 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 528.80 tests/s, 2898.41 assertions/s /usr/bin/ruby3.4 /usr/bin/gem2deb-test-runner ┌──────────────────────────────────────────────────────────────────────────────┐ │ Run tests for ruby3.4 from debian/ruby-tests.rake │ └──────────────────────────────────────────────────────────────────────────────┘ RUBYLIB=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/lib/ruby/vendor_ruby:. GEM_PATH=/build/reproducible-path/ruby-bio-2.0.6/debian/ruby-bio/usr/share/rubygems-integration/all:/build/reproducible-path/ruby-bio-2.0.6/debian/.debhelper/generated/_source/home/.local/share/gem/ruby/3.4.0:/var/lib/gems/3.4.0:/usr/local/lib/ruby/gems/3.4.0:/usr/lib/ruby/gems/3.4.0:/usr/lib/x86_64-linux-gnu/ruby/gems/3.4.0:/usr/share/rubygems-integration/3.4.0:/usr/share/rubygems-integration/all:/usr/lib/x86_64-linux-gnu/rubygems-integration/3.4.0 ruby3.4 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake /usr/bin/ruby3.4 -w -I"test" /usr/lib/ruby/gems/3.4.0/gems/rake-13.2.1/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_P03589.rb" "test/unit/bio/db/embl/test_uniprotkb_P28907.rb" "test/unit/bio/db/embl/test_uniprotkb_P49144.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 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/3.4.0/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: test_db_ids: .: (0.000270) test_dbs: .: (0.000097) test_go_ids: .: (0.000087) test_go_terms: .: (0.000085) test_parser: .: (0.000196) test_set_date: .: (0.000093) test_set_desc: .: (0.000087) test_to_str: .: (0.000095) Bio::FuncTestCommandBackports: test_mktmpdir_with_block: .: (0.000329) test_mktmpdir_without_block: .: (0.000237) test_remove_entry_secure: .: (0.000173) Bio::FuncTestCommandCallMisc1: test_call_command: .: (0.001687) test_call_command_fork: .: (0.000058) test_call_command_open3: .: (0.001372) test_call_command_popen: .: (0.001354) Bio::FuncTestCommandCallSimple: test_call_command: .: (0.001318) test_call_command_fork: .: (0.000055) test_call_command_open3: .: (0.001459) test_call_command_popen: .: (0.001277) Bio::FuncTestCommandCallWithSpace: test_call_command: .: (0.001311) test_call_command_fork: .: (0.000059) test_call_command_open3: .: (0.001329) test_call_command_popen: .: (0.001268) Bio::FuncTestCommandChdir: test_call_command_chdir: .: (0.001197) test_call_command_fork_chdir: .: (0.000112) test_call_command_popen_chdir: .: (0.001085) test_query_command_chdir: .: (0.001059) test_query_command_fork_chdir: .: (0.000103) test_query_command_popen_chdir: .: (0.001010) Bio::FuncTestCommandQuery: test_query_command: .: (0.002471) test_query_command_fork: .: (0.000699) test_query_command_open3: .: (0.002320) test_query_command_popen: .: (0.002192) Bio::FuncTestCommandTmpdir: test_close!: .: (0.000363) test_initialize: .: (0.000143) test_path: .: (0.000095) test_path_after_close: .: (0.000194) Bio::FuncTestSequenceOutputEMBL: test_output_embl: .: (0.005381) test_output_fasta: .: (0.002747) Bio::NCBIDB::TestCommon: test_acc_version: .: (0.000157) test_accession: .: (0.000127) test_accessions: .: (0.000067) test_comment: .: (0.000053) test_common_name: .: (0.000077) test_definition: .: (0.000119) test_features: .: (0.000149) test_gi: .: (0.000064) test_keywords: .: (0.000059) test_locus: .: (0.000038) test_nid: .: (0.000059) test_organism: .: (0.000070) test_origin: .: (0.000055) test_references: .: (0.000315) test_segment: .: (0.000065) test_source: .: (0.000116) test_taxonomy: .: (0.000068) test_version: .: (0.000062) test_versions: .: (0.000058) Bio::TestAA: test_13: .: (0.000092) test_1n: .: (0.000035) test_name2one: .: (0.000122) test_name2three: .: (0.000043) test_one2name: .: (0.000082) test_one2three: .: (0.000033) test_three2name: .: (0.000031) test_three2one: .: (0.000102) test_to_1_1: .: (0.000035) test_to_1_3: .: (0.000042) test_to_1_name: .: (0.000042) test_to_3_1: .: (0.000033) test_to_3_3: .: (0.000031) test_to_3_name: .: (0.000040) test_to_re: .: (0.000053) Bio::TestAAConstants: test_bio_aminoacid: .: (0.000091) Bio::TestAAindex: test_api: .: (0.000125) test_auto_aax1: .: (0.000116) test_auto_aax2: .: (0.000093) Bio::TestAAindex1: test_author: .: (0.000140) test_comment: .: (0.000084) test_correlation_coefficient: .: (0.000177) test_dblinks: .: (0.000084) test_definition: .: (0.000143) test_entry_id: .: (0.000083) test_index: .: (0.000180) test_journal: .: (0.000102) test_title: .: (0.000142) Bio::TestAAindex2: test_access_A_R: .: (0.000360) test_access_R_A: .: (0.000274) test_author: .: (0.000093) test_cols: .: (0.000148) test_comment: .: (0.000137) test_dblinks: .: (0.000137) test_definition: .: (0.000086) test_entry_id: .: (0.000101) test_journal: .: (0.000095) test_matrix: .: (0.000268) test_matrix_1_2: .: (0.000335) test_matrix_2_2: .: (0.000380) test_matrix_A_R: .: (0.000270) test_matrix_R_A: .: (0.000318) test_matrix_determinant: .: (0.001182) test_matrix_rank: .: (0.001090) test_matrix_transpose: .: (0.000451) test_rows: .: (0.000094) test_title: .: (0.000090) Bio::TestAAindexConstant: test_delimiter: .: (0.000090) test_tagsize: .: (0.000035) Bio::TestAbif: test_complement: .: (0.006780) test_seq: .: (0.006266) test_to_biosequence: .: (0.006679) Bio::TestActsLikeMap: test_mixin: .: (0.000141) Bio::TestActsLikeMapAndMarker: test_mixin: .: (0.000202) Bio::TestActsLikeMarker: test_mixin: .: (0.000101) Bio::TestAlignment: test_add_seq_no_key: .: (0.000141) test_add_seq_using_seq_with_aaseq_method: .: (0.000067) test_add_seq_using_seq_with_definition_method: .: (0.000043) test_add_seq_using_seq_with_entry_id_method: .: (0.000051) test_add_seq_using_seq_with_naseq_method: .: (0.000055) test_add_seq_using_seq_with_seq_method: .: (0.000047) test_consensus_iupac_gap_modes: .: (0.000262) test_consensus_iupac_missing_char: .: (0.000083) test_consensus_iupac_missing_char_option: .: (0.000089) test_consensus_iupac_no_gaps: .: (0.000105) test_consensus_iupac_of_ambiguous_bases: .: (0.000159) test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.010636) test_consensus_opt_gap_mode: .: (0.000383) test_consensus_opt_missing_char: .: (0.000113) test_consensus_string_no_gaps: .: (0.000968) test_consensus_threshold_four_sequences: .: (0.000149) test_consensus_threshold_two_sequences: .: (0.000158) test_convert_match: .: (0.000098) test_convert_unmatch: .: (0.000257) test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000072) test_convert_unmatch_different_match_char: .: (0.000650) test_convert_unmatch_multiple_sequences: .: (0.000091) test_default_gap_char: .: (0.000035) test_default_gap_regexp_matches_default_gap_char: .: (0.000040) test_default_missing_char: .: (0.000034) test_each_site_equal_length: .: (0.000069) test_each_site_unequal_length: .: (0.000068) test_equals: .: (0.000177) test_match_line_protein: .: (0.000222) test_normalizebang_extends_sequences_with_gaps: .: (0.000487) test_seq_length_is_max_seq_length: .: (0.000051) test_seq_length_when_one_sequence: .: (0.000037) test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000039) test_seqclass_when_seqclass_set: .: (0.000051) test_seqclass_when_sequence_used: .: (0.000112) test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000040) test_set_and_get_gap_char: .: (0.000036) test_store_cannot_override_key: .: (0.000040) test_store_with_default_keys_and_user_defined_keys: .: (0.000047) test_store_with_nil_key_uses_next_number_for_key: .: (0.000040) Bio::TestAlignmentEnumerableExtension: test_alignment_collect: .: (0.000120) test_alignment_concat: .: (0.000065) test_alignment_length: .: (0.000035) test_alignment_lstrip!: .: (0.000072) test_alignment_lstrip_nil: .: (0.000048) test_alignment_normalize!: .: (0.000039) test_alignment_rstrip!: .: (0.000072) test_alignment_rstrip_nil: .: (0.000044) test_alignment_site: .: (0.000042) test_alignment_slice: .: (0.000062) test_alignment_strip!: .: (0.000099) test_alignment_strip_nil: .: (0.000052) test_alignment_subseq: .: (0.000062) test_alignment_window: .: (0.000041) test_collect_each_site: .: (0.000057) test_consensus_each_site_default: .: (0.000066) test_consensus_each_site_gap_mode_1: .: (0.000064) test_consensus_each_site_gap_mode_minus1: .: (0.000067) test_consensus_iupac: .: (0.000166) test_consensus_string_default: .: (0.000065) test_consensus_string_half: .: (0.000058) test_convert_match: .: (0.000054) test_convert_unmatch: .: (0.000044) test_each_seq: .: (0.000048) test_each_site: .: (0.000076) test_each_site_step: .: (0.000055) test_each_window: .: (0.000247) test_match_line: .: (0.000378) test_match_line_amino: .: (0.000795) test_match_line_nuc: .: (0.000081) test_private_alignment_site: .: (0.000045) test_remove_all_gaps!: .: (0.000054) test_seqclass: .: (0.000039) test_seqclass=: .: (0.000051) test_seqclass_default: .: (0.000033) Bio::TestAlignmentMultiFastaFormat: test_alignment: .: (0.001624) test_determine_seq_method: .: (0.000902) test_entries: .: (0.000174) Bio::TestAlignmentOutput: test_avoid_same_name: .: (0.000139) test_avoid_same_name_numbering: .: (0.000063) test_clustal_have_same_name_true: .: (0.000047) test_have_same_name_false: .: (0.000044) Bio::TestAlignmentPropertyMethods: test_gap_char=: .: (0.000089) test_gap_char_default: .: (0.000040) test_gap_char_never_nil: .: (0.000036) test_gap_regexp: .: (0.000035) test_gap_regexp=: .: (0.000037) test_gap_regexp_never_nil: .: (0.000034) test_get_all_property_default: .: (0.000035) test_get_all_property_nodefault: .: (0.000042) test_is_gap_default_false: .: (0.000037) test_is_gap_default_true: .: (0.000037) test_is_gap_nodefault_false: .: (0.000037) test_is_gap_nodefault_true: .: (0.000036) test_missing_char=: .: (0.000035) test_missing_char_default: .: (0.000250) test_missing_char_never_nil: .: (0.000038) test_seqclass=: .: (0.000038) test_seqclass_default: .: (0.000035) test_seqclass_never_nil: .: (0.000034) test_set_all_property: .: (0.000040) Bio::TestAlignmentSite: test_consensus_iupac: .: (0.000265) test_consensus_string_50percent: .: (0.000045) test_consensus_string_50percent_nil: .: (0.000041) test_consensus_string_default: .: (0.000036) test_consensus_string_default_nil: .: (0.000035) test_has_gap_false: .: (0.000038) test_has_gap_true: .: (0.000035) test_match_line_amino_100percent: .: (0.000048) test_match_line_amino_missing: .: (0.000075) test_match_line_amino_strong: .: (0.000049) test_match_line_amino_weak: .: (0.000062) test_match_line_nuc_100percent: .: (0.000044) test_match_line_nuc_missing: .: (0.000045) test_remove_gaps!: .: (0.000038) test_remove_gaps_bang_not_removed: .: (0.000034) Bio::TestAtomFinder: test_atoms: .: (0.009592) test_each_atom: .: (0.000113) test_find_atom: .: (0.000080) Bio::TestBioFastaDefline: test_acc_version: .: (0.000240) test_accession: .: (0.000230) test_accessions: .: (0.000159) test_description: .: (0.000135) test_descriptions: .: (0.000141) test_entry_id: .: (0.000126) test_get: .: (0.000217) test_get_all_by_type: .: (0.000123) test_get_by_type: .: (0.000129) test_gi: .: (0.000117) test_id_strings: .: (0.000286) test_locus: .: (0.000112) test_method_missing: .: (0.000156) test_to_s: .: (0.000148) test_words: .: (0.000337) Bio::TestBioGOOntology: test_dag_edit_format_parser: .: (0.000434) test_goid2term: .: (0.000184) test_parse_goids: .: (0.000182) Bio::TestBioGenBank: test_basecount: .: (0.000190) test_circular: .: (0.000146) test_classification: .: (0.000156) test_date: .: (0.000110) test_date_modified: .: (0.000417) test_division: .: (0.000123) test_each_cds_feature: .: (0.000367) test_each_cds_qualifiers: .: (0.000351) test_each_gene: .: (0.000344) test_entry_id: .: (0.000115) test_length: .: (0.000106) test_locus_circular: .: (0.000120) test_locus_class: .: (0.000117) test_locus_date: .: (0.000112) test_locus_division: .: (0.000113) test_locus_entry_id: .: (0.000112) test_locus_length: .: (0.000114) test_locus_natype: .: (0.000115) test_locus_strand: .: (0.000112) test_natype: .: (0.000100) test_seq: .: (0.000138) test_seq_len: .: (0.000130) test_strand: .: (0.000105) test_strandedness: .: (0.000110) test_to_biosequence: .: (0.001009) Bio::TestBioGenPept: test_circular: .: (0.000177) test_date: .: (0.000089) test_dbsource: .: (0.000079) test_division: .: (0.000080) test_entry_id: .: (0.000081) test_length: .: (0.000082) test_locus: .: (0.000081) test_seq: .: (0.000094) test_seq_len: .: (0.000086) Bio::TestBioKEGGGENES_b0529: test_aalen: .: (0.000185) test_aaseq: .: (0.000130) test_chromosome: .: (0.000101) test_codon_usage: .: (0.000161) test_cu_list: .: (0.000092) test_dblinks_as_hash: .: (0.000123) test_dblinks_as_strings: .: (0.000102) test_definition: .: (0.000114) test_division: .: (0.000104) test_eclinks: .: (0.000122) test_entry: .: (0.000094) test_entry_id: .: (0.000110) test_gbposition: .: (0.000103) test_gene: .: (0.000102) test_genes: .: (0.000099) test_keggclass: .: (0.000112) test_keggclasses: .: (0.000130) test_locations: .: (0.000189) test_motifs_as_hash: .: (0.000137) test_motifs_as_strings: .: (0.000099) test_name: .: (0.000103) test_names_as_array: .: (0.000110) test_new: .: (0.000099) test_ntlen: .: (0.000153) test_ntseq: .: (0.000179) test_organism: .: (0.000100) test_orthologs_as_hash: .: (0.000118) test_orthologs_as_strings: .: (0.000103) test_pathway: .: (0.000121) test_pathway_after_pathways_as_strings: .: (0.000204) test_pathway_before_pathways_as_strings: .: (0.000135) test_pathways_as_hash: .: (0.000108) test_pathways_as_strings: .: (0.000091) test_position: .: (0.000102) test_structure: .: (0.000101) Bio::TestBioKEGGGENOME_T00005: test_chromosomes: .: (0.007588) test_comment: .: (0.000298) test_data_source: .: (0.000176) test_definition: .: (0.000172) test_disease: .: (0.000197) test_entry_id: .: (0.000180) test_lineage: .: (0.000918) test_nalen: .: (0.000183) test_name: .: (0.000189) test_new: .: (0.000221) test_num_gene: .: (0.000175) test_num_rna: .: (0.000170) test_original_databases: .: (0.000174) test_original_db: .: (0.000665) test_plasmids: .: (0.000168) test_references: .: (0.001788) test_statistics: .: (0.000295) test_taxid: .: (0.000185) test_taxonomy: .: (0.000176) Bio::TestBioKEGGGENOME_T00070: test_chromosomes: .: (0.000221) test_comment: .: (0.000114) test_data_source: .: (0.000096) test_definition: .: (0.000093) test_disease: .: (0.000106) test_entry_id: .: (0.000328) test_lineage: .: (0.000132) test_nalen: .: (0.000101) test_name: .: (0.000095) test_new: .: (0.000088) test_num_gene: .: (0.000089) test_num_rna: .: (0.000094) test_original_databases: .: (0.000088) test_original_db: .: (0.000114) test_plasmids: .: (0.000154) test_references: .: (0.000167) test_statistics: .: (0.000096) test_taxid: .: (0.000124) test_taxonomy: .: (0.000111) Bio::TestBioKEGGPATHWAY_ec00072: test_compounds_as_hash: .: (0.000174) test_compounds_as_strings: .: (0.000279) test_dblinks_as_hash: .: (0.000078) test_dblinks_as_strings: .: (0.000072) test_description: .: (0.000084) test_diseases_as_hash: .: (0.000074) test_diseases_as_strings: .: (0.000072) test_entry_id: .: (0.000081) test_enzymes_as_strings: .: (0.000081) test_genes_as_hash: .: (0.000128) test_genes_as_strings: .: (0.000072) test_keggclass: .: (0.000082) test_ko_pathway: .: (0.000080) test_modules_as_hash: .: (0.000081) test_modules_as_strings: .: (0.000072) test_name: .: (0.000081) test_new: .: (0.000078) test_organism: .: (0.000079) test_orthologs_as_hash: .: (0.000072) test_orthologs_as_strings: .: (0.000068) test_pathways_as_hash: .: (0.000077) test_pathways_as_strings: .: (0.000072) test_reactions_as_hash: .: (0.000091) test_reactions_as_strings: .: (0.000071) test_references: .: (0.000071) test_rel_pathways_as_hash: .: (0.000088) test_rel_pathways_as_strings: .: (0.000102) Bio::TestBioKEGGPATHWAY_hsa00790: test_compounds_as_hash: .: (0.000233) test_compounds_as_strings: .: (0.000127) test_dblinks_as_hash: .: (0.000104) test_dblinks_as_strings: .: (0.000087) test_description: .: (0.000093) test_diseases_as_hash: .: (0.000094) test_diseases_as_strings: .: (0.000087) test_entry_id: .: (0.000096) test_enzymes_as_strings: .: (0.000082) test_genes_as_hash: .: (0.000115) test_genes_as_strings: .: (0.000275) test_keggclass: .: (0.000100) test_ko_pathway: .: (0.000092) test_modules_as_hash: .: (0.000092) test_modules_as_strings: .: (0.000086) test_name: .: (0.000093) test_new: .: (0.000088) test_organism: .: (0.000093) test_orthologs_as_hash: .: (0.000082) test_orthologs_as_strings: .: (0.000081) test_pathways_as_hash: .: (0.000087) test_pathways_as_strings: .: (0.000084) test_reactions_as_hash: .: (0.000080) test_reactions_as_strings: .: (0.000080) test_references: .: (0.000079) test_rel_pathways_as_hash: .: (0.000096) test_rel_pathways_as_strings: .: (0.000255) Bio::TestBioKEGGPATHWAY_ko00312: test_compounds_as_hash: .: (0.000159) test_compounds_as_strings: .: (0.000098) test_dblinks_as_hash: .: (0.000074) test_dblinks_as_strings: .: (0.000070) test_description: .: (0.000080) test_diseases_as_hash: .: (0.000069) test_diseases_as_strings: .: (0.000068) test_entry_id: .: (0.000080) test_enzymes_as_strings: .: (0.000073) test_genes_as_hash: .: (0.000069) test_genes_as_strings: .: (0.000067) test_keggclass: .: (0.000082) test_ko_pathway: .: (0.000077) test_modules_as_hash: .: (0.000068) test_modules_as_strings: .: (0.000067) test_name: .: (0.000078) test_new: .: (0.000073) test_organism: .: (0.000382) test_orthologs_as_hash: .: (0.000155) test_orthologs_as_strings: .: (0.000085) test_pathways_as_hash: .: (0.000074) test_pathways_as_strings: .: (0.000070) test_reactions_as_hash: .: (0.000067) test_reactions_as_strings: .: (0.000066) test_references: .: (0.000069) test_rel_pathways_as_hash: .: (0.000074) test_rel_pathways_as_strings: .: (0.000070) Bio::TestBioKEGGPATHWAY_map00030: test_compounds_as_hash: .: (0.000150) test_compounds_as_strings: .: (0.000141) test_dblinks_as_hash: .: (0.000093) test_dblinks_as_strings: .: (0.000135) test_description: .: (0.000162) test_diseases_as_hash: .: (0.000090) test_diseases_as_strings: .: (0.000084) test_entry_id: .: (0.000093) test_enzymes_as_strings: .: (0.000098) test_genes_as_hash: .: (0.000100) test_genes_as_strings: .: (0.000080) test_keggclass: .: (0.000095) test_ko_pathway: .: (0.000096) test_modules_as_hash: .: (0.000124) test_modules_as_strings: .: (0.000094) test_name: .: (0.000092) test_new: .: (0.000088) test_organism: .: (0.000091) test_orthologs_as_hash: .: (0.000082) test_orthologs_as_strings: .: (0.000080) test_pathways_as_hash: .: (0.000087) test_pathways_as_strings: .: (0.000081) test_reactions_as_hash: .: (0.000080) test_reactions_as_strings: .: (0.000077) test_references: .: (0.000484) test_rel_pathways_as_hash: .: (0.000127) test_rel_pathways_as_strings: .: (0.000094) Bio::TestBioKeggDRUG: test_activity: .: (0.000178) test_comment: .: (0.000106) test_dblinks_as_hash: .: (0.000136) test_dblinks_as_strings: .: (0.000102) test_entry_id: .: (0.000102) test_formula: .: (0.000098) test_kcf: .: (0.000088) test_mass: .: (0.000097) test_name: .: (0.000107) test_names: .: (0.000131) test_pathways_as_hash: .: (0.000106) test_pathways_as_strings: .: (0.000089) test_products: .: (0.000103) test_remark: .: (0.000112) Bio::TestBioKeggGLYCAN: test_comment: .: (0.000174) test_composition: .: (0.000114) test_compounds: .: (0.000100) test_dblinks_as_hash: .: (0.000196) test_dblinks_as_strings: .: (0.000118) test_entry_id: .: (0.000103) test_enzymes: .: (0.000106) test_kcf: .: (0.000086) test_keggclass: .: (0.000095) test_mass: .: (0.000101) test_name: .: (0.000095) test_orthologs_as_hash: .: (0.000134) test_orthologs_as_strings: .: (0.000106) test_pathways_as_hash: .: (0.000105) test_pathways_as_strings: .: (0.000091) test_reactions: .: (0.000101) test_references: .: (0.000116) test_remark: .: (0.000098) Bio::TestBioKeggGLYCAN_G01366: test_comment: .: (0.000152) test_composition: .: (0.000094) test_compounds: .: (0.000081) test_dblinks_as_hash: .: (0.000097) test_dblinks_as_strings: .: (0.000076) test_entry_id: .: (0.000080) test_enzymes: .: (0.000077) test_kcf: .: (0.000072) test_keggclass: .: (0.000080) test_mass: .: (0.000080) test_name: .: (0.000077) test_orthologs_as_hash: .: (0.000075) test_orthologs_as_strings: .: (0.000071) test_pathways_as_hash: .: (0.000077) test_pathways_as_strings: .: (0.000069) test_reactions: .: (0.000077) test_references: .: (0.000071) test_remark: .: (0.000078) Bio::TestBioKeggPathway_rn00250: test_compounds_as_hash: .: (0.000246) test_compounds_as_strings: .: (0.000149) test_dblinks_as_hash: .: (0.000121) test_dblinks_as_strings: .: (0.000108) test_description: .: (0.000116) test_diseases_as_hash: .: (0.000122) test_diseases_as_strings: .: (0.000112) test_entry_id: .: (0.000116) test_enzymes_as_strings: .: (0.000104) test_genes_as_hash: .: (0.000107) test_genes_as_strings: .: (0.000104) test_keggclass: .: (0.000114) test_ko_pathway: .: (0.000118) test_modules_as_hash: .: (0.000142) test_modules_as_strings: .: (0.000125) test_name: .: (0.000119) test_new: .: (0.000113) test_organism: .: (0.000117) test_orthologs_as_hash: .: (0.000108) test_orthologs_as_strings: .: (0.000128) test_pathways_as_hash: .: (0.000118) test_pathways_as_strings: .: (0.000106) test_reactions_as_hash: .: (0.000231) test_reactions_as_strings: .: (0.000187) test_references: .: (0.000253) test_rel_pathways_as_hash: .: (0.000184) test_rel_pathways_as_strings: .: (0.000145) Bio::TestBioLITDB: test_author: .: (0.000175) test_entry_id: .: (0.000090) test_field: .: (0.000083) test_journal: .: (0.000083) test_keyword: .: (0.000099) test_reference: .: (0.000165) test_title: .: (0.000106) test_volume: .: (0.000084) Bio::TestBioNBRF: test_aalen: .: (0.000149) test_aaseq: .: (0.000077) test_entry: .: (0.000063) test_length: .: (0.000067) test_nalen: .: (0.000107) test_naseq: .: (0.000087) test_seq: .: (0.000070) test_seq_class: .: (0.000069) test_to_nbrf: .: (0.000076) Bio::TestBioTreeOutputPrivate: test_to_newick_format_label: .: (0.000164) test_to_newick_format_leaf: .: (0.000206) test_to_newick_format_leaf_NHX: .: (0.000090) Bio::TestBl2seqReport: test_db_len: .: (0.007348) test_db_num: .: (0.000442) test_new: .: (0.000160) test_undefed_methods: .: (0.000537) test_undefed_methods_for_iteration: .: (0.000489) Bio::TestBl2seqReportConstants: test_rs: .: (0.000096) Bio::TestBl2seqReportHit: test_empty_hits: .: (0.000200) test_hits: .: (0.000153) Bio::TestBlast: test_blast_reports_format0: .: (0.003906) test_blast_reports_format0_with_block: .: (0.000416) test_blast_reports_format7: .: (0.007229) test_blast_reports_format7_with_block: .: (0.016065) test_blast_reports_format7_with_parser: .: (0.019331) test_blast_reports_format7_with_parser_with_block: .: (0.005376) test_blast_reports_format8: .: (0.000425) test_blast_reports_format8_with_block: .: (0.000645) test_blast_reports_format8_with_parser: .: (0.000136) test_blast_reports_format8_with_parser_with_block: .: (0.000105) test_blast_reports_xml: .: (0.007702) test_blast_reports_xml_with_block: .: (0.005883) test_blastll: .: (0.000081) test_db: .: (0.000065) test_exec_genomenet: .: (0.000051) test_exec_local: .: (0.000050) test_exec_ncbi: .: (0.000049) test_filter: .: (0.000056) test_format: .: (0.000061) test_make_command_line: .: (0.000280) test_make_command_line_2: .: (0.000161) test_matrix: .: (0.000060) test_new: .: (0.000100) test_new_opt_string: .: (0.000103) test_option: .: (0.000071) test_option_set: .: (0.000104) test_option_set_m0: .: (0.000088) test_options: .: (0.000058) test_output: .: (0.000057) test_parse_result: .: (0.005279) test_parser: .: (0.000081) test_program: .: (0.000062) test_query: .: (0.000051) test_self_local: .: (0.000080) test_self_remote: .: (0.000984) test_server: .: (0.000082) Bio::TestBlastNCBIOptions: test_add_options: .: (0.000180) test_delete: .: (0.000139) test_equal_equal: .: (0.000146) test_get: .: (0.000133) test_make_command_line_options: .: (0.000124) test_normalize!: .: (0.000080) test_parse: .: (0.000089) test_set: .: (0.000173) Bio::TestBlastReport: test_db: .: (0.007328) test_db_len: .: (0.005240) test_db_num: .: (0.005301) test_each_hit: .: (0.006713) test_each_iteration: .: (0.005393) test_eff_space: .: (0.006336) test_entrez_query: .: (0.005042) test_entropy: .: (0.004976) test_expect: .: (0.006401) test_filter: .: (0.005626) test_gap_extend: .: (0.005416) test_gap_open: .: (0.005686) test_hits: .: (0.005247) test_hsp_len: .: (0.006224) test_inclusion: .: (0.005059) test_iterations: .: (0.005018) test_kappa: .: (0.006224) test_lambda: .: (0.005599) test_matrix: .: (0.005540) test_message: .: (0.005574) test_parameters: .: (0.005203) test_pattern: .: (0.006237) test_program: .: (0.005045) test_query_def: .: (0.005025) test_query_id: .: (0.006284) test_query_len: .: (0.005422) test_reference: .: (0.006108) test_sc_match: .: (0.004976) test_sc_mismatch: .: (0.005008) test_statistics: .: (0.006148) test_version: .: (0.005482) Bio::TestBlastReportDefault: test_db: .: (0.000344) test_db_len: .: (0.000252) test_db_num: .: (0.000229) test_each_hit: .: (0.000231) test_each_iteration: .: (0.000203) test_eff_space: .: (0.000261) test_entropy: .: (0.000247) test_expect: .: (0.000253) test_gap_extend: .: (0.000242) test_gap_open: .: (0.000241) test_gapped_entropy: .: (0.000227) test_gapped_kappa: .: (0.000221) test_gapped_lambda: .: (0.000218) test_hits: .: (0.000218) test_iterations: .: (0.000203) test_kappa: .: (0.000238) test_lambda: .: (0.000218) test_matrix: .: (0.000266) test_message: .: (0.000210) test_pattern: .: (0.000203) test_program: .: (0.000210) test_query_def: .: (0.000221) test_query_len: .: (0.000212) test_reference: .: (0.000229) test_sc_match: .: (0.000249) test_sc_mismatch: .: (0.000240) test_version: .: (0.000208) Bio::TestBlastReportHit: test_Hit_accession: .: (0.006563) test_Hit_bit_score: .: (0.005620) test_Hit_definition: .: (0.004639) test_Hit_evalue: .: (0.006449) test_Hit_hit_id: .: (0.005366) test_Hit_hsps: .: (0.006267) test_Hit_identity: .: (0.004991) test_Hit_lap_at: .: (0.005018) test_Hit_len: .: (0.006453) test_Hit_midline: .: (0.005478) test_Hit_num: .: (0.006224) test_Hit_overlap: .: (0.005032) test_Hit_query_def: .: (0.005128) test_Hit_query_end: .: (0.006501) test_Hit_query_id: .: (0.005461) test_Hit_query_len: .: (0.006167) test_Hit_query_seq: .: (0.005013) test_Hit_query_start: .: (0.005079) test_Hit_taeget_def: .: (0.006306) test_Hit_target_end: .: (0.005421) test_Hit_target_id: .: (0.006070) test_Hit_target_len: .: (0.005036) test_Hit_target_seq: .: (0.004997) test_Hit_target_start: .: (0.006249) Bio::TestBlastReportHitDefault: test_Hit_bit_score: .: (0.000535) test_Hit_definition: .: (0.000249) test_Hit_evalue: .: (0.000247) test_Hit_hsps: .: (0.000289) test_Hit_identity: .: (0.000233) test_Hit_lap_at: .: (0.000305) test_Hit_len: .: (0.000226) test_Hit_midline: .: (0.000293) test_Hit_overlap: .: (0.000222) test_Hit_query_end: .: (0.000350) test_Hit_query_seq: .: (0.000302) test_Hit_query_start: .: (0.000291) test_Hit_taeget_def: .: (0.000222) test_Hit_target_end: .: (0.000398) test_Hit_target_id: .: (0.000296) test_Hit_target_len: .: (0.000240) test_Hit_target_seq: .: (0.000295) test_Hit_target_start: .: (0.000293) Bio::TestBlastReportHitMulti: test_Hit_accession: .: (0.016517) test_Hit_bit_score: .: (0.017160) test_Hit_definition: .: (0.016400) test_Hit_evalue: .: (0.039900) test_Hit_hit_id: .: (0.016738) test_Hit_hsps: .: (0.016249) test_Hit_identity: .: (0.015489) test_Hit_lap_at: .: (0.015395) test_Hit_len: .: (0.016254) test_Hit_midline: .: (0.015716) test_Hit_num: .: (0.015844) test_Hit_overlap: .: (0.016000) test_Hit_query_def: .: (0.015865) test_Hit_query_end: .: (0.015782) test_Hit_query_id: .: (0.014924) test_Hit_query_len: .: (0.016325) test_Hit_query_seq: .: (0.015949) test_Hit_query_start: .: (0.016043) test_Hit_taeget_def: .: (0.016161) test_Hit_target_end: .: (0.016147) test_Hit_target_id: .: (0.015812) test_Hit_target_len: .: (0.014891) test_Hit_target_seq: .: (0.016372) test_Hit_target_start: .: (0.015870) Bio::TestBlastReportHitMultiREXML: test_Hit_accession: .: (0.016164) test_Hit_bit_score: .: (0.016353) test_Hit_definition: .: (0.016222) test_Hit_evalue: .: (0.016040) test_Hit_hit_id: .: (0.015937) test_Hit_hsps: .: (0.014935) test_Hit_identity: .: (0.016513) test_Hit_lap_at: .: (0.016106) test_Hit_len: .: (0.016119) test_Hit_midline: .: (0.016244) test_Hit_num: .: (0.016114) test_Hit_overlap: .: (0.015970) test_Hit_query_def: .: (0.014862) test_Hit_query_end: .: (0.016489) test_Hit_query_id: .: (0.016216) test_Hit_query_len: .: (0.017065) test_Hit_query_seq: .: (0.017013) test_Hit_query_start: .: (0.016769) test_Hit_taeget_def: .: (0.017127) test_Hit_target_end: .: (0.016694) test_Hit_target_id: .: (0.015357) test_Hit_target_len: .: (0.017259) test_Hit_target_seq: .: (0.016610) test_Hit_target_start: .: (0.017002) Bio::TestBlastReportHitREXML: test_Hit_accession: .: (0.005443) test_Hit_bit_score: .: (0.007055) test_Hit_definition: .: (0.005340) test_Hit_evalue: .: (0.005440) test_Hit_hit_id: .: (0.004681) test_Hit_hsps: .: (0.007190) test_Hit_identity: .: (0.005507) test_Hit_lap_at: .: (0.005400) test_Hit_len: .: (0.004733) test_Hit_midline: .: (0.007071) test_Hit_num: .: (0.005281) test_Hit_overlap: .: (0.005346) test_Hit_query_def: .: (0.004784) test_Hit_query_end: .: (0.007246) test_Hit_query_id: .: (0.005406) test_Hit_query_len: .: (0.005376) test_Hit_query_seq: .: (0.004814) test_Hit_query_start: .: (0.007192) test_Hit_taeget_def: .: (0.005289) test_Hit_target_end: .: (0.005179) test_Hit_target_id: .: (0.005828) test_Hit_target_len: .: (0.006130) test_Hit_target_seq: .: (0.005408) test_Hit_target_start: .: (0.005055) Bio::TestBlastReportHitTabular: test_Hit_accession: .: (0.000201) test_Hit_bit_score: .: (0.000082) test_Hit_definition: .: (0.000065) test_Hit_evalue: .: (0.000065) test_Hit_hit_id: .: (0.000069) test_Hit_hsps: .: (0.000062) test_Hit_identity: .: (0.000059) test_Hit_lap_at: .: (0.000069) test_Hit_len: .: (0.000060) test_Hit_midline: .: (0.000062) test_Hit_num: .: (0.000062) test_Hit_overlap: .: (0.000062) test_Hit_query_def: .: (0.000064) test_Hit_query_end: .: (0.000060) test_Hit_query_id: .: (0.000061) test_Hit_query_len: .: (0.000059) test_Hit_query_seq: .: (0.000059) test_Hit_query_start: .: (0.000063) test_Hit_taeget_def: .: (0.000061) test_Hit_target_end: .: (0.000061) test_Hit_target_id: .: (0.000059) test_Hit_target_len: .: (0.000058) test_Hit_target_seq: .: (0.000059) test_Hit_target_start: .: (0.000061) Bio::TestBlastReportHsp: test_Hsp_align_len: .: (0.007377) test_Hsp_bit_score: .: (0.005507) test_Hsp_density: .: (0.005414) test_Hsp_evalue: .: (0.004758) test_Hsp_gaps: .: (0.007072) test_Hsp_hit_frame: .: (0.005474) test_Hsp_hit_from: .: (0.005324) test_Hsp_hit_to: .: (0.004787) test_Hsp_hseq: .: (0.007091) test_Hsp_identity: .: (0.005245) test_Hsp_midline: .: (0.005307) test_Hsp_mismatch_count: .: (0.006142) test_Hsp_num: .: (0.006063) test_Hsp_pattern_from: .: (0.005188) test_Hsp_pattern_to: .: (0.004932) test_Hsp_percent_identity: .: (0.007023) test_Hsp_positive: .: (0.005365) test_Hsp_qseq: .: (0.005501) test_Hsp_query_frame: .: (0.004733) test_Hsp_query_from: .: (0.007252) test_Hsp_query_to: .: (0.005628) test_Hsp_score: .: (0.005434) Bio::TestBlastReportHspDefault: test_Hsp_align_len: .: (0.000401) test_Hsp_bit_score: .: (0.000243) test_Hsp_evalue: .: (0.000233) test_Hsp_gaps: .: (0.000233) test_Hsp_hit_frame: .: (0.000234) test_Hsp_hit_from: .: (0.000332) test_Hsp_hit_to: .: (0.000303) test_Hsp_hseq: .: (0.000317) test_Hsp_identity: .: (0.000235) test_Hsp_midline: .: (0.000311) test_Hsp_percent_identity: .: (0.000234) test_Hsp_positive: .: (0.000235) test_Hsp_qseq: .: (0.000307) test_Hsp_query_frame: .: (0.000232) test_Hsp_query_from: .: (0.000299) test_Hsp_query_to: .: (0.000302) test_Hsp_score: .: (0.000233) Bio::TestBlastReportHspMulti: test_Hsp_align_len: .: (0.017779) test_Hsp_bit_score: .: (0.016330) test_Hsp_density: .: (0.016650) test_Hsp_evalue: .: (0.016844) test_Hsp_gaps: .: (0.016558) test_Hsp_hit_frame: .: (0.017015) test_Hsp_hit_from: .: (0.017198) test_Hsp_hit_to: .: (0.016863) test_Hsp_hseq: .: (0.016995) test_Hsp_identity: .: (0.017211) test_Hsp_midline: .: (0.017232) test_Hsp_mismatch_count: .: (0.016920) test_Hsp_num: .: (0.017077) test_Hsp_pattern_from: .: (0.016997) test_Hsp_pattern_to: .: (0.016941) test_Hsp_percent_identity: .: (0.017062) test_Hsp_positive: .: (0.017045) test_Hsp_qseq: .: (0.016950) test_Hsp_query_frame: .: (0.016506) test_Hsp_query_from: .: (0.016384) test_Hsp_query_to: .: (0.016324) test_Hsp_score: .: (0.016249) Bio::TestBlastReportHspMultiREXML: test_Hsp_align_len: .: (0.016600) test_Hsp_bit_score: .: (0.016433) test_Hsp_density: .: (0.016251) test_Hsp_evalue: .: (0.016137) test_Hsp_gaps: .: (0.016281) test_Hsp_hit_frame: .: (0.016332) test_Hsp_hit_from: .: (0.016213) test_Hsp_hit_to: .: (0.016204) test_Hsp_hseq: .: (0.016107) test_Hsp_identity: .: (0.016120) test_Hsp_midline: .: (0.016111) test_Hsp_mismatch_count: .: (0.016144) test_Hsp_num: .: (0.016095) test_Hsp_pattern_from: .: (0.016110) test_Hsp_pattern_to: .: (0.016234) test_Hsp_percent_identity: .: (0.016094) test_Hsp_positive: .: (0.016114) test_Hsp_qseq: .: (0.016142) test_Hsp_query_frame: .: (0.016201) test_Hsp_query_from: .: (0.016144) test_Hsp_query_to: .: (0.016147) test_Hsp_score: .: (0.016117) Bio::TestBlastReportHspREXML: test_Hsp_align_len: .: (0.005138) test_Hsp_bit_score: .: (0.004629) test_Hsp_density: .: (0.006865) test_Hsp_evalue: .: (0.005172) test_Hsp_gaps: .: (0.005324) test_Hsp_hit_frame: .: (0.005714) test_Hsp_hit_from: .: (0.005974) test_Hsp_hit_to: .: (0.005436) test_Hsp_hseq: .: (0.004589) test_Hsp_identity: .: (0.006545) test_Hsp_midline: .: (0.005125) test_Hsp_mismatch_count: .: (0.005300) test_Hsp_num: .: (0.004634) test_Hsp_pattern_from: .: (0.006606) test_Hsp_pattern_to: .: (0.005182) test_Hsp_percent_identity: .: (0.005176) test_Hsp_positive: .: (0.005586) test_Hsp_qseq: .: (0.005852) test_Hsp_query_frame: .: (0.005550) test_Hsp_query_from: .: (0.004644) test_Hsp_query_to: .: (0.006744) test_Hsp_score: .: (0.005339) Bio::TestBlastReportHspTabular: test_Hsp_align_len: .: (0.000182) test_Hsp_bit_score: .: (0.000072) test_Hsp_density: .: (0.000085) test_Hsp_evalue: .: (0.000066) test_Hsp_gaps: .: (0.000065) test_Hsp_hit_frame: .: (0.000061) test_Hsp_hit_from: .: (0.000060) test_Hsp_hit_to: .: (0.000059) test_Hsp_hseq: .: (0.000059) test_Hsp_identity: .: (0.000067) test_Hsp_midline: .: (0.000060) test_Hsp_mismatch_count: .: (0.000059) test_Hsp_num: .: (0.000060) test_Hsp_pattern_from: .: (0.000059) test_Hsp_pattern_to: .: (0.000057) test_Hsp_percent_identity: .: (0.000057) test_Hsp_positive: .: (0.000256) test_Hsp_qseq: .: (0.000062) test_Hsp_query_frame: .: (0.000059) test_Hsp_query_from: .: (0.000061) test_Hsp_query_to: .: (0.000059) test_Hsp_score: .: (0.000057) Bio::TestBlastReportIteration: test_hits: .: (0.005084) test_message: .: (0.006067) test_num: .: (0.006102) test_statistics: .: (0.005571) Bio::TestBlastReportIterationDefault: test_hits: .: (0.000359) test_message: .: (0.000216) test_num: .: (0.000207) Bio::TestBlastReportIterationMulti: test_each: .: (0.016272) test_hits: .: (0.016417) test_message: .: (0.016308) test_num: .: (0.016128) test_query_def: .: (0.016171) test_query_id: .: (0.016275) test_query_len: .: (0.016120) test_statistics: .: (0.016212) Bio::TestBlastReportIterationMultiREXML: test_each: .: (0.016337) test_hits: .: (0.016120) test_message: .: (0.016202) test_num: .: (0.016209) test_query_def: .: (0.016284) test_query_id: .: (0.016225) test_query_len: .: (0.016117) test_statistics: .: (0.016139) Bio::TestBlastReportIterationREXML: test_hits: .: (0.005183) test_message: .: (0.006535) test_num: .: (0.005263) test_statistics: .: (0.005328) Bio::TestBlastReportIterationTabular: test_hits: .: (0.000174) test_message: .: (0.000070) test_num: .: (0.000062) test_statistics: .: (0.000060) Bio::TestBlastReportMulti: test_db: .: (0.016319) test_db_len: .: (0.016186) test_db_num: .: (0.016313) test_each_hit: .: (0.016223) test_each_iteration: .: (0.016171) test_eff_space: .: (0.016280) test_entropy: .: (0.016184) test_expect: .: (0.016137) test_filter: .: (0.016078) test_gap_extend: .: (0.016152) test_gap_open: .: (0.016262) test_hits: .: (0.016127) test_hsp_len: .: (0.016308) test_iterations: .: (0.016353) test_kappa: .: (0.016256) test_lambda: .: (0.016120) test_matrix: .: (0.016013) test_message: .: (0.016249) test_parameters: .: (0.016375) test_pattern: .: (0.016253) test_program: .: (0.016164) test_query_def: .: (0.016054) test_query_id: .: (0.015938) test_query_len: .: (0.016086) test_reference: .: (0.016061) test_reports: .: (0.016024) test_statistics: .: (0.016003) test_version: .: (0.016077) Bio::TestBlastReportMultiREXML: test_db: .: (0.016235) test_db_len: .: (0.016119) test_db_num: .: (0.016158) test_each_hit: .: (0.016145) test_each_iteration: .: (0.016084) test_eff_space: .: (0.016210) test_entropy: .: (0.015977) test_expect: .: (0.016780) test_filter: .: (0.016218) test_gap_extend: .: (0.016935) test_gap_open: .: (0.016489) test_hits: .: (0.040026) test_hsp_len: .: (0.016452) test_iterations: .: (0.016225) test_kappa: .: (0.016963) test_lambda: .: (0.016782) test_matrix: .: (0.016517) test_message: .: (0.039773) test_parameters: .: (0.016430) test_pattern: .: (0.016810) test_program: .: (0.016644) test_query_def: .: (0.017254) test_query_id: .: (0.039351) test_query_len: .: (0.016607) test_reference: .: (0.014738) test_reports: .: (0.016780) test_statistics: .: (0.016398) test_version: .: (0.016403) Bio::TestBlastReportREXML: test_db: .: (0.005404) test_db_len: .: (0.005393) test_db_num: .: (0.004633) test_each_hit: .: (0.006880) test_each_iteration: .: (0.005357) test_eff_space: .: (0.005250) test_entrez_query: .: (0.004686) test_entropy: .: (0.005726) test_expect: .: (0.006132) test_filter: .: (0.005279) test_gap_extend: .: (0.004950) test_gap_open: .: (0.004595) test_hits: .: (0.006929) test_hsp_len: .: (0.005317) test_inclusion: .: (0.005262) test_iterations: .: (0.004715) test_kappa: .: (0.004579) test_lambda: .: (0.007110) test_matrix: .: (0.005180) test_message: .: (0.005233) test_parameters: .: (0.004654) test_pattern: .: (0.006376) test_program: .: (0.005802) test_query_def: .: (0.005184) test_query_id: .: (0.004875) test_query_len: .: (0.004583) test_reference: .: (0.006927) test_sc_match: .: (0.005299) test_sc_mismatch: .: (0.005138) test_statistics: .: (0.004641) test_version: .: (0.006292) Bio::TestBlastReportTabular: test_db: .: (0.000230) test_db_len: .: (0.000070) test_db_num: .: (0.000067) test_each_hit: .: (0.000065) test_each_iteration: .: (0.000058) test_eff_space: .: (0.000059) test_entrez_query: .: (0.000062) test_entropy: .: (0.000057) test_expect: .: (0.000057) test_filter: .: (0.000056) test_gap_extend: .: (0.000055) test_gap_open: .: (0.000056) test_hits: .: (0.000579) test_hsp_len: .: (0.000171) test_inclusion: .: (0.000067) test_iterations: .: (0.000060) test_kappa: .: (0.000058) test_lambda: .: (0.000057) test_matrix: .: (0.000056) test_message: .: (0.000060) test_parameters: .: (0.000058) test_pattern: .: (0.000057) test_program: .: (0.000055) test_query_def: .: (0.000058) test_query_id: .: (0.000058) test_query_len: .: (0.000055) test_reference: .: (0.000056) test_sc_match: .: (0.000057) test_sc_mismatch: .: (0.000056) test_statistics: .: (0.000057) test_version: .: (0.000055) Bio::TestChain: test_aaseq: .: (0.000328) test_addLigand: .: (0.000049) test_addResidue: .: (0.000057) test_atom_seq: .: (0.000048) test_comp: .: (0.000062) test_each: .: (0.000048) test_each_heterogen: .: (0.000046) test_each_residue: .: (0.000044) test_get_heterogen_by_id: .: (0.000042) test_get_residue_by_id: .: (0.000041) test_inspect: .: (0.000055) test_rehash: .: (0.000051) test_rehash_heterogens: .: (0.000038) test_rehash_residues: .: (0.000040) test_square_brace: .: (0.000044) test_to_s: .: (0.000053) Bio::TestChainFinder: test_chains: .: (0.000245) test_each_chain: .: (0.000056) test_find_chain: .: (0.000046) Bio::TestClustalWReport::TestClustalWReport: test_alignment: .: (0.004039) test_header: .: (0.000273) test_match_line: .: (0.000297) test_sequence0: .: (0.000253) test_sequence1: .: (0.000295) Bio::TestClustalWReport::TestClustalWReportSeqnos: test_alignment: .: (0.004036) test_header: .: (0.000380) test_match_line: .: (0.000414) test_sequence0: .: (0.000394) test_sequence1: .: (0.000417) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: test_alignment: .: (0.005770) test_header: .: (0.000331) test_match_line: .: (0.000249) test_sequence0: .: (0.000256) test_sequence1: .: (0.000251) Bio::TestCodonTable: test_Tables: .: (0.000110) test_accessor: .: (0.000056) test_definition: .: (0.000035) test_each: .: (0.000638) test_revtrans: .: (0.000088) test_self_accessor: .: (0.000039) test_self_copy: .: (0.000371) test_set_accessor: .: (0.040134) test_start: .: (0.000072) test_start_codon?: .: (0.000048) test_stop: .: (0.000035) test_stop_codon?: .: (0.000039) test_table: .: (0.000037) Bio::TestCodonTableConstants: test_Definitions: .: (0.000119) test_Starts: .: (0.000042) test_Tables: .: (0.000033) test_stops: .: (0.000037) Bio::TestColorScheme: test_buried: .: (0.000529) Bio::TestCommand: test_command_constants: .: (0.000110) test_escape_shell: .: (0.000067) test_escape_shell_unix: .: (0.000047) test_escape_shell_windows: .: (0.000052) test_make_cgi_params_by_array_of_array: .: (0.000156) test_make_cgi_params_by_array_of_hash: .: (0.000131) test_make_cgi_params_by_array_of_string: .: (0.000064) test_make_cgi_params_by_hash_in_string: .: (0.000192) test_make_cgi_params_by_hash_in_symbol: .: (0.000181) test_make_cgi_params_by_string: .: (0.000100) test_make_command_line: .: (0.000055) test_make_command_line_unix: .: (0.000045) test_make_command_line_windows: .: (0.000048) test_safe_command_line_array: .: (0.000055) test_safe_command_line_array_passthrough: .: (0.000048) Bio::TestContingencyTable: test_lite_example: .: (0.063334) Bio::TestDB: test_entry_id: .: (0.000170) test_exists: .: (0.000043) test_fetch: .: (0.000077) test_get: .: (0.000040) test_open: .: (0.000036) test_tags: .: (0.000038) Bio::TestDataType: test_const_like_method: .: (0.000284) test_pdb_achar: .: (0.000107) test_pdb_atom: .: (0.000083) test_pdb_character: .: (0.000081) test_pdb_date: .: (0.000081) test_pdb_idcode: .: (0.000081) test_pdb_integer: .: (0.000045) test_pdb_list: .: (0.000043) test_pdb_lstring: .: (0.000078) test_pdb_real: .: (0.000061) test_pdb_resudue_name: .: (0.000082) test_pdb_slist: .: (0.000042) test_pdb_string: .: (0.000080) test_pdb_stringrj: .: (0.000039) test_pdb_symop: .: (0.000075) test_specification_list: .: (0.000049) Bio::TestEMBL: test_ac: .: (0.000271) test_accession: .: (0.000151) test_cc: .: (0.000126) test_de: .: (0.000146) test_division: .: (0.000154) test_dr: .: (0.000127) test_dt: .: (0.000134) test_dt_created: .: (0.000130) test_dt_iterator: /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/db/embl/test_embl.rb:103: warning: the block passed to 'Bio::EMBL#dt' defined at /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl.rb:182 may be ignored .: (0.000141) test_dt_updated: .: (0.000125) test_each_cds: .: (0.000250) test_each_gene: .: (0.000201) test_entry: .: (0.000175) test_fh: .: (0.000144) test_ft: .: (0.000219) test_ft_accessor: .: (0.000211) test_ft_iterator: .: (0.000222) test_id_line: .: (0.000161) test_id_line_data_class: .: (0.000153) test_id_line_division: .: (0.000146) test_id_line_entry_name: .: (0.000155) test_id_line_iterator: /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/db/embl/test_embl.rb:32: warning: the block passed to 'Bio::EMBL#id_line' defined at /build/reproducible-path/ruby-bio-2.0.6/lib/bio/db/embl/embl.rb:89 may be ignored .: (0.000170) test_id_line_molecule_type: .: (0.002021) test_id_line_sequence_length: .: (0.000215) test_kw: .: (0.000155) test_molecule: .: (0.000156) test_oc: .: (0.000176) test_og: .: (0.000129) test_os: .: (0.000159) test_ref: .: (0.000749) test_references: .: (0.000345) test_seq: .: (0.000274) test_sequence_length: .: (0.000152) test_sq: .: (0.000143) test_sq_get: .: (0.000137) test_sv: .: (0.001027) test_version: .: (0.000152) Bio::TestEMBL89: test_ac: .: (0.000219) test_accession: .: (0.000140) test_cc: .: (0.000119) test_de: .: (0.000141) test_division: .: (0.000328) test_dr: .: (0.000139) test_dt: .: (0.000130) test_dt_created: .: (0.000121) test_dt_iterator: .: (0.000115) test_dt_updated: .: (0.000119) test_each_cds: .: (0.000206) test_each_gene: .: (0.000190) test_entry: .: (0.000315) test_fh: .: (0.000133) test_ft: .: (0.000193) test_ft_accessor: .: (0.000220) test_ft_iterator: .: (0.000206) test_id_line: .: (0.000148) test_id_line_data_class: .: (0.000285) test_id_line_division: .: (0.000153) test_id_line_entry_name: .: (0.000140) test_id_line_iterator: .: (0.000138) test_id_line_molecule_type: .: (0.000138) test_id_line_sequence_length: .: (0.000137) test_id_line_sequence_version: .: (0.000137) test_kw: .: (0.000132) test_molecule: .: (0.000360) test_oc: .: (0.000174) test_og: .: (0.000116) test_os: .: (0.000143) test_ref: .: (0.000173) test_references: .: (0.000232) test_seq: .: (0.000460) test_sequence_length: .: (0.000158) test_sq: .: (0.000154) test_sq_get: .: (0.000143) test_sv: .: (0.000158) test_version: .: (0.000158) Bio::TestEMBLAPI: test_ac: .: (0.000198) test_accessions: .: (0.000067) Bio::TestEMBLCommon: test_ac: .: (0.000288) test_accession: .: (0.000040) test_accessions: .: (0.000038) test_de: .: (0.000035) test_definition: .: (0.000035) test_description: .: (0.000034) test_dr: .: (0.000036) test_keywords: .: (0.000036) test_kw: .: (0.000037) test_oc: .: (0.000035) test_og: .: (0.000035) test_os: .: (0.000035) test_ref: .: (0.000036) test_references: .: (0.000037) Bio::TestEMBLDB: test_fetch: .: (0.000129) test_p_entry2hash: .: (0.000037) Bio::TestEMBLToBioSequence: test_classification: .: (0.001748) test_date_created: .: (0.000281) test_date_modified: .: (0.000226) test_definition: .: (0.000172) test_division: .: (0.000170) test_entry_id: .: (0.000338) test_entry_version: .: (0.000184) test_features: .: (0.000225) test_keywords: .: (0.000160) test_molecule_type: .: (0.000167) test_primary_accession: .: (0.000153) test_references: .: (0.000264) test_release_created: .: (0.000162) test_release_modified: .: (0.000149) test_secondary_accessions: .: (0.000183) test_sequence_version: .: (0.000179) test_species: .: (0.000156) test_topology: .: (0.000189) Bio::TestEMBLToBioSequenceRoundTrip: test_classification: .: (0.001444) test_date_created: .: (0.001293) test_date_modified: .: (0.001327) test_definition: .: (0.001268) test_division: .: (0.003682) test_entry_id: .: (0.001958) test_entry_version: .: (0.001890) test_features: .: (0.001380) test_keywords: .: (0.001387) test_molecule_type: .: (0.001425) test_primary_accession: .: (0.001375) test_references: .: (0.001554) test_release_created: .: (0.001391) test_release_modified: .: (0.001414) test_secondary_accessions: .: (0.001199) test_sequence_version: .: (0.001186) test_species: .: (0.001185) test_topology: .: (0.003331) Bio::TestFasta: test_db: .: (0.000229) test_format: .: (0.000043) test_format_arg_integer: .: (0.000047) test_format_arg_str: .: (0.000040) test_ktup: .: (0.000040) test_matrix: .: (0.000038) test_option: .: (0.000063) test_options: .: (0.000042) test_output: .: (0.000033) test_program: .: (0.000038) test_server: .: (0.000038) Bio::TestFastaDeflineEmb: test_acc_version: .: (0.000118) test_accession: .: (0.000050) test_accessions: .: (0.000636) test_description: .: (0.000057) test_descriptions: .: (0.000054) test_entry_id: .: (0.000044) test_get_all_by_type: .: (0.000044) test_gi: .: (0.000045) test_id_strings: .: (0.000079) test_list_ids: .: (0.000046) test_locus: .: (0.000045) test_words: .: (0.000062) Bio::TestFastaDeflineGI1: test_acc_version: .: (0.000120) test_accession: .: (0.000053) test_accessions: .: (0.000052) test_description: .: (0.000048) test_descriptions: .: (0.000047) test_emb: .: (0.000057) test_entry_id: .: (0.000495) test_get_all_by_type: .: (0.000049) test_get_emb: .: (0.000051) test_gi: .: (0.000046) test_id_strings: .: (0.000072) test_list_ids: .: (0.000047) test_locus: .: (0.000048) test_words: .: (0.000068) Bio::TestFastaDeflineGI2: test_acc_version: .: (0.000105) test_accession: .: (0.000050) test_accessions: .: (0.000046) test_description: .: (0.000041) test_descriptions: .: (0.000041) test_entry_id: .: (0.000040) test_get_all_by_type: .: (0.000041) test_gi: .: (0.000042) test_id_strings: .: (0.000061) test_list_ids: .: (0.000043) test_locus: .: (0.000043) test_sp: .: (0.000049) test_words: .: (0.000182) Bio::TestFastaDeflineGIMultiple: test_acc_version: .: (0.000122) test_accession: .: (0.000065) test_accessions: .: (0.000069) test_description: .: (0.000058) test_descriptions: .: (0.000058) test_entry_id: .: (0.000064) test_get_all_by_type: .: (0.000060) test_gi: .: (0.000059) test_id_strings: .: (0.000120) test_list_ids: .: (0.000062) test_locus: .: (0.000061) test_words: .: (0.000122) Bio::TestFastaDeflineSce: test_acc_version: .: (0.000111) test_accession: .: (0.000058) test_accessions: .: (0.000054) test_description: .: (0.000227) test_descriptions: .: (0.000055) test_entry_id: .: (0.000052) test_get_all_by_type: .: (0.000053) test_gi: .: (0.000053) test_id_strings: .: (0.000094) test_list_ids: .: (0.000056) test_locus: .: (0.000052) test_words: .: (0.000093) Bio::TestFastaDeflineSimple: test_acc_version: .: (0.000091) test_accession: .: (0.000042) test_accessions: .: (0.000040) test_description: .: (0.000038) test_descriptions: .: (0.000038) test_entry_id: .: (0.000037) test_get_all_by_type: .: (0.000038) test_gi: .: (0.000038) test_id_strings: .: (0.000051) test_list_ids: .: (0.000038) test_locus: .: (0.000038) test_words: .: (0.000238) Bio::TestFastaDeflineSwissProt: test_acc_version: .: (0.000099) test_accession: .: (0.000050) test_accessions: .: (0.000045) test_description: .: (0.000041) test_descriptions: .: (0.000041) test_entry_id: .: (0.000040) test_get: .: (0.000065) test_get_all_by_type: .: (0.000041) test_id_strings: .: (0.000075) test_list_ids: .: (0.000042) test_locus: .: (0.000042) test_sp: .: (0.000046) test_words: .: (0.000077) Bio::TestFastaDeflineTrembl: test_acc_version: .: (0.000101) test_accession: .: (0.000048) test_accessions: .: (0.000246) test_description: .: (0.000045) test_descriptions: .: (0.000042) test_entry_id: .: (0.000040) test_get: .: (0.000046) test_get_all_by_type: .: (0.000042) test_id_strings: .: (0.000088) test_list_ids: .: (0.000042) test_locus: .: (0.000042) test_tr: .: (0.000047) test_words: .: (0.000091) Bio::TestFastaFirstName: test_first_name1: .: (0.000096) test_first_name_multi_identifier: .: (0.000041) test_first_name_single_worded_defintion: .: (0.000037) test_no_definition: .: (0.000036) test_space_before_first_name: .: (0.000037) test_tabbed_defintion: .: (0.000038) Bio::TestFastaFormat: test_aalen: .: (0.000104) test_aaseq: .: (0.000049) test_acc_version: .: (0.000076) test_accession: .: (0.000060) test_accessions: .: (0.000061) test_data: .: (0.000042) test_definition: .: (0.000041) test_entry: .: (0.000042) test_entry_id: .: (0.000055) test_entry_overrun: .: (0.000041) test_first_name: .: (0.000042) test_gi: .: (0.000056) test_identifiers: .: (0.000059) test_length: .: (0.000047) test_query: .: (0.000055) test_seq: .: (0.000045) Bio::TestFastaFormatConst: test_delimiter: .: (0.000088) Bio::TestFastaFormatKeggGenesAA: test_acc_version: .: (0.000113) test_data: .: (0.000045) test_definition: .: (0.000045) test_entry: .: (0.000043) test_entry_id: .: (0.000064) test_first_name: .: (0.000044) Bio::TestFastaFormatKeggGenesNT: test_nalen: .: (0.000092) test_naseq: .: (0.000043) test_naseq_class: .: (0.000043) Bio::TestFastaFormatSwissProt: test_locus: .: (0.000107) Bio::TestFastaInitialize: test_new_1: .: (0.000317) test_option: .: (0.000041) test_option_backward_compatibility: .: (0.000056) Bio::TestFastaNumericFormat: test_arg: .: (0.000117) test_data: .: (0.000060) test_definition: .: (0.000039) test_each: .: (0.000055) test_entry: .: (0.000037) test_entry_id: .: (0.000044) test_length: .: (0.000052) test_to_biosequence: .: (0.000400) Bio::TestFastaQuery: test_query: .: (0.000812) test_self_local: .: (0.000031) test_self_parser: .: (0.000026) test_self_remote: .: (0.000025) Bio::TestFastacmd: test_database: .: (0.001210) test_fastacmd: .: (0.000039) test_methods: .: (0.000050) Bio::TestFastq::TestFastq_error_diff_ids: test_validate_format: .: (0.001480) Bio::TestFastq::TestFastq_error_double_qual: test_validate_format: .: (0.000964) Bio::TestFastq::TestFastq_error_double_seq: test_validate_format: .: (0.000600) Bio::TestFastq::TestFastq_error_long_qual: test_validate_format: .: (0.001847) Bio::TestFastq::TestFastq_error_no_qual: test_validate_format: .: (0.001760) Bio::TestFastq::TestFastq_error_qual_del: test_validate_format: .: (0.000980) Bio::TestFastq::TestFastq_error_qual_escape: test_validate_format: .: (0.000951) Bio::TestFastq::TestFastq_error_qual_null: test_validate_format: .: (0.002071) Bio::TestFastq::TestFastq_error_qual_space: test_validate_format: .: (0.001559) Bio::TestFastq::TestFastq_error_qual_tab: test_validate_format: .: (0.001453) Bio::TestFastq::TestFastq_error_qual_unit_sep: test_validate_format: .: (0.000701) Bio::TestFastq::TestFastq_error_qual_vtab: test_validate_format: .: (0.000529) Bio::TestFastq::TestFastq_error_short_qual: test_validate_format: .: (0.001493) Bio::TestFastq::TestFastq_error_spaces: test_validate_format: .: (0.001542) Bio::TestFastq::TestFastq_error_tabs: test_validate_format: .: (0.002265) Bio::TestFastq::TestFastq_error_trunc_at_plus: test_validate_format: .: (0.002371) Bio::TestFastq::TestFastq_error_trunc_at_qual: test_validate_format: .: (0.000955) Bio::TestFastq::TestFastq_error_trunc_at_seq: test_validate_format: .: (0.000860) Bio::TestFastq::TestFastq_illumina_full_range: test_error_probabilities_as_illumina: .: (0.003200) test_error_probabilities_as_sanger: .: (0.001525) test_error_probabilities_as_solexa: .: (0.001411) test_quality_scores_as_illumina: .: (0.000176) test_quality_scores_as_sanger: .: (0.000138) test_quality_scores_as_solexa: .: (0.000147) test_validate_format: .: (0.000259) Bio::TestFastq::TestFastq_longreads_original_sanger: test_definition: .: (0.000619) test_entry_id: .: (0.000407) test_error_probabilities: .: (0.035672) test_nalen: .: (0.000431) test_naseq: .: (0.000372) test_quality_scores: .: (0.000982) test_quality_string: .: (0.000327) test_roundtrip: .: (0.037132) test_seq: .: (0.000402) test_sequence_string: .: (0.000490) test_to_biosequence: .: (0.032592) test_to_biosequence_and_output: .: (0.002119) test_to_s: .: (0.000351) test_validate_format: .: (0.000364) test_validate_format_with_array: .: (0.000547) Bio::TestFastq::TestFastq_mask: test_mask_20: .: (0.000295) test_mask_20_with_empty_string: .: (0.000169) test_mask_20_with_longer_string: .: (0.000162) test_mask_20_with_x: .: (0.000165) test_mask_60: .: (0.000197) Bio::TestFastq::TestFastq_sanger_full_range: test_error_probabilities_as_illumina: .: (0.001675) test_error_probabilities_as_sanger: .: (0.001699) test_error_probabilities_as_solexa: .: (0.001507) test_quality_scores_as_illumina: .: (0.000165) test_quality_scores_as_sanger: .: (0.000132) test_quality_scores_as_solexa: .: (0.000164) test_validate_format: .: (0.000263) Bio::TestFastq::TestFastq_solexa_full_range: test_error_probabilities_as_illumina: .: (0.001147) test_error_probabilities_as_sanger: .: (0.001118) test_error_probabilities_as_solexa: .: (0.001069) test_quality_scores_as_illumina: .: (0.000170) test_quality_scores_as_sanger: .: (0.000151) test_quality_scores_as_solexa: .: (0.000122) test_validate_format: .: (0.000256) Bio::TestFeature: test_append: .: (0.000108) test_append_nil: .: (0.000041) test_assoc: .: (0.000047) test_each: .: (0.000037) test_feature: .: (0.000033) test_locations: .: (0.000081) test_new: .: (0.000035) test_position: .: (0.000034) test_qualifiers: .: (0.000034) Bio::TestFeatures: test_append: .: (0.000125) test_arg: .: (0.000044) test_each: .: (0.000040) test_features: .: (0.000062) Bio::TestFlatFile::TestDefaultAutoDetect: test_aaindex1: .: (0.000532) test_aaindex2: .: (0.000136) test_blast: .: (0.000103) test_blastxml: .: (0.000488) test_embl: .: (0.000157) test_embl_oldrelease: .: (0.000139) test_fastaformat: .: (0.000235) test_fastanumericformat: .: (0.000067) test_fastq: .: (0.000082) test_genbank: .: (0.000114) test_genpept: .: (0.000127) test_hmmer: .: (0.000100) test_maxml_cluster: .: (0.001514) test_maxml_sequence: .: (0.000058) test_medline: .: (0.000074) test_prosite: .: (0.002837) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. .: (0.002112) test_transfac: .: (0.000769) Bio::TestFlatFile::TestFlatFileClassMethod: test_auto_0arg: .: (0.000138) test_auto_1arg_filename: .: (0.000199) test_auto_1arg_io: .: (0.000160) test_auto_1arg_io_with_block: .: (0.000322) test_auto_1arg_with_block: .: (0.000294) test_auto_2arg_filename_mode: .: (0.000170) test_auto_2arg_filename_mode_with_block: .: (0.000315) test_auto_3arg: .: (0.000170) test_auto_3arg_with_block: .: (0.000299) test_foreach: .: (0.000280) test_new_2arg_class: .: (0.000089) test_new_2arg_nil: .: (0.000150) test_open_0arg: .: (0.000059) test_open_1arg_class: .: (0.000050) test_open_1arg_filename: .: (0.000158) test_open_1arg_io: .: (0.000151) test_open_1arg_io_with_block: .: (0.000322) test_open_1arg_nil: .: (0.000063) test_open_1arg_with_block: .: (0.001979) test_open_2arg_autodetect: .: (0.000191) test_open_2arg_autodetect_io: .: (0.000150) test_open_2arg_autodetect_io_with_block: .: (0.000302) test_open_2arg_autodetect_with_block: .: (0.000296) test_open_2arg_class: .: (0.000085) test_open_2arg_class_io: .: (0.000583) test_open_2arg_class_io_with_block: .: (0.000244) test_open_2arg_class_with_block: .: (0.000217) test_open_2arg_filename_mode: .: (0.000168) test_open_2arg_filename_mode_with_block: .: (0.000293) test_open_3arg: .: (0.000311) test_open_3arg_with_block: .: (0.001346) test_open_4arg: .: (0.000622) test_to_a: .: (0.000272) Bio::TestFlatFile::TestFlatFileFastaFormat: test_autodetect: .: (0.000736) test_close: .: (0.000073) test_dbclass: .: (0.000061) test_dbclass_eq: .: (0.000075) test_dbclass_nil: .: (0.000097) test_each: .: (0.000131) test_each_entry: .: (0.000200) test_ended_pos: .: (0.000138) test_entry_pos_flag: .: (0.000077) test_entry_raw: .: (0.000167) test_eof?: .: (0.000150) test_next_entry: .: (0.000200) test_path: .: (0.000075) test_pos: .: (0.000110) test_raw: .: (0.000655) test_rewind: .: (0.000143) test_start_pos: .: (0.000113) test_start_pos_ended_pos_not_recorded: .: (0.000115) test_to_io: .: (0.000070) Bio::TestFlatFile::TestFlatFileWithCustomClass: test_simpleformat: .: (0.000149) test_simpleformat2: .: (0.000090) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: test_close: .: (0.000102) test_eof_false_after_prefetch: .: (0.000080) test_eof_false_first: .: (0.000044) test_eof_true: .: (0.000070) test_getc: .: (0.000046) test_getc_after_prefetch: .: (0.000047) test_gets: .: (0.000045) test_gets_equal_prefetch_gets: .: (0.000049) test_gets_paragraph_mode: .: (0.000579) test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000176) test_gets_paragraph_mode_within_buffer: .: (0.000167) test_gets_rs: .: (0.000063) test_gets_rs_equal_prefetch_gets: .: (0.000064) test_gets_rs_within_buffer: .: (0.000120) test_pos: .: (0.000050) test_pos=: .: (0.000054) test_prefetch_buffer: .: (0.000066) test_prefetch_gets: .: (0.000050) test_prefetch_gets_with_arg: .: (0.000059) test_rewind: .: (0.000044) test_skip_spaces: .: (0.000052) test_to_io: .: (0.000053) test_ungetc: .: (0.000051) test_ungetc_after_prefetch: .: (0.000052) test_ungets: .: (0.000078) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: test_self_for_io: .: (0.000112) test_self_open_file: .: (0.027194) test_self_open_file_with_block: .: (0.000073) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: test_parse_file_open_arg_int_opt: .: (0.000544) test_parse_file_open_arg_int_perm: .: (0.000041) test_parse_file_open_arg_int_perm_opt: .: (0.000038) test_parse_file_open_arg_integer: .: (0.000035) test_parse_file_open_arg_nil: .: (0.000033) test_parse_file_open_arg_opt: .: (0.000054) test_parse_file_open_arg_opt_with_integer_mode: .: (0.000043) test_parse_file_open_arg_str: .: (0.000044) test_parse_file_open_arg_str_opt: .: (0.000044) test_parse_file_open_arg_str_perm: .: (0.000039) test_parse_file_open_arg_str_perm_opt: .: (0.000044) test_parse_file_open_arg_str_with_enc: .: (0.000043) test_parse_file_open_arg_str_with_ext_enc: .: (0.000040) test_parse_file_open_mode_integer: .: (0.000036) test_parse_file_open_mode_nil: .: (0.000042) test_parse_file_open_mode_str: .: (0.000040) test_parse_file_open_mode_str_with_enc: .: (0.000039) test_parse_file_open_mode_str_with_ext_enc: .: (0.000042) Bio::TestFlatFileSplitter::TestTemplate: test_dbclass: .: (0.000104) test_entry: .: (0.000045) test_entry_ended_pos: .: (0.000042) test_entry_pos_flag: .: (0.000047) test_entry_start_pos: .: (0.000298) test_get_entry: .: (0.000068) test_rewind: .: (0.000048) test_skip_leader: .: (0.000047) test_stream: .: (0.000036) test_stream_pos: .: (0.000047) Bio::TestFlatFileSplitter::TestDefault: test_delimiter: .: (0.000100) test_delimiter_overrun: .: (0.000037) test_entry: .: (0.000056) test_entry_ended_pos: .: (0.000049) test_entry_ended_pos_default_nil: .: (0.000046) test_entry_start_pos: .: (0.000047) test_entry_start_pos_default_nil: .: (0.000044) test_get_entry: .: (0.000086) test_get_parsed_entry: .: (0.000095) test_header: .: (0.000037) test_skip_leader: .: (0.000055) test_skip_leader_without_header: .: (0.000056) Bio::TestFlatFileSplitter::TestLineOriented: test_dbclass: .: (0.000157) test_entry_ended_pos: .: (0.000270) test_entry_start_pos: .: (0.000086) test_flag_to_fetch_header: .: (0.000081) test_get_entry: .: (0.000121) test_get_parsed_entry: .: (0.000121) test_rewind: .: (0.000089) test_skip_leader: .: (0.000054) Bio::TestGCGMsf: test_alignment: .: (0.000491) test_checksum: .: (0.000099) test_compcheck: .: (0.000092) test_date: .: (0.000255) test_description: .: (0.000092) test_entry_id: .: (0.000089) test_gap_length_weight: .: (0.000090) test_gap_weight: .: (0.000088) test_heading: .: (0.000086) test_length: .: (0.000086) test_seq_type: .: (0.000086) test_symbol_comparison_table: .: (0.000088) test_validate_checksum: .: (0.000572) Bio::TestGFF: test_record_class: .: (0.000255) test_records: .: (0.000341) Bio::TestGFF2: test_const_version: .: (0.000288) test_gff_version: .: (0.000192) test_metadata: .: (0.000194) test_metadata_size: .: (0.000362) test_records_size: .: (0.000183) test_to_s: .: (0.000309) Bio::TestGFF2ComplexAttributes: test_attributes_case1: .: (0.000117) test_attributes_case2: .: (0.000081) test_attributes_incompatible_backslash_semicolon: .: (0.000100) Bio::TestGFF2MetaData: test_data: .: (0.000079) test_directive: .: (0.000035) test_parse: .: (0.000044) Bio::TestGFF2Record: test_attribute: .: (0.000220) test_attribute_nonexistent: .: (0.000122) test_attributes: .: (0.000133) test_attributes_to_hash: .: (0.000135) test_comment_only?: .: (0.000119) test_delete_attribute: .: (0.000339) test_delete_attribute_multiple: .: (0.000143) test_delete_attribute_multiple2: .: (0.000148) test_delete_attribute_multiple_nil: .: (0.000133) test_delete_attribute_nil: .: (0.000140) test_delete_attribute_nonexistent: .: (0.000131) test_delete_attributes: .: (0.000314) test_delete_attributes_multiple: .: (0.000135) test_delete_attributes_nonexistent: .: (0.000130) test_end: .: (0.000119) test_eqeq: .: (0.000307) test_eqeq_false: .: (0.000436) test_feature: .: (0.000121) test_frame: .: (0.000116) test_get_attribute: .: (0.000158) test_get_attribute_nonexistent: .: (0.000120) test_get_attributes: .: (0.000160) test_get_attributes_nonexistent: .: (0.000187) test_replace_attributes: .: (0.000139) test_replace_attributes_multiple_multiple_over: .: (0.000140) test_replace_attributes_multiple_multiple_same: .: (0.000133) test_replace_attributes_multiple_multiple_two: .: (0.000149) test_replace_attributes_multiple_single: .: (0.000134) test_replace_attributes_nonexistent: .: (0.000132) test_replace_attributes_nonexistent_multiple: .: (0.000134) test_replace_attributes_single_multiple: .: (0.000148) test_score: .: (0.000121) test_self_parse: .: (0.000298) test_seqname: .: (0.000121) test_set_attribute: .: (0.000135) test_set_attribute_multiple: .: (0.000134) test_set_attribute_nonexistent: .: (0.000133) test_sort_attributes_by_tag!: .: (0.000170) test_sort_attributes_by_tag_bang_test2: .: (0.000160) test_sort_attributes_by_tag_bang_with_block: .: (0.000152) test_source: .: (0.000117) test_start: .: (0.000118) test_strand: .: (0.000115) test_to_s: .: (0.000182) Bio::TestGFF2RecordEmpty: test_comment: .: (0.000101) test_comment_eq: .: (0.000040) test_comment_only?: .: (0.000039) test_comment_only_false: .: (0.000036) test_to_s: .: (0.000041) test_to_s_not_empty: .: (0.000068) Bio::TestGFF3: test_const_version: .: (0.000335) test_gff_version: .: (0.000231) test_records: .: (0.000292) test_sequence_regions: .: (0.000229) test_sequences: .: (0.000263) test_to_s: .: (0.000422) Bio::TestGFF3MetaData: test_data: .: (0.000094) test_directive: .: (0.000035) test_parse: .: (0.000042) Bio::TestGFF3Record: test_attributes: .: (0.000165) test_end: .: (0.000096) test_feature: .: (0.000092) test_frame: .: (0.000088) test_id: .: (0.000091) test_score: .: (0.000087) test_seqname: .: (0.000087) test_source: .: (0.000090) test_start: .: (0.000094) test_strand: .: (0.000094) test_to_s: .: (0.000167) test_to_s_attr_order_changed: .: (0.000194) Bio::TestGFF3RecordEscape: test_escape: .: (0.000112) test_escape_attribute: .: (0.000057) test_escape_seqid: .: (0.000055) test_unescape: .: (0.000057) Bio::TestGFF3RecordGap: test___scan_gap: .: (0.000168) test_eqeq: .: (0.000099) test_new_from_sequences_na: .: (0.002644) test_new_from_sequences_na_aa: .: (0.000148) test_new_from_sequences_na_aa_boundary_gap: .: (0.000209) test_new_from_sequences_na_aa_example: .: (0.000147) test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000126) test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000616) test_process_sequences_na: .: (0.000099) test_process_sequences_na_aa: .: (0.000090) test_process_sequences_na_aa_reverse_frameshift: .: (0.000086) test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000094) test_process_sequences_na_aa_tooshort: .: (0.000150) test_process_sequences_na_tooshort: .: (0.000117) test_to_s: .: (0.000089) Bio::TestGFF3RecordMisc: test_attributes_none: .: (0.000177) test_attributes_one: .: (0.000054) test_attributes_with_escaping: .: (0.000063) test_id_multiple: .: (0.000109) test_id_multiple2: .: (0.000092) test_id_replace: .: (0.000061) test_id_set: .: (0.000071) test_initialize_9: .: (0.000037) test_phase: .: (0.000059) test_score: .: (0.000051) test_to_s_void: .: (0.000046) Bio::TestGFF3RecordTarget: test_end: .: (0.000098) test_parse: .: (0.000456) test_start: .: (0.000049) test_strand: .: (0.000041) test_target_id: .: (0.000043) test_to_s: .: (0.000077) Bio::TestGFF3SequenceRegion: test_end: .: (0.000098) test_parse: .: (0.000083) test_seqid: .: (0.000044) test_start: .: (0.000041) test_to_s: .: (0.000069) Bio::TestGFFRecord: test_attributes: .: (0.000117) test_comment: .: (0.000054) test_end: .: (0.000050) test_feature: .: (0.000451) test_frame: .: (0.000054) test_score: .: (0.000048) test_seqname: .: (0.000048) test_source: .: (0.000048) test_start: .: (0.000046) test_strand: .: (0.000048) Bio::TestGFFRecordConstruct: test_add_seqname: .: (0.000096) Bio::TestGeneAssociation: test_aspect: .: (0.000130) test_assigned_by: .: (0.000048) test_date: .: (0.000045) test_db: .: (0.000045) test_db_object_id: .: (0.000043) test_db_object_name: .: (0.000042) test_db_object_symbol: .: (0.000561) test_db_object_synonym: .: (0.000056) test_db_object_type: .: (0.000047) test_db_reference: .: (0.000045) test_evidence: .: (0.000044) test_goid: .: (0.000053) test_parser: .: (0.000262) test_qualifier: .: (0.000049) test_taxon: .: (0.000047) test_to_str: .: (0.000050) test_with: .: (0.000047) Bio::TestGenscanReport: test_date_run: .: (0.000486) test_gccontent: .: (0.000833) test_genscan_version: .: (0.000333) test_isochore: .: (0.000317) test_length: .: (0.000321) test_matrix: .: (0.000312) test_predictions_size: .: (0.000565) test_query_name: .: (0.000323) test_time: .: (0.000310) Bio::TestGenscanReportExon: test_acceptor_score: .: (0.000470) test_donor_score: .: (0.000327) test_exon_type: .: (0.000489) test_exon_type_long: .: (0.000327) test_first: .: (0.000313) test_initiation_score: .: (0.000308) test_last: .: (0.000301) test_number: .: (0.000462) test_p_value: .: (0.000319) test_phase: .: (0.000305) test_range: .: (0.000312) test_score: .: (0.000324) test_strand: .: (0.000472) test_t_score: .: (0.000331) test_termination_score: .: (0.000308) Bio::TestGenscanReportGene: test_aaseq: .: (0.000401) test_naseq: .: (0.000331) test_number: .: (0.000463) test_polyA: .: (0.000329) test_promoter: .: (0.000315) Bio::TestHMMERReportClassMethods: test_reports_ary: .: (0.000498) test_reports_ary_contents: .: (0.000448) Bio::TestHMMERReportConstants: test_rs: .: (0.000102) Bio::TestHMMERReportHit: test_accession: .: (0.000418) test_append_hsp: .: (0.000522) test_bit_score: .: (0.000359) test_definition: .: (0.000413) test_description: .: (0.000355) test_each: .: (0.000373) test_each_hsp: .: (0.000366) test_entry_id: .: (0.000368) test_evalue: .: (0.000420) test_hit: .: (0.000525) test_hit_id: .: (0.000373) test_hsps: .: (0.000368) test_num: .: (0.000371) test_score: .: (0.000419) test_target_def: .: (0.000371) test_target_id: .: (0.000365) Bio::TestHMMERReportHmmpfam: test_domain_top_hits: .: (0.000454) test_each: .: (0.000524) test_each_hit: .: (0.000437) test_histogram: .: (0.000374) test_hits: .: (0.000369) test_hsps: .: (0.000372) test_parameter: .: (0.000378) test_program: .: (0.000437) test_query_info: .: (0.000389) test_statistical_detail: .: (0.000363) test_total_seq_searched: .: (0.000492) test_whole_seq_top_hits: .: (0.000386) Bio::TestHMMERReportHmmsearch: test_domain_top_hits: .: (0.000541) test_histogram: .: (0.000441) test_statistical_detail: .: (0.000446) test_total_seq_searched: .: (0.000429) test_whole_seq_top_hit: .: (0.000454) Bio::TestHMMERReportHsp: test_accession: .: (0.000431) test_bit_score: .: (0.032520) test_csline: .: (0.000394) test_domain: .: (0.000375) test_evalue: .: (0.000375) test_flatseq: .: (0.000380) test_hmm_f: .: (0.000382) test_hmm_t: .: (0.000377) test_hmmseq: .: (0.000374) test_hsp: .: (0.000380) test_midline: .: (0.000401) test_query_frame: .: (0.000387) test_query_from: .: (0.000386) test_query_seq: .: (0.000370) test_query_to: .: (0.000376) test_rfline: .: (0.000369) test_score: .: (0.000368) test_seq_f: .: (0.000374) test_seq_ft: .: (0.000428) test_seq_t: .: (0.000373) test_set_alignment: .: (0.000381) test_targat_to: .: (0.000388) test_target_frame: .: (0.000373) test_target_from: .: (0.000422) test_target_seq: .: (0.000372) Bio::TestHetatmFinder: test_each_hetatm: .: (0.000261) test_find_hetatm: .: (0.000111) test_hetatms: .: (0.000139) Bio::TestHeterogen: test_addAtom: .: (0.000178) test_each: .: (0.000107) test_each_hetatm: .: (0.000090) test_get_residue_id_from_atom: .: (0.000077) test_het_atom: .: (0.000065) test_iCode: .: (0.000065) test_inspect: .: (0.000084) test_resSeq: .: (0.000068) test_sort: .: (0.000095) test_square_bracket: .: (0.000082) test_to_s: .: (0.000124) test_update_resudue_id: .: (0.000070) Bio::TestHeterogenFinder: test_each_heterogen: .: (0.000152) test_find_heterogen: .: (0.000059) test_heterogens: .: (0.000060) Bio::TestIprscanPTxtReport: test_match_accession: .: (0.000147) test_match_description: .: (0.000074) test_match_evalue: .: (0.000065) test_match_ipr_description: .: (0.000061) test_match_ipr_id: .: (0.000064) test_match_match_end: .: (0.000063) test_match_match_start: .: (0.000062) test_match_method: .: (0.000061) test_matches_size: .: (0.000062) test_query_id: .: (0.000059) test_query_length: .: (0.000062) Bio::TestIprscanRawReport: test_entry_id: .: (0.001134) test_match_accession: .: (0.005428) test_match_crc64: .: (0.002298) test_match_date: .: (0.002141) test_match_description: .: (0.001837) test_match_evalue: .: (0.001741) test_match_go_terms: .: (0.001085) test_match_ipr_description: .: (0.001049) test_match_ipr_id: .: (0.001269) test_match_match_end: .: (0.001120) test_match_match_start: .: (0.001094) test_match_method: .: (0.002389) test_match_query_id: .: (0.006358) test_match_query_length: .: (0.007797) test_match_status: .: (0.006097) test_obj: .: (0.007036) test_query_id: .: (0.005922) test_query_length: .: (0.001394) test_self_reports_in_raw: .: (0.003250) Bio::TestIprscanReport: test_output_raw: .: (0.000807) test_to_raw: .: (0.000231) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.000303) test_match_accession: .: (0.000223) test_match_date: .: (0.000212) test_match_description: .: (0.000220) test_match_evalue: .: (0.000214) test_match_go_terms: .: (0.000212) test_match_ipr_description: .: (0.000613) test_match_ipr_id: .: (0.000216) test_match_match_end: .: (0.000217) test_match_match_start: .: (0.000213) test_match_method: .: (0.000209) test_match_status: .: (0.000207) test_matches_size: .: (0.000219) test_query_id: .: (0.000220) test_query_length: .: (0.000214) Bio::TestIprscanTxtEntryList: test_to_hash: .: (0.000479) test_to_hash_match?: .: (0.000306) Bio::TestIprscanTxtReport: test_parse_txt: .: (0.000592) Bio::TestKeggCompound: test_comment: .: (0.000233) test_dblinks_as_hash: .: (0.000178) test_dblinks_as_strings: .: (0.000142) test_entry_id: .: (0.000126) test_enzymes: .: (0.000301) test_formula: .: (0.000129) test_kcf: .: (0.000110) test_mass: .: (0.000122) test_name: .: (0.000131) test_names: .: (0.000130) test_pathways_as_hash: .: (0.000205) test_pathways_as_strings: .: (0.000147) test_reactions: .: (0.000302) test_remark: .: (0.000278) test_rpairs: .: (0.000137) Bio::TestKeggEnzyme: test_all_reac: .: (0.000423) test_classes: .: (0.000334) test_cofactors: .: (0.000452) test_comment: .: (0.000339) test_dblinks_as_hash: .: (0.000354) test_dblinks_as_strings: .: (0.000383) test_diseases: .: (0.000314) test_entry: .: (0.000323) test_entry_id: .: (0.000482) test_genes: .: (0.005759) test_genes_as_hash: .: (0.010552) test_genes_as_strings: .: (0.001468) test_inhibitors: .: (0.000350) test_iubmb_reactions: .: (0.000347) test_kegg_reactions: .: (0.000347) test_motifs: .: (0.000312) test_name: .: (0.000386) test_names: .: (0.000982) test_obsolete?: .: (0.000343) test_orthologs_as_hash: .: (0.000339) test_orthologs_as_strings: .: (0.000324) test_pathways_as_hash: .: (0.000364) test_pathways_as_strings: .: (0.000329) test_products: .: (0.000337) test_reaction: .: (0.000330) test_structures: .: (0.000451) test_substrates: .: (0.001031) test_sysname: .: (0.000514) Bio::TestKeggGenesDblinks: test_data: .: (0.000155) test_dblinks_0: .: (0.000062) test_dblinks_1: .: (0.000051) test_dblinks_2: .: (0.000050) Bio::TestKeggGenesStructure: test_data: .: (0.000108) test_ids: .: (0.000075) test_ids_in_array: .: (0.000062) Bio::TestKeggKGML::TestKGMLEntry1: test_components: .: (0.004805) test_graphics__size: .: (0.003580) test_id: .: (0.003049) test_link: .: (0.002955) test_name: .: (0.006406) test_reaction: .: (0.004761) test_type: .: (0.003941) Bio::TestKeggKGML::TestKGMLEntry1234: test_components: .: (0.003703) test_graphics__size: .: (0.002988) test_id: .: (0.002906) test_link: .: (0.003090) test_name: .: (0.003146) test_reaction: .: (0.003109) test_type: .: (0.003198) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: test_bgcolor=: .: (0.003248) test_category: .: (0.003194) test_entry_id: .: (0.003133) test_fgcolor=: .: (0.003143) test_height=: .: (0.003244) test_label=: .: (0.003196) test_shape=: .: (0.003233) test_width=: .: (0.007046) test_x=: .: (0.004698) test_y=: .: (0.003706) Bio::TestKeggKGML::TestKGMLEntry567: test_components: .: (0.003493) test_graphics__size: .: (0.003224) test_id: .: (0.003195) test_link: .: (0.003370) test_name: .: (0.003218) test_reaction: .: (0.003214) test_type: .: (0.003216) Bio::TestKeggKGML::TestKGMLEntrySetter: test_components=: .: (0.000129) test_graphics=: .: (0.000049) test_id=: .: (0.000053) test_link=: .: (0.000049) test_name=: .: (0.000050) test_reaction=: .: (0.000049) test_type=: .: (0.000046) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: test_bgcolor=: .: (0.000117) test_category=: .: (0.000061) test_entry_id=: .: (0.000057) test_fgcolor=: .: (0.000060) test_height=: .: (0.000058) test_label=: .: (0.000062) test_pathway=: .: (0.000050) test_shape=: .: (0.000063) test_width=: .: (0.000057) test_x=: .: (0.000057) test_y=: .: (0.000056) Bio::TestKeggKGML::TestKGMLGraphics1234: test_bgcolor: .: (0.003115) test_coords: .: (0.002888) test_fgcolor: .: (0.002883) test_height: .: (0.002901) test_name: .: (0.002920) test_type: .: (0.002965) test_width: .: (0.006001) test_x: .: (0.004666) test_y: .: (0.003884) Bio::TestKeggKGML::TestKGMLGraphics1_0: test_bgcolor: .: (0.003490) test_coords: .: (0.003204) test_fgcolor: .: (0.003208) test_height: .: (0.003204) test_name: .: (0.003348) test_type: .: (0.003223) test_width: .: (0.003231) test_x: .: (0.003251) test_y: .: (0.002898) Bio::TestKeggKGML::TestKGMLGraphicsSetter: test_bgcolor=: .: (0.000129) test_coords=: .: (0.000051) test_fgcolor=: .: (0.000048) test_height=: .: (0.000046) test_name=: .: (0.000047) test_type=: .: (0.000046) test_width=: .: (0.000045) test_x=: .: (0.000043) test_y=: .: (0.000044) Bio::TestKeggKGML::TestKGMLPathway: test_entries=: .: (0.002994) test_entries__size: .: (0.002885) test_image: .: (0.002918) test_link: .: (0.002932) test_name: .: (0.004943) test_number: .: (0.004646) test_org: .: (0.004389) test_reactions=: .: (0.003771) test_reactions__size: .: (0.003199) test_relations=: .: (0.003233) test_relations__size: .: (0.003363) test_title: .: (0.003175) Bio::TestKeggKGML::TestKGMLProduct: test_id: .: (0.006485) test_name: .: (0.006204) Bio::TestKeggKGML::TestKGMLProductSetter: test_id=: .: (0.000123) test_initialize_0: .: (0.000038) test_initialize_1: .: (0.000041) test_initialize_2: .: (0.000040) test_name=: .: (0.000049) Bio::TestKeggKGML::TestKGMLReaction: test_id: .: (0.002936) test_name: .: (0.002881) test_products: .: (0.002899) test_substrates: .: (0.002918) test_type: .: (0.002979) Bio::TestKeggKGML::TestKGMLReactionSetter: test_id=: .: (0.000120) test_name=: .: (0.000060) test_products=: .: (0.000055) test_substraces=: .: (0.000053) test_type=: .: (0.000054) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: test_direction=: .: (0.000119) test_entry_id=: .: (0.000067) Bio::TestKeggKGML::TestKGMLRelation: test_entry1: .: (0.006264) test_entry2: .: (0.004289) test_name: .: (0.003551) test_type: .: (0.003389) test_value: .: (0.003200) Bio::TestKeggKGML::TestKGMLRelationDeprecated: test_edge: .: (0.000098) test_node1=: .: (0.000062) test_node2=: .: (0.000056) test_rel=: .: (0.000058) Bio::TestKeggKGML::TestKGMLRelationSetter: test_entry1=: .: (0.000093) test_entry2=: .: (0.000050) test_name=: .: (0.000050) test_type=: .: (0.000047) test_value=: .: (0.000047) Bio::TestKeggKGML::TestKGMLSubstrate: test_id: .: (0.006389) test_name: .: (0.006297) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: test_id=: .: (0.000123) test_initialize_0: .: (0.000039) test_initialize_1: .: (0.000038) test_initialize_2: .: (0.000038) test_name=: .: (0.000049) Bio::TestKeggKGML::TestKGMLSubstrateSetter: test_id=: .: (0.000100) test_initialize_0: .: (0.000036) test_initialize_1: .: (0.000035) test_initialize_2: .: (0.000036) test_name=: .: (0.000047) Bio::TestKeggModule: test_compounds: .: (0.000235) test_compounds_as_hash: .: (0.000122) test_compounds_as_strings: .: (0.000098) test_definition: .: (0.000106) test_entry_id: .: (0.000091) test_keggclass: .: (0.000089) test_name: .: (0.000085) test_new: .: (0.000086) test_orthologs: .: (0.000130) test_orthologs_as_array: .: (0.000288) test_orthologs_as_hash: .: (0.000127) test_orthologs_as_strings: .: (0.000099) test_pathways: .: (0.000085) test_pathways_as_hash: .: (0.000080) test_pathways_as_strings: .: (0.000075) test_reactions: .: (0.000117) test_reactions_as_hash: .: (0.000113) test_reactions_as_strings: .: (0.000094) Bio::TestKeggOrthology: test_dblinks: .: (0.000323) test_dblinks_as_hash: .: (0.000252) test_dblinks_as_strings: .: (0.000206) test_definition: .: (0.000221) test_entry_id: .: (0.000209) test_genes_as_hash: .: (0.004717) test_genes_as_strings: .: (0.001261) test_keggclass: .: (0.000277) test_keggclasses: .: (0.000274) test_modules: .: (0.000209) test_modules_as_hash: .: (0.000221) test_modules_as_strings: .: (0.000197) test_name: .: (0.000205) test_names: .: (0.000217) test_pathways_as_strings: .: (0.000207) test_pathways_in_keggclass: .: (0.000265) test_references: .: (0.000298) Bio::TestKeggPathway_map00052: test_compounds_as_hash: .: (0.000177) test_compounds_as_strings: .: (0.000094) test_dblinks_as_hash: .: (0.000090) test_dblinks_as_strings: .: (0.000086) test_description: .: (0.000100) test_diseases_as_hash: .: (0.000088) test_diseases_as_strings: .: (0.000085) test_entry_id: .: (0.000097) test_enzymes_as_strings: .: (0.000087) test_genes_as_hash: .: (0.000084) test_genes_as_strings: .: (0.000085) test_keggclass: .: (0.000097) test_ko_pathway: .: (0.000093) test_modules_as_hash: .: (0.000121) test_modules_as_strings: .: (0.000094) test_name: .: (0.000095) test_organism: .: (0.000093) test_orthologs_as_hash: .: (0.000086) test_orthologs_as_strings: .: (0.000085) test_pathways_as_hash: .: (0.000110) test_pathways_as_strings: .: (0.000091) test_reactions_as_hash: .: (0.000086) test_reactions_as_strings: .: (0.000083) test_references: .: (0.000086) test_rel_pathways_as_hash: .: (0.000108) test_rel_pathways_as_strings: .: (0.000096) Bio::TestKeggReaction: test_definition: .: (0.000190) test_entry_id: .: (0.000108) test_enzymes: .: (0.000104) test_equation: .: (0.000103) test_name: .: (0.000107) test_orthologs_as_hash: .: (0.000120) test_orthologs_as_strings: .: (0.000100) test_pathways_as_hash: .: (0.000106) test_pathways_as_strings: .: (0.000093) test_rpairs_as_hash: .: (0.000120) test_rpairs_as_strings: .: (0.000097) test_rpairs_as_tokens: .: (0.000121) Bio::TestLasergene: test_methods: .: (0.005342) Bio::TestLocations: test_complement: .: (0.000187) test_hat: .: (0.000063) test_normal: .: (0.000057) test_replace_single_base: .: (0.000049) test_should_not_modify_argument: .: (0.000049) Bio::TestLocationsRoundTrip: test_locations_roundtrip: .: (0.003061) test_locations_to_s: .: (0.001384) Bio::TestMEDLINE: test_authors: .: (0.000520) test_authors_with_last_name_all_caps: .: (0.000054) test_authors_with_suffix: .: (0.000049) Bio::TestMEDLINE_20146148: test_ab: .: (0.000241) test_ad: .: (0.000149) test_au: .: (0.000142) test_authors: .: (0.000196) test_doi: .: (0.000146) test_dp: .: (0.000135) test_ip: .: (0.000133) test_mh: .: (0.000146) test_pages: .: (0.000141) test_pg: .: (0.000131) test_pii: .: (0.000272) test_pmid: .: (0.000142) test_pt: .: (0.000140) test_reference: .: (0.000266) test_self_new: .: (0.000155) test_so: .: (0.000139) test_ta: .: (0.000231) test_ti: .: (0.000146) test_ui: .: (0.000132) test_vi: .: (0.000135) test_year: .: (0.000133) Bio::TestMapSimple: test_attributes: .: (0.000149) Bio::TestMapping: test_add_mapping_as_map: .: (0.000254) test_add_mapping_as_marker: .: (0.000077) test_contains_marker?: .: (0.000058) test_mapped_to?: .: (0.000051) test_mapping_location_comparison: .: (0.000154) test_mappings_as_map_each: .: (0.000053) test_mappings_as_marker_each: .: (0.000076) test_mappings_on: .: (0.000076) test_multiple_mappings_between_same_marker_and_map: .: (0.000139) test_positions_on: .: (0.000080) test_raise_error_kind_of: .: (0.000270) Bio::TestMast: test_check_options_with_empty_opts: .: (0.000195) test_check_options_with_invalid_opts: .: (0.000096) test_check_options_with_valid_opts: .: (0.000081) test_command_to_be_run: .: (0.000084) test_config_defaults: .: (0.000061) test_minimal_config: .: (0.000069) test_more_config: .: (0.000071) test_run: .: (0.000180) Bio::TestMastReport: test_parse_hit_list_with_bad_data: .: (0.000211) test_report_has_motifs: .: (0.000111) Bio::TestModel: test_addChain: .: (0.000106) test_comp: .: (0.000058) test_each: .: (0.000058) test_each_chain: .: (0.000045) test_inspect: .: (0.000043) test_rehash: .: (0.000039) test_square_brace: .: (0.000042) test_to_s: .: (0.000044) Bio::TestModelFinder: test_find_model: .: (0.000108) Bio::TestMotif: test_creation_and_attributes: .: (0.000109) test_length: .: (0.000037) Bio::TestMyGraph: test_cliquishness: .: (0.000206) Bio::TestNA: test_accessor: .: (0.000091) test_na: .: (0.000039) test_name: .: (0.000036) test_names: .: (0.000033) test_to_re: .: (0.000101) test_weight: .: (0.000042) test_weight_rna: .: (0.000038) Bio::TestNAConstants: test_NAMES: .: (0.000076) test_NAMES_1_to_name: .: (0.000034) test_WEIGHT: .: (0.000039) Bio::TestNATranslate: test_translate: .: (0.000175) test_translate_1: .: (0.000075) test_translate_2: .: (0.000043) test_translate_3: .: (0.000041) test_translate_4: .: (0.000091) test_translate_5: .: (0.000044) test_translate_6: .: (0.000041) Bio::TestNCBIDB: test_fetch: .: (0.000225) test_p_entry2hash: .: (0.000036) test_p_subtag2array: .: (0.000030) test_p_toptag2array: .: (0.000030) Bio::TestNewick: test_reparse: .: (0.000622) test_reparse_before_lazy_parsing: .: (0.000199) test_string_tree: .: (0.000480) Bio::TestNewick2: test_string_tree: .: (0.000333) Bio::TestNewickPrivate: test_parse_newick_get_tokens_for_leaf: .: (0.000100) test_parse_newick_leaf: .: (0.000088) test_parse_newick_tokenize: .: (0.000156) Bio::TestNexus: test_nexus: .: (0.006454) Bio::TestOSLine: test_period_trancation_O63147: .: (0.000141) test_uncapitalized_letter_Q32725_9POAL: .: (0.000058) Bio::TestPAMLCodeml::TestCodeml: test_dump_parameters: .: (0.000106) test_load_parameters: .: (0.000054) test_parameters: .: (0.000035) test_set_default_parameters: .: (0.000048) Bio::TestPAMLCodeml::TestCodemlControlGeneration: test_control_file_generated: .: (0.000347) test_expected_parameters_set_in_control_file: .: (0.000281) Bio::TestPAMLCodeml::TestCodemlInitialize: test_new_with_one_argument: .: (0.000110) test_new_with_parameters: .: (0.000053) test_new_with_two_argument: .: (0.000049) test_new_without_argument: .: (0.000042) Bio::TestPAMLCodeml::TestCodemlRates: test_rates_first_position: .: (0.000555) test_rates_hundred_and_fiftieth_position: .: (0.000495) test_rates_last_position: .: (0.000492) Bio::TestPAMLCodeml::TestCodemlReport: test_alpha: .: (0.000440) test_tree: .: (0.000367) test_tree_length: .: (0.000351) test_tree_log_likelihood: .: (0.000349) Bio::TestPAMLCodeml::TestControlFileUsage: test_correct_parameters_should_be_loaded: .: (0.000198) test_parameters_should_be_loaded_from_control: .: (0.000120) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: test_error_thrown_if_seqfile_does_not_specified: .: (0.000630) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: test_alpha: .: (0.000147) test_dN_dS: .: (0.000104) test_kappa: .: (0.000079) test_lnL: .: (0.000067) test_m3_classes: .: (0.000117) test_m3_lnL: .: (0.000069) test_m3_to_s: .: (0.000067) test_m3_tree: .: (0.000119) test_omega: .: (0.000067) test_to_s: .: (0.000065) test_tree: .: (0.000107) test_tree_length: .: (0.000067) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: test_dN_dS: .: (0.000259) test_p: .: (0.000180) test_position: .: (0.000171) test_probability: .: (0.000167) test_w: .: (0.000163) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: test_graph: .: (0.000266) test_graph_omega: .: (0.000213) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: test_descr: .: (0.000135) test_footer: .: (0.000071) test_header: .: (0.000065) test_initialize: .: (0.000074) test_models: .: (0.000077) test_nb_sites: .: (0.000276) test_num_codons: .: (0.000085) test_num_sequences: .: (0.000079) test_significant: .: (0.000079) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: test_models: .: (0.000149) test_nb_sites: .: (0.000126) test_significant: .: (0.000081) test_sites: .: (0.000503) Bio::TestPDB: test_accession: .: (0.000574) test_addModel: .: (0.000350) test_authors: .: (0.000322) test_bracket: .: (0.000325) test_classification: .: (0.000338) test_dbref: .: (0.000374) test_definition: .: (0.000343) test_each: .: (0.000372) test_each_model: .: (0.000341) test_entry_id: .: (0.003843) test_helix: .: (0.000411) test_inspect: .: (0.000964) test_jrnl: .: (0.000354) test_keywords: .: (0.000345) test_record: .: (0.000892) test_remark: .: (0.000477) test_seqres: .: (0.000472) test_sheet: .: (0.001045) test_ssbond: .: (0.000595) test_to_s: .: (0.001130) test_turn: .: (0.000361) test_version: .: (0.000378) Bio::TestPDBRecord::TestANISOU: test_U11: .: (0.000138) test_U12: .: (0.000058) test_U13: .: (0.000061) test_U22: .: (0.000065) test_U23: .: (0.000053) test_U33: .: (0.000050) test_altLoc: .: (0.000054) test_chainID: .: (0.000050) test_charge: .: (0.000052) test_element: .: (0.000052) test_iCode: .: (0.000050) test_name: .: (0.000050) test_resName: .: (0.000052) test_resSeq: .: (0.000051) test_segID: .: (0.000051) test_serial: .: (0.000050) Bio::TestPDBRecord::TestATOM: test_altLoc: .: (0.000101) test_anisou: .: (0.000042) test_chainID: .: (0.000038) test_charge: .: (0.000039) test_comparable: .: (0.000159) test_do_parse: .: (0.000041) test_element: .: (0.000038) test_iCode: .: (0.000038) test_name: .: (0.000036) test_occupancy: .: (0.000056) test_original_data: .: (0.000041) test_record_name: .: (0.000039) test_resName: .: (0.000038) test_resSeq: .: (0.000037) test_residue: .: (0.000039) test_segID: .: (0.000038) test_serial: .: (0.000037) test_sigatm: .: (0.000037) test_tempFactor: .: (0.000044) test_ter: .: (0.000039) test_to_a: .: (0.000040) test_to_s: .: (0.000052) test_x: .: (0.000044) test_xyz: .: (0.000058) test_y: .: (0.000045) test_z: .: (0.000042) Bio::TestPDBRecord::TestAUTHOR: test_authorList: .: (0.000110) Bio::TestPDBRecord::TestCAVEAT: test_comment: .: (0.000221) test_idcode: .: (0.000048) Bio::TestPDBRecord::TestCISPEP: test_chainID1: .: (0.000116) test_chainID2: .: (0.000052) test_icode1: .: (0.000048) test_icode2: .: (0.000048) test_measure: .: (0.000056) test_modNum: .: (0.000048) test_pep1: .: (0.000049) test_pep2: .: (0.000048) test_seqNum1: .: (0.000047) test_seqNum2: .: (0.000048) test_serNum: .: (0.000047) Bio::TestPDBRecord::TestCOMPND: test_compound: .: (0.000105) Bio::TestPDBRecord::TestCONECT: test_serial: .: (0.000223) Bio::TestPDBRecord::TestCRYST1: test_a: .: (0.000105) test_alpha: .: (0.000045) test_b: .: (0.000042) test_beta: .: (0.000041) test_c: .: (0.000041) test_gamma: .: (0.000042) test_sGroup: .: (0.000042) test_z: .: (0.000041) Bio::TestPDBRecord::TestDBREF: test_chainID: .: (0.000111) test_database: .: (0.000058) test_dbAccession: .: (0.000056) test_dbIdCode: .: (0.000056) test_dbseqBegin: .: (0.000055) test_dbseqEnd: .: (0.000055) test_idCode: .: (0.000057) test_idbnsBeg: .: (0.000058) test_insertBegin: .: (0.000055) test_insertEnd: .: (0.000055) test_seqBegin: .: (0.000055) test_seqEnd: .: (0.000054) Bio::TestPDBRecord::TestDefault: test_text: .: (0.000099) Bio::TestPDBRecord::TestENDMDL: test_serial: .: (0.000085) Bio::TestPDBRecord::TestEXPDTA: test_technique: .: (0.000089) Bio::TestPDBRecord::TestEnd: test_serial: .: (0.000084) Bio::TestPDBRecord::TestHEADER: test_classification: .: (0.000090) test_depDate: .: (0.000066) test_idCode: .: (0.000043) Bio::TestPDBRecord::TestHET: test_ChainID: .: (0.000103) test_hetID: .: (0.000047) test_iCode: .: (0.000046) test_numHetAtoms: .: (0.000213) test_seqNum: .: (0.000052) test_text: .: (0.000045) Bio::TestPDBRecord::TestHETATM: test_altLoc: .: (0.000095) test_anisou: .: (0.000042) test_chainID: .: (0.000040) test_charge: .: (0.000038) test_comparable: .: (0.000052) test_do_parse: .: (0.000041) test_element: .: (0.000039) test_iCode: .: (0.000040) test_name: .: (0.000037) test_occupancy: .: (0.000051) test_original_data: .: (0.000043) test_record_name: .: (0.000039) test_resName: .: (0.000038) test_resSeq: .: (0.000038) test_residue: .: (0.000038) test_segID: .: (0.000039) test_serial: .: (0.000038) test_sigatm: .: (0.000038) test_tempFactor: .: (0.000050) test_ter: .: (0.000040) test_to_a: .: (0.000041) test_to_s: .: (0.000052) test_x: .: (0.000044) test_xyz: .: (0.000048) test_y: .: (0.000043) test_z: .: (0.000042) Bio::TestPDBRecord::TestHYDBND: test_Chain1: .: (0.000132) test_ChainH: .: (0.000062) test_ICode1: .: (0.000061) test_altLoc1: .: (0.000061) test_altLoc2: .: (0.000060) test_altLocH: .: (0.000059) test_chainID2: .: (0.000059) test_iCode2: .: (0.000059) test_iCodeH: .: (0.000059) test_name1: .: (0.000060) test_name2: .: (0.000060) test_nameH: .: (0.000060) test_resName1: .: (0.000060) test_resName2: .: (0.000189) test_resSeq1: .: (0.000065) test_resSeq2: .: (0.000058) test_resSeqH: .: (0.000059) test_sym1: .: (0.000060) test_sym2: .: (0.000058) Bio::TestPDBRecord::TestKEYWDS: test_keywds: .: (0.000098) Bio::TestPDBRecord::TestLINK: test_altLoc1: .: (0.000113) test_altLoc2: .: (0.000058) test_chainID1: .: (0.000054) test_chainID2: .: (0.000055) test_iCode1: .: (0.000054) test_iCode2: .: (0.000053) test_name1: .: (0.000053) test_name2: .: (0.000052) test_resName1: .: (0.000052) test_resName2: .: (0.000053) test_resSeq1: .: (0.000054) test_resSeq2: .: (0.000054) test_sym1: .: (0.000054) test_sym2: .: (0.000053) Bio::TestPDBRecord::TestMASTER: test_numConect: .: (0.000222) test_numCoord: .: (0.000043) test_numHelix: .: (0.000041) test_numHet: .: (0.000040) test_numRemark: .: (0.000040) test_numSeq: .: (0.000042) test_numSheet: .: (0.000040) test_numSite: .: (0.000041) test_numTer: .: (0.000040) test_numTurn: .: (0.000040) test_numXform: .: (0.000040) Bio::TestPDBRecord::TestMODEL: test_serial: .: (0.000086) Bio::TestPDBRecord::TestMODRES: test_chainID: .: (0.000103) test_comment: .: (0.000051) test_iCode: .: (0.000048) test_idCode: .: (0.000048) test_resName: .: (0.000047) test_seqNum: .: (0.000047) test_stdRes: .: (0.000046) Bio::TestPDBRecord::TestMTRIX1: test_Mn1: .: (0.000100) test_Mn2: .: (0.000042) test_Mn3: .: (0.000040) test_Vn: .: (0.000039) test_iGiven: .: (0.000043) test_serial: .: (0.000039) Bio::TestPDBRecord::TestMTRIX2: test_Mn1: .: (0.000108) test_Mn2: .: (0.000043) test_Mn3: .: (0.000040) test_Vn: .: (0.000039) test_iGiven: .: (0.000039) test_serial: .: (0.000038) Bio::TestPDBRecord::TestMTRIX3: test_Mn1: .: (0.000090) test_Mn2: .: (0.000042) test_Mn3: .: (0.000039) test_Vn: .: (0.000039) test_iGiven: .: (0.000039) test_serial: .: (0.000039) Bio::TestPDBRecord::TestOBSLTE: test_idCode: .: (0.000098) test_rIdCode: .: (0.000047) test_repDate: .: (0.000043) Bio::TestPDBRecord::TestORIGX1: test_On1: .: (0.000094) test_On2: .: (0.000039) test_On3: .: (0.000037) test_Tn: .: (0.000038) Bio::TestPDBRecord::TestREVDAT: test_modDate: .: (0.000091) test_modId: .: (0.000049) test_modNum: .: (0.000043) test_modType: .: (0.000043) test_record: .: (0.000043) Bio::TestPDBRecord::TestRemarkN: test_remarkNum: .: (0.000088) test_text: .: (0.000041) Bio::TestPDBRecord::TestSCALE1: test_Sn1: .: (0.000093) test_Sn2: .: (0.000040) test_Sn3: .: (0.000038) test_Un: .: (0.000038) Bio::TestPDBRecord::TestSCALE2: test_Sn1: .: (0.000085) test_Sn2: .: (0.000040) test_Sn3: .: (0.000037) test_Un: .: (0.000037) Bio::TestPDBRecord::TestSCALE3: test_Sn1: .: (0.000084) test_Sn2: .: (0.000039) test_Sn3: .: (0.000037) test_Un: .: (0.000036) Bio::TestPDBRecord::TestSEQADV: test_chainID: .: (0.000104) test_conflict: .: (0.000053) test_database: .: (0.000051) test_dbIdCode: .: (0.000049) test_dbRes: .: (0.000049) test_dbSeq: .: (0.000051) test_iCode: .: (0.000050) test_idCode: .: (0.000049) test_resName: .: (0.000049) test_seqNum: .: (0.000050) Bio::TestPDBRecord::TestSEQRES: test_chainID: .: (0.000122) test_numRes: .: (0.000054) test_resName: .: (0.000055) Bio::TestPDBRecord::TestSHEET: test_curAtom: .: (0.000113) test_curChainId: .: (0.000065) test_curICode: .: (0.000063) test_curResName: .: (0.000070) test_curResSeq: .: (0.000062) test_endChainID: .: (0.000062) test_endICode: .: (0.000062) test_endResName: .: (0.000062) test_endSeqNum: .: (0.000060) test_initChainID: .: (0.000062) test_initICode: .: (0.000061) test_initResName: .: (0.000147) test_initSeqNum: .: (0.000061) test_numStrands: .: (0.000060) test_prevAtom: .: (0.000061) test_prevChainId: .: (0.000060) test_prevICode: .: (0.000061) test_prevResName: .: (0.000060) test_prevResSeq: .: (0.000060) test_sense: .: (0.000062) test_sheetID: .: (0.000062) test_strand: .: (0.000062) Bio::TestPDBRecord::TestSIGATM: test_altLoc: .: (0.000125) test_chainID: .: (0.000054) test_charge: .: (0.000052) test_element: .: (0.000052) test_iCode: .: (0.000051) test_name: .: (0.000050) test_resName: .: (0.000051) test_resSeq: .: (0.000140) test_segID: .: (0.000051) test_serial: .: (0.000051) test_sigOcc: .: (0.000051) test_sigTemp: .: (0.000051) test_sigX: .: (0.000050) test_sigY: .: (0.000050) test_sigZ: .: (0.000048) Bio::TestPDBRecord::TestSIGUIJ: test_SigmaU11: .: (0.000116) test_SigmaU12: .: (0.000053) test_SigmaU13: .: (0.000051) test_SigmaU22: .: (0.000050) test_SigmaU23: .: (0.000050) test_SigmaU33: .: (0.000064) test_altLoc: .: (0.000053) test_chainID: .: (0.000051) test_charge: .: (0.000050) test_element: .: (0.000050) test_iCode: .: (0.000052) test_name: .: (0.000051) test_resName: .: (0.000179) test_resSeq: .: (0.000053) test_segID: .: (0.000050) test_serial: .: (0.000051) Bio::TestPDBRecord::TestSITE: test_chainID1: .: (0.000123) test_chainID2: .: (0.000059) test_chainID3: .: (0.000056) test_chainID4: .: (0.000057) test_iCode1: .: (0.000055) test_iCode2: .: (0.000056) test_iCode3: .: (0.000056) test_iCode4: .: (0.000056) test_numRes: .: (0.000056) test_resName1: .: (0.000055) test_resName2: .: (0.000055) test_resName3: .: (0.000055) test_resName4: .: (0.000055) test_seq1: .: (0.000057) test_seq2: .: (0.000056) test_seq3: .: (0.000055) test_seq4: .: (0.000055) test_seqNum: .: (0.000055) test_siteID: .: (0.000198) Bio::TestPDBRecord::TestSLTBRG: test_altLoc1: .: (0.000111) test_altLoc2: .: (0.000050) test_atom1: .: (0.000049) test_atom2: .: (0.000049) test_chainID1: .: (0.000048) test_chainID2: .: (0.000047) test_iCode1: .: (0.000048) test_iCode2: .: (0.000047) test_resName1: .: (0.000045) test_resName2: .: (0.000047) test_resSeq1: .: (0.000046) test_resSeq2: .: (0.000046) test_sym1: .: (0.000047) test_sym2: .: (0.000047) Bio::TestPDBRecord::TestSOURCE: test_srcName: .: (0.000103) Bio::TestPDBRecord::TestSPRSDE: test_idCode: .: (0.000096) test_sIdCode: .: (0.000047) test_sprsdeDate: .: (0.000046) Bio::TestPDBRecord::TestTER: test_chainID: .: (0.000105) test_iCode: .: (0.000046) test_resName: .: (0.000043) test_resSeq: .: (0.000043) test_serial: .: (0.000044) Bio::TestPDBRecord::TestTITLE: test_title: .: (0.000093) Bio::TestPDBRecord::TestTVECT: test_serial: .: (0.000099) test_t1: .: (0.000046) test_t2: .: (0.000043) test_t3: .: (0.000043) test_text: .: (0.000042) Bio::TestPROSITE: test_ac: .: (0.000749) test_cc: .: (0.000669) test_de: .: (0.000643) test_division: .: (0.000739) test_dr: .: (0.013992) test_dt: .: (0.001307) test_false_neg: .: (0.000822) test_false_pos: .: (0.000661) test_false_positive_sequences: .: (0.001039) test_list_falsenegative: .: (0.009862) test_list_falsepositive: .: (0.013638) test_list_potentialhit: .: (0.012487) test_list_truepositive: .: (0.012384) test_list_unknown: .: (0.008525) test_list_xref: .: (0.010390) test_ma: .: (0.000563) test_max_repeat: .: (0.000544) test_name: .: (0.000534) test_nr: .: (0.000593) test_pa: .: (0.000572) test_pa2re: .: (0.000575) test_partial: .: (0.000564) test_pdb_xref: .: (0.000536) test_pdoc_xref: .: (0.000651) test_positive: .: (0.000674) test_positive_hits: .: (0.000675) test_positive_sequences: .: (0.000735) test_release: .: (0.000707) test_ru: .: (0.000675) test_self_pa2re: .: (0.000735) test_site: .: (0.001112) test_skip_flag: .: (0.000637) test_swissprot_release_number: .: (0.000683) test_swissprot_release_sequences: .: (0.000687) test_taxon_range: .: (0.000679) test_total: .: (0.000709) test_total_hits: .: (0.000709) test_total_sequences: .: (0.000703) test_unknown: .: (0.000708) test_unknown_hits: .: (0.000716) test_unknown_sequences: .: (0.002857) Bio::TestPROSITEConst: test_delimiter: .: (0.000129) test_tagsize: .: (0.000038) Bio::TestPTS1: test_function_set: .: (0.000108) test_function_set_number_1: .: (0.000050) test_function_set_number_2: .: (0.000039) test_function_set_number_3: .: (0.000039) test_function_show: .: (0.000036) Bio::TestPTS1Constant: test_FUNCTION: .: (0.000087) Bio::TestPTS1New: test_fungi: .: (0.000085) test_general: .: (0.000041) test_metazoa: .: (0.000675) Bio::TestQualifier: test_qualifier: .: (0.000100) test_value: .: (0.000034) Bio::TestREBASE: test_methods: .: (0.000411) Bio::TestRPSBlast::TestRPSBlastHSP: test_align_len: .: (0.001315) test_bit_score: .: (0.000375) test_evalue: .: (0.000316) test_gaps: .: (0.000310) test_hit_from: .: (0.000329) test_hit_to: .: (0.000344) test_hseq: .: (0.000319) test_identity: .: (0.000320) test_midline: .: (0.000323) test_percent_identity: .: (0.000813) test_positive: .: (0.000476) test_qseq: .: (0.000327) test_query_from: .: (0.000317) test_query_to: .: (0.000313) test_score: .: (0.000311) Bio::TestRPSBlast::TestRPSBlastReport: test_db: .: (0.000356) test_hits_size: .: (0.000704) test_iterations_size: .: (0.000983) test_program: .: (0.000278) test_query_def: .: (0.000646) test_query_len: .: (0.000637) test_version: .: (0.000285) test_version_date: .: (0.000264) test_version_number: .: (0.000266) Bio::TestRPSBlast::TestRPSBlastReportHit: test_bit_score: .: (0.000505) test_definition: .: (0.000341) test_evalue: .: (0.000322) test_hsps_size: .: (0.000286) test_identity: .: (0.000316) test_lap_at: .: (0.000349) test_len: .: (0.000321) test_midline: .: (0.000339) test_overlap: .: (0.000335) test_query_end: .: (0.000336) test_query_seq: .: (0.000460) test_query_start: .: (0.000342) test_target_def: .: (0.000321) test_target_end: .: (0.000331) test_target_len: .: (0.000314) test_target_seq: .: (0.000328) test_target_start: .: (0.000329) Bio::TestRPSBlast::TestRPSBlastSplitter: test_entry_pos: .: (0.000240) test_get_entry: .: (0.000208) test_rewind: .: (0.000052) test_skip_leader: .: (0.000193) Bio::TestReference: test_abstract: .: (0.000102) test_affiliations: .: (0.000041) test_authors: .: (0.000038) test_format_bibitem: .: (0.000071) test_format_bibtex: .: (0.000102) test_format_bibtex_with_arguments: .: (0.000086) test_format_cell: .: (0.000052) test_format_current: .: (0.000051) test_format_endnote: .: (0.000062) test_format_general: .: (0.000055) test_format_genome_biol: .: (0.000050) test_format_genome_res: .: (0.000049) test_format_nar: .: (0.000048) test_format_nature: .: (0.000057) test_format_rd: .: (0.000052) test_format_science: .: (0.000141) test_format_trends: .: (0.000043) test_issue: .: (0.000037) test_journal: .: (0.000038) test_mesh: .: (0.000038) test_pages: .: (0.000036) test_pubmed: .: (0.000035) test_pubmed_url: .: (0.000037) test_url: .: (0.000036) test_volume: .: (0.000035) test_year: .: (0.000036) Bio::TestReference_noURL: test_format_endnote: .: (0.000113) test_url: .: (0.000038) Bio::TestReferences: test_append: .: (0.000121) test_each: .: (0.000050) Bio::TestRelation: test_comparison_operator: .: (0.000109) test_uniq: .: (0.000060) Bio::TestResidue: test_addAtom: .: (0.000210) test_each: .: (0.000099) test_each_atom: .: (0.000084) test_get_residue_id_from_atom: .: (0.000076) test_het_atom: .: (0.000064) test_iCode: .: (0.000066) test_inspect: .: (0.000074) test_resSeq: .: (0.000066) test_sort: .: (0.000095) test_square_bracket: .: (0.000077) test_to_s: .: (0.000104) test_update_resudue_id: .: (0.000068) Bio::TestResidueFinder: test_each_residue: .: (0.000159) test_find_residue: .: (0.000053) test_residues: .: (0.000060) Bio::TestRestrictionEnzyme::TestAnalysis: test_cut: .: (0.108667) test_cut_from_bio_sequence_na: .: (0.014335) test_cut_without_permutations: .: (0.011287) test_view_ranges: .: (0.018469) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: test_cuts: .: (0.000889) test_cuts_after_remove_incomplete_cuts: .: (0.000334) test_strands_for_display: .: (0.001672) test_strands_for_display_current: .: (0.000325) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: test_fragments: .: (0.000296) test_fragments_for_display_1: .: (0.000527) test_fragments_for_display_10: .: (0.000433) test_fragments_for_display_2: .: (0.000361) test_fragments_for_display_3: .: (0.000666) test_fragments_for_display_4: .: (0.000435) test_fragments_for_display_5: .: (0.000320) test_fragments_for_display_6: .: (0.000454) test_fragments_for_display_7: .: (0.000290) test_fragments_for_display_8: .: (0.000253) test_fragments_for_display_9: .: (0.000270) Bio::TestRestrictionEnzyme::TestCutRanges: test_obj_2: .: (0.000196) test_obj_3: .: (0.000269) test_obj_7: .: (0.000099) test_obj_z: .: (0.000098) Bio::TestRestrictionEnzyme::TestCutSymbol: test_methods: .: (0.000179) Bio::TestRestrictionEnzyme::TestDenseIntArray: test_bracket: .: (0.000132) test_bracket_eq: .: (0.000091) test_concat: .: (0.000060) test_delete: .: (0.000056) test_dup: .: (0.000078) test_each: .: (0.000073) test_eqeq: .: (0.000052) test_eqeq_false: .: (0.000045) test_eqeq_other: .: (0.000041) test_eqeq_self: .: (0.000042) test_include?: .: (0.000046) test_internal_data: .: (0.000044) test_internal_data_eq: .: (0.000073) test_length: .: (0.000043) test_ltlt: .: (0.000049) test_ltlt_larger: .: (0.000048) test_ltlt_middle: .: (0.000047) test_plus: .: (0.000059) test_plus_error: .: (0.000342) test_push: .: (0.000058) test_reverse_each: .: (0.000076) test_self_bracket: .: (0.000043) test_self_new: .: (0.000055) test_size: .: (0.000042) test_sort!: .: (0.000040) test_to_a: .: (0.000043) test_uniq!: .: (0.000040) test_unshift: .: (0.000059) Bio::TestRestrictionEnzyme::TestDoubleStranded: test_argument_error: .: (0.002407) test_complement: .: (0.002190) test_complement_with_cut_symbols: .: (0.002262) test_cut_locations: .: (0.001904) test_cut_locations_in_enzyme_notation: .: (0.001907) test_primary: .: (0.001898) test_primary_with_cut_symbols: .: (0.001975) test_to_re: .: (0.001890) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: test_align: .: (0.000577) test_align_with_cuts: .: (0.000378) test_argument_error: .: (0.000667) test_ds: .: (0.000439) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: test_argument_error: .: (0.000248) test_complement: .: (0.000095) test_contents: .: (0.000084) test_primary: .: (0.000083) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: test_argument_error: .: (0.000180) test_complement: .: (0.000087) test_contents: .: (0.000079) test_primary: .: (0.000078) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: test_complement: .: (0.000123) test_contents: .: (0.000066) test_primary: .: (0.000060) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: test_complement: .: (0.000132) test_complement_to_array_index: .: (0.000165) test_complement_to_array_index_class: .: (0.000099) test_contents: .: (0.000072) test_primary: .: (0.000065) test_primary_to_array_index: .: (0.000099) test_primary_to_array_index_class: .: (0.000091) test_to_array_index: .: (0.000208) test_to_array_index_class: .: (0.000186) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: test_enzyme_name: .: (0.000239) test_rebase: .: (0.000073) Bio::TestRestrictionEnzyme::TestSingleStrand: test_argument_error: .: (0.000452) test_creation_with_no_cuts: .: (0.000241) test_cut_locations: .: (0.000231) test_cut_locations_in_enzyme_notation: .: (0.000287) test_orientation: .: (0.000226) test_pattern: .: (0.000302) test_pattern_palindromic?: .: (0.000245) test_stripped: .: (0.000188) test_to_re: .: (0.000171) test_with_cut_symbols: .: (0.000200) test_with_spaces: .: (0.000287) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: test_argument_error: .: (0.000411) test_creation_with_no_cuts: .: (0.000330) test_cut_locations: .: (0.000226) test_cut_locations_in_enzyme_notation: .: (0.000205) test_orientation: .: (0.000250) test_pattern: .: (0.000211) test_pattern_palindromic?: .: (0.000301) test_stripped: .: (0.000189) test_to_re: .: (0.000162) test_with_cut_symbols: .: (0.000266) test_with_spaces: .: (0.000221) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: test_argument_error: .: (0.000291) test_initialize_with_pattern: .: (0.000160) test_max: .: (0.000062) test_min: .: (0.000058) test_to_array_index: .: (0.000069) Bio::TestRestrictionEnzyme::TestSortedNumArray: test_bracket: .: (0.000121) test_bracket_eq: .: (0.000064) test_concat: .: (0.000049) test_delete: .: (0.000044) test_dup: .: (0.000066) test_each: .: (0.000132) test_eqeq: .: (0.000046) test_eqeq_false: .: (0.000039) test_eqeq_other: .: (0.000036) test_eqeq_self: .: (0.000035) test_include?: .: (0.000042) test_internal_data_hash: .: (0.000038) test_internal_data_hash_eq: .: (0.000047) test_length: .: (0.000058) test_ltlt: .: (0.000093) test_ltlt_noeffect: .: (0.000044) test_plus: .: (0.000044) test_plus_error: .: (0.000059) test_private_push_element: .: (0.000043) test_private_push_element_intermediate: .: (0.000100) test_private_push_element_last: .: (0.000043) test_private_push_element_noeffect: .: (0.000042) test_private_sorted_keys: .: (0.000038) test_private_unshift_element: .: (0.000042) test_private_unshift_element_first: .: (0.000044) test_private_unshift_element_intermediate: .: (0.000042) test_private_unshift_element_noeffect: .: (0.000041) test_push: .: (0.000044) test_reverse_each: .: (0.000070) test_self_bracket: .: (0.000037) test_self_new: .: (0.000050) test_size: .: (0.000037) test_sort!: .: (0.000036) test_to_a: .: (0.000096) test_uniq!: .: (0.000037) test_unshift: .: (0.000091) Bio::TestRestrictionEnzyme::TestStringFormatting: test_add_spacing: .: (0.000111) test_left_padding: .: (0.000056) test_right_padding: .: (0.000051) test_strip_padding: .: (0.000054) Bio::TestSOFT: test_dataset: .: (0.009963) test_series: .: (0.004355) Bio::TestSOSUIReport: test_entry_id: .: (0.000184) test_prediction: .: (0.000071) test_tmh: .: (0.000065) test_tmhs: .: (0.000079) Bio::TestSOSUIReportConst: test_delimiter: .: (0.000086) test_rs: .: (0.000035) Bio::TestSOSUITMH: test_grade: .: (0.000126) test_range: .: (0.000069) test_sequence: .: (0.000066) Bio::TestSampleGraph: test_bellman_ford: .: (0.000232) test_bfs_shortest_path: .: (0.000085) test_breadth_first_search: .: (0.000076) test_depth_first_search: .: (0.000136) test_dijkstra: .: (0.000111) test_dump_list: .: (0.000113) test_dump_matrix: .: (0.000165) test_extract_subgraph_by_label: .: (0.000246) test_extract_subgraph_by_list: .: (0.000091) test_extract_subgraph_retains_disconnected_nodes: .: (0.000069) test_small_world_aka_node_degree_histogram: .: (0.000066) test_to_matrix: .: (0.000153) test_to_matrix_fixed_index: .: (0.000109) test_undirected_cliquishness: .: (0.000133) Bio::TestScf_version_2: test_complement: .: (0.004599) test_seq: .: (0.004444) test_to_biosequence: .: (0.004265) Bio::TestScf_version_3: test_complement: .: (0.010951) test_seq: .: (0.010688) test_to_biosequence: .: (0.010966) Bio::TestSequence: test_AA_new_blank_sequence: .: (0.000144) test_AA_new_sequence_all_legal_symbols: .: (0.000046) test_AA_new_sequence_removes_whitespace: .: (0.000040) test_AA_new_sequence_upcases_symbols: .: (0.000043) test_DNA_new_blank_sequence: .: (0.000040) test_DNA_new_sequence_downcases_symbols: .: (0.000040) test_DNA_new_sequence_removes_whitespace: .: (0.000039) test_NA_randomize_with_counts: .: (0.000538) test_NA_randomize_with_counts_and_block: .: (0.000598) test_RNA_new_sequence: .: (0.000051) test_ambiguous_dna_sequence_complement: .: (0.000046) test_ambiguous_rna_sequence_complement: .: (0.000040) test_amino_acid_codes: .: (0.000065) test_amino_acid_molecular_weight: .: (0.000093) test_amino_acid_names: .: (0.000054) test_amino_acid_randomize_can_be_chained: .: (0.000732) test_amino_acid_randomize_has_same_composition: .: (0.000265) test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000473) test_dna_composition: .: (0.000055) test_dna_gc_percent: .: (0.000059) test_dna_molecular_weight: .: (0.000077) test_dna_pikachu: .: (0.000048) test_dna_sequence_complement: .: (0.000041) test_dna_sequence_translate: .: (0.000205) test_dna_to_re: .: (0.000083) test_element_reference_operator_with_one_argument: .: (0.000042) test_element_reference_operator_with_two_arguments: .: (0.000040) test_invalid_nucleic_acid_illegal_bases: .: (0.000064) test_invalid_nucleic_acid_illegal_bases_more: .: (0.000279) test_nucleic_acid_names: .: (0.000057) test_randomize_dna_can_be_chained: .: (0.000155) test_randomize_dna_retains_composition: .: (0.000114) test_randomize_dna_with_block: .: (0.000140) test_rna_composition: .: (0.000051) test_rna_gc_percent: .: (0.000073) test_rna_molecular_weight: .: (0.000069) test_rna_pikachu: .: (0.000046) test_rna_sequence_complement: .: (0.000041) test_rna_sequence_translate: .: (0.000169) test_rna_to_re: .: (0.000080) test_total: .: (0.000056) test_two_consecutive_dna_randomizations_not_equal: .: (0.000340) test_valid_dna_sequence_illegal_bases: .: (0.000044) Bio::TestSequenceAA: test_codes: .: (0.000129) test_molecular_weight: .: (0.000063) test_names: .: (0.000051) test_to_re: .: (0.000071) test_to_s: .: (0.000038) Bio::TestSequenceAACompat: test_aa_self_randomize: .: (0.000135) Bio::TestSequenceAANew: test_new: .: (0.000085) test_new_n: .: (0.000042) test_new_r: .: (0.000035) test_new_t: .: (0.000037) Bio::TestSequenceCommon::TestSequenceCommon: test_composition: .: (0.000110) test_concat: .: (0.000042) test_push: .: (0.000037) test_seq: .: (0.000036) test_splicing: .: (0.000107) test_sum: .: (0.000040) test_to_s: .: (0.000034) test_to_str: .: (0.000033) test_total: .: (0.000041) test_window_search: .: (0.000115) Bio::TestSequenceCommon::TestSequenceCommonNormalize: test_no_normalize: .: (0.000100) test_normalize_A: .: (0.000041) test_normalize_a: .: (0.000037) Bio::TestSequenceCommon::TestSequenceCommonRandomize: test_randomize: .: (0.000665) test_randomize_with_block: .: (0.001911) test_randomize_with_hash: .: (0.000678) test_randomize_with_hash_block: .: (0.002152) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:325:in 'Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2#test_randomize_equiprobability' =============================================================================== : (0.003219) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:331:in 'Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2#test_randomize_with_hash_equiprobability' =============================================================================== : (0.005445) Bio::TestSequenceCommon::TestSequenceCommonSubseq: test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000166) test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000078) test_subseq_returns_subsequence: .: (0.000051) test_to_s_returns_self_as_string: .: (0.000054) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: test_window_search_with_width_3_default_step_no_residual: .: (0.001462) test_window_search_with_width_3_step_two_with_residual: .: (0.000067) Bio::TestSequenceCompat::TestSequenceCommonCompat: test_to_fasta: .: (0.000921) Bio::TestSequenceCompat::TestSequenceCompat: test_to_s: .: (0.000113) Bio::TestSequenceCompat::TestSequenceNACompat: test_aa_self_randomize: .: (0.000831) test_na_self_randomize: .: (0.000089) Bio::TestSequenceDBLink: test_database: .: (0.000113) test_id: .: (0.000039) test_secondary_ids: .: (0.000781) Bio::TestSequenceDBLinkClassMethods: test_parse_embl_DR_line: .: (0.001549) test_parse_uniprot_DR_line: .: (0.000077) Bio::TestSequenceFormatFormatterFasta_numeric: test_output: .: (0.003545) test_output_width_35: .: (0.001342) test_output_width_nil: .: (0.000788) Bio::TestSequenceFormatFormatterQual: test_output: .: (0.001487) test_output_after_adding_sequence: .: (0.000863) test_output_after_truncating_sequence: .: (0.000807) test_output_from_error_probabilities: .: (0.009314) test_output_width45: .: (0.000332) test_output_with_converting_score_phred2solexa: .: (0.000937) test_output_with_converting_score_solexa2phred: .: (0.000559) test_output_with_default_score: .: (0.000481) Bio::TestSequenceMasker: test_mask: .: (0.000185) test_mask_with_enumerator: .: (0.000082) test_mask_with_enumerator_empty_mask_char: .: (0.000471) test_mask_with_enumerator_excess: .: (0.000224) test_mask_with_enumerator_longer_mask_char: .: (0.000067) test_mask_with_enumerator_shorter: .: (0.000697) test_mask_with_error_probability: .: (0.000369) test_mask_with_quality_score: .: (0.000065) Bio::TestSequenceNA: test_at_content: .: (0.000461) test_at_skew: .: (0.000461) test_codon_usage: .: (0.000074) test_complement: .: (0.000368) test_dna: .: (0.000060) test_dna!: .: (0.000044) test_forward_complement: .: (0.000392) test_gc_content: .: (0.000116) test_gc_percent: .: (0.000414) test_gc_skew: .: (0.000785) test_iliegal_bases: .: (0.000057) test_molecular_weight: .: (0.000071) test_names: .: (0.000491) test_reverse_complement: .: (0.000072) test_rna: .: (0.000457) test_rna!: .: (0.000043) test_splicing: .: (0.000109) test_to_re: .: (0.000492) test_to_s: .: (0.000049) Bio::TestSequenceNACommon: test_composition: .: (0.000514) test_concat: .: (0.000049) test_push: .: (0.000039) test_seq: .: (0.000431) test_splicing: .: (0.000458) test_sum: .: (0.000051) test_to_s: .: (0.000387) test_to_str: .: (0.000045) test_total: .: (0.000047) test_window_search: .: (0.000438) Bio::TestSequenceNANew: test_new: .: (0.000487) test_new_n: .: (0.000068) test_new_r: .: (0.000038) test_new_t: .: (0.000036) Bio::TestSequenceNATranslation: test_translate: .: (0.000566) test_translate_0: .: (0.002309) test_translate_1: .: (0.000808) test_translate_2: .: (0.000142) test_translate_3: .: (0.000110) test_translate_4: .: (0.000736) test_translate_5: .: (0.000772) test_translate_6: .: (0.000111) test_translate_7: .: (0.000642) test_translate_given_codon_table: .: (0.025154) test_translate_n1: .: (0.000358) test_translate_n2: .: (0.000256) test_translate_n3: .: (0.000253) test_translate_unknown_o: .: (0.000130) test_translate_unknown_x: .: (0.000127) Bio::TestSequenceQualityScore::TestConverter: test_convert_nothing: .: (0.000136) test_convert_scores_from_phred_to_solexa: .: (0.000332) test_convert_scores_from_solexa_to_phred: .: (0.000077) Bio::TestSequenceQualityScore::TestPhred: test_convert_nothing: .: (0.000094) test_convert_scores_from_phred: .: (0.000040) test_convert_scores_from_phred_to_solexa: .: (0.000173) test_convert_scores_from_solexa: .: (0.000072) test_convert_scores_from_solexa_to_phred: .: (0.000069) test_convert_scores_to_phred: .: (0.000035) test_convert_scores_to_solexa: .: (0.000173) test_p2q: .: (0.000073) test_phred_p2q: .: (0.000063) test_phred_q2p: .: (0.001089) test_q2p: .: (0.001083) test_quality_score_type: .: (0.000049) test_self_convert_scores_to_solexa: .: (0.000186) test_self_p2q: .: (0.000247) test_self_q2p: .: (0.000900) Bio::TestSequenceQualityScore::TestSolexa: test_convert_nothing: .: (0.000164) test_convert_scores_from_phred: .: (0.000357) test_convert_scores_from_phred_to_solexa: .: (0.000172) test_convert_scores_from_solexa: .: (0.000036) test_convert_scores_from_solexa_to_phred: .: (0.000088) test_convert_scores_to_phred: .: (0.000070) test_convert_scores_to_solexa: .: (0.000032) test_p2q: .: (0.000090) test_q2p: .: (0.001176) test_quality_score_type: .: (0.000048) test_self_convert_scores_to_phred: .: (0.000080) test_self_p2q: .: (0.000087) test_self_q2p: .: (0.001155) test_solexa_p2q: .: (0.000098) test_solexa_q2p: .: (0.001148) Bio::TestSequenceRuby3::TestSequenceCommon: test_capitalize: .: (0.000143) test_center: .: (0.000051) test_chomp: .: (0.000068) test_chop: .: (0.000058) test_delete: .: (0.000044) test_delete_prefix: .: (0.000042) test_delete_suffix: .: (0.000047) test_downcase: .: (0.000043) test_each_char: .: (0.000083) test_each_char_enum: .: (0.000070) test_each_grapheme_cluster: .: (0.000436) test_each_grapheme_cluster_enum: .: (0.000077) test_each_line: .: (0.000069) test_each_line_enum: .: (0.000062) test_gsub: .: (0.000057) test_gsub_with_block: .: (0.000225) test_ljust: .: (0.000048) test_lstrip: .: (0.000045) test_multiply: .: (0.000044) test_next: .: (0.000048) test_reverse: .: (0.000053) test_rjust: .: (0.000046) test_rstrip: .: (0.000045) test_slice: .: (0.000047) test_slice2: .: (0.000044) test_split: .: (0.000062) test_squeeze: .: (0.000048) test_strip: .: (0.000046) test_sub: .: (0.000092) test_sub_with_block: .: (0.000126) test_succ: .: (0.000045) test_swapcase: .: (0.000062) test_tr: .: (0.000048) test_tr_s: .: (0.000042) test_upcase: .: (0.000044) Bio::TestSequenceRuby3::TestSequenceCommonPartition: test_partition: .: (0.000194) test_partition_nomatch: .: (0.000063) test_partition_sep_TSeq: .: (0.000064) test_partition_sep_regexp: .: (0.000064) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: test_rpartition: .: (0.000119) test_rpartition_nomatch: .: (0.000060) test_rpartition_sep_TSeq: .: (0.000057) test_rpartition_sep_regexp: .: (0.000059) Bio::TestShRNA: test_blocK_it: .: (0.029273) test_blocK_it_: .: (0.018749) test_blocK_it_BLOCK_IT: .: (0.017371) test_blocK_it_BLOCK_iT: .: (0.014959) test_blocK_it_piGene: .: (0.014260) test_bottom_strand: .: (0.015250) test_bottom_strand_class: .: (0.013898) test_bottom_strand_nil: .: (0.014422) test_design: .: (0.013993) test_design_BLOCK_IT: .: (0.014215) test_report: .: (0.014496) test_report_before_design: .: (0.014367) test_top_strand: .: (0.014500) test_top_strand_class: .: (0.013570) test_top_strand_nil: .: (0.013805) Bio::TestShRNANew: test_new: .: (0.000625) Bio::TestSiRNA: test_antisense_size: .: (0.000107) test_design: .: (0.014770) test_design_reynolds: .: (0.017484) test_design_uitei: .: (0.014048) test_max_gc_percent: .: (0.000061) test_min_gc_percent: .: (0.000039) test_reynolds: .: (0.016691) test_reynolds?: .: (0.000079) test_uitei: .: (0.014920) test_uitei?: .: (0.000069) Bio::TestSiRNANew: test_new: .: (0.000682) Bio::TestSiRNAPair: test_antisense: .: (0.013778) test_gc_percent: .: (0.014718) test_report: .: (0.013630) test_rule: .: (0.014825) test_sense: .: (0.013688) test_start: .: (0.014934) test_stop: .: (0.013668) test_target: .: (0.014671) Bio::TestSiRNAPairNew: test_new: .: (0.000294) Bio::TestSim4Report: test_all_hits: .: (0.000234) test_each: .: (0.000105) test_each_hit: .: (0.000089) test_hits: .: (0.000255) test_num_hits: .: (0.000099) test_query_def: .: (0.000077) test_query_id: .: (0.000073) test_query_len: .: (0.000071) test_seq1: .: (0.000098) Bio::TestSim4Report2: test_all_hits: .: (0.000163) test_each: .: (0.000090) test_each_hit: .: (0.000082) test_hits: .: (0.000082) test_num_hits: .: (0.000077) test_query_def: .: (0.000071) test_query_id: .: (0.000068) test_query_len: .: (0.000070) test_seq1: .: (0.000088) Bio::TestSim4Report4: test_all_hits: .: (0.000158) test_each: .: (0.000181) test_each_hit: .: (0.000100) test_hits: .: (0.000090) test_num_hits: .: (0.000075) test_query_def: .: (0.000077) test_query_id: .: (0.000076) test_query_len: .: (0.000075) test_seq1: .: (0.000101) Bio::TestSim4ReportHit: test_align: .: (0.000191) test_complement?: .: (0.000081) test_definition: .: (0.000074) test_each: .: (0.000213) test_exons: .: (0.000160) test_hit_id: .: (0.000083) test_hsps: .: (0.000137) test_introns: .: (0.000135) test_len: .: (0.000077) test_query_def: .: (0.000075) test_query_id: .: (0.000073) test_query_len: .: (0.000072) test_segmentpairs: .: (0.000161) test_seq1: .: (0.000100) test_seq2: .: (0.000092) test_target_def: .: (0.000128) test_target_id: .: (0.000075) test_target_len: .: (0.000081) Bio::TestSim4ReportHit2: test_align: .: (0.000926) test_complement?: .: (0.000088) test_definition: .: (0.000072) test_each: .: (0.000137) test_exons: .: (0.000133) test_hit_id: .: (0.000074) test_hsps: .: (0.000131) test_introns: .: (0.000125) test_len: .: (0.000072) test_query_def: .: (0.000071) test_query_id: .: (0.000070) test_query_len: .: (0.000069) test_segmentpairs: .: (0.000133) test_seq1: .: (0.000094) test_seq2: .: (0.000089) test_target_def: .: (0.000070) test_target_id: .: (0.000069) test_target_len: .: (0.000069) Bio::TestSim4ReportHit4: test_align: .: (0.000200) test_complement?: .: (0.000082) test_definition: .: (0.000081) test_each: .: (0.000190) test_exons: .: (0.000184) test_hit_id: .: (0.000093) test_hsps: .: (0.000176) test_introns: .: (0.000174) test_len: .: (0.000081) test_query_def: .: (0.000078) test_query_id: .: (0.000074) test_query_len: .: (0.000074) test_segmentpairs: .: (0.000189) test_seq1: .: (0.000105) test_seq2: .: (0.000098) test_target_def: .: (0.000075) test_target_id: .: (0.000074) test_target_len: .: (0.000075) Bio::TestSim4ReportSegment: test_from: .: (0.000087) test_self_new: .: (0.000051) test_seq: .: (0.000034) test_to: .: (0.000032) Bio::TestSim4ReportSegmentPair2_exon: test_align_len: .: (0.000179) test_direction: .: (0.000119) test_hit_from: .: (0.000116) test_hit_to: .: (0.000111) test_hseq: .: (0.000111) test_midline: .: (0.000110) test_percent_identity: .: (0.000112) test_qseq: .: (0.000113) test_query_from: .: (0.000113) test_query_to: .: (0.000110) test_seq1: .: (0.000152) test_seq2: .: (0.000131) Bio::TestSim4ReportSegmentPair2_intron: test_align_len: .: (0.000177) test_direction: .: (0.000125) test_hit_from: .: (0.000114) test_hit_to: .: (0.000112) test_hseq: .: (0.000111) test_midline: .: (0.000111) test_percent_identity: .: (0.000113) test_qseq: .: (0.000111) test_query_from: .: (0.000111) test_query_to: .: (0.000111) test_seq1: .: (0.000130) test_seq2: .: (0.000131) Bio::TestSim4ReportSegmentPair4_exon: test_align_len: .: (0.000215) test_direction: .: (0.000158) test_hit_from: .: (0.000152) test_hit_to: .: (0.000151) test_hseq: .: (0.000153) test_midline: .: (0.000149) test_percent_identity: .: (0.000151) test_qseq: .: (0.000149) test_query_from: .: (0.000150) test_query_to: .: (0.001680) test_seq1: .: (0.000326) test_seq2: .: (0.000185) Bio::TestSim4ReportSegmentPair4_intron: test_align_len: .: (0.000230) test_direction: .: (0.000165) test_hit_from: .: (0.000159) test_hit_to: .: (0.000801) test_hseq: .: (0.000163) test_midline: .: (0.000150) test_percent_identity: .: (0.000168) test_qseq: .: (0.000151) test_query_from: .: (0.000151) test_query_to: .: (0.000160) test_seq1: .: (0.000174) test_seq2: .: (0.000703) Bio::TestSim4ReportSegmentPair4_intron1: test_align_len: .: (0.000365) test_direction: .: (0.000160) test_hit_from: .: (0.000154) test_hit_to: .: (0.000149) test_hseq: .: (0.000150) test_midline: .: (0.000150) test_percent_identity: .: (0.000149) test_qseq: .: (0.000272) test_query_from: .: (0.000157) test_query_to: .: (0.000166) test_seq1: .: (0.000173) test_seq2: .: (0.000171) Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.000192) test_direction: .: (0.000354) test_hit_from: .: (0.000147) test_hit_to: .: (0.000187) test_hseq: .: (0.000118) test_midline: .: (0.000111) test_percent_identity: .: (0.000110) test_qseq: .: (0.000114) test_query_from: .: (0.000113) test_query_to: .: (0.000111) test_seq1: .: (0.000129) test_seq2: .: (0.000127) Bio::TestSim4ReportSegmentPair_intron: test_align_len: .: (0.000449) test_direction: .: (0.000129) test_hit_from: .: (0.000116) test_hit_to: .: (0.000112) test_hseq: .: (0.000113) test_midline: .: (0.000110) test_percent_identity: .: (0.000149) test_qseq: .: (0.000119) test_query_from: .: (0.000112) test_query_to: .: (0.000109) test_seq1: .: (0.000136) test_seq2: .: (0.000132) Bio::TestSim4ReportSeqDesc: test_definition: .: (0.000237) test_entry_id: .: (0.000041) test_filename: .: (0.000037) test_len: .: (0.000036) test_self_new: .: (0.000045) test_self_parse: .: (0.000054) Bio::TestTMHMMReport: test_entry_id: .: (0.000223) test_exp_aas_in_tmhs: .: (0.000151) test_exp_first_60aa: .: (0.000148) test_helix: .: (0.000163) test_predicted_tmhs: .: (0.000143) test_query_len: .: (0.000224) test_tmhs: .: (0.000156) test_to_s: .: (0.000259) test_total_prob_of_N_in: .: (0.000150) Bio::TestTMHMMReport_reports: test_reports: .: (0.000109) Bio::TestTMHMMTMH: test_entry_id: .: (0.000197) test_pos: .: (0.000150) test_range: .: (0.001401) test_status: .: (0.000156) test_version: .: (0.000143) Bio::TestTargetPReport: test_cleavage_site_prediction: .: (0.000172) test_cutoff: .: (0.000096) test_entry_id: .: (0.000089) test_length: .: (0.000088) test_loc: .: (0.000087) test_name: .: (0.000086) test_networks: .: (0.000085) test_prediction: .: (0.000095) test_query_len: .: (0.000086) test_query_sequences: .: (0.000086) test_rc: .: (0.000087) test_version: .: (0.000087) Bio::TestTargetPReportConst: test_delimiter: .: (0.000080) test_rs: .: (0.000035) Bio::TestTogoWSAccessWait: test_reset_togows_access_wait: .: (0.000080) test_togows_access_wait: .: (2.000196) Bio::TestTogoWSREST: test_debug: .: (0.000382) test_debug_default: .: (0.000093) test_internal_http: .: (0.000085) Bio::TestTogoWSRESTclassMethod: test_convert: .: (0.000107) test_entry: .: (0.000040) test_entry_database_list: .: (0.000038) test_new: .: (0.000089) test_new_with_uri_object: .: (0.000099) test_new_with_uri_string: .: (0.000086) test_retrieve: .: (0.000038) test_search: .: (0.000036) test_search_database_list: .: (0.000036) Bio::TestTogoWSRESTprivate: test_make_path: .: (0.000168) test_prepare_return_value: .: (0.000107) Bio::TestTopologicalSort: test_dfs_topological_sort: .: (0.000211) Bio::TestTree: test_get_edge_distance: .: (0.000129) test_get_edge_distance_string: .: (0.000067) test_get_node_name: .: (0.000047) test_initialize: .: (0.000053) test_options: .: (0.000046) test_root: .: (0.000035) test_root=: .: (0.000042) Bio::TestTree2: test_add_edge: .: (0.000178) test_add_node: .: (0.000099) test_adjacency_matrix: .: (0.000113) test_adjacency_matrix_with_block: .: (0.000098) test_adjacent_nodes: .: (0.000104) test_adjacent_nodes_nonexistent: .: (0.000064) test_ancestors: .: (0.000087) test_children: .: (0.000075) test_clear: .: (0.000082) test_clear_node: .: (0.000097) test_clear_node_nonexistent: .: (0.000104) test_collect_edge!: .: (0.000145) test_collect_node!: .: (0.000129) test_concat: .: (0.000127) test_descendents: .: (0.000087) test_distance_matrix: .: (0.000235) test_each_edge: .: (0.000103) test_each_node: .: (0.000091) test_each_out_edge: .: (0.000083) test_each_out_edge_chimpanzee: .: (0.000079) test_each_out_edge_human: .: (0.000077) test_each_out_edge_mammals: .: (0.000096) test_each_out_edge_nonexistent: .: (0.000068) test_each_out_edge_primates: .: (0.000104) test_each_out_edge_rat: .: (0.000078) test_each_out_edge_rodents: .: (0.000102) test_edges: .: (0.000074) test_get_edge: .: (0.000156) test_get_edge_indirect: .: (0.000062) test_get_edge_merged: .: (0.000069) test_get_edge_nonexistent: .: (0.000061) test_get_node_bootstrap: .: (0.000067) test_get_node_bootstrap_string=: .: (0.000069) test_get_node_by_name: .: (0.000099) test_get_node_by_name_noexistent: .: (0.000061) test_include?: .: (0.000086) test_include_nonexistent: .: (0.000058) test_insert_node: .: (0.000108) test_leaves: .: (0.000092) test_leaves_noargs: .: (0.000071) test_lowest_common_ancestor: .: (0.000075) test_nodes: .: (0.000066) test_number_of_edges: .: (0.000061) test_number_of_nodes: .: (0.000059) test_out_degree: .: (0.000084) test_out_degree_nonexistent: .: (0.000062) test_out_edges: .: (0.000084) test_out_edges_mammals: .: (0.000095) test_out_edges_nonexistent: .: (0.000080) test_out_edges_primates: .: (0.000108) test_out_edges_rodents: .: (0.000107) test_parent: .: (0.000085) test_path: .: (0.000075) test_remove_edge: .: (0.000087) test_remove_edge_if: .: (0.000089) test_remove_edge_if_nothing_removed: .: (0.000093) test_remove_edge_nonexistent: .: (0.000088) test_remove_node: .: (0.000094) test_remove_node_if: .: (0.000072) test_remove_node_if_false: .: (0.000082) test_remove_node_nonexistent: .: (0.000078) test_remove_nonsense_nodes: .: (0.000088) test_subtree: .: (0.000104) test_subtree_with_all_paths: .: (0.003486) test_total_distance: .: (0.000105) Bio::TestTreeEdge: test_distance: .: (0.000104) test_distance=: .: (0.000057) test_distance_string: .: (0.000037) test_distance_string=: .: (0.000055) test_initialize: .: (0.000053) test_inspect: .: (0.000038) test_to_s: .: (0.000038) Bio::TestTreeNode: test_bootstrap: .: (0.000085) test_bootstrap=: .: (0.000056) test_bootstrap_string: .: (0.000033) test_bootstrap_string=: .: (0.000065) test_initialize: .: (0.000050) test_inspect: .: (0.000051) test_name: .: (0.000039) test_to_s: .: (0.000035) Bio::TestUniProt: test_gene_name: .: (0.003467) Bio::TestUniProtKB: test_ac: .: (0.002136) test_accession: .: (0.001701) test_cc: .: (0.006080) test_cc_alternative_products: .: (0.015906) test_cc_database: .: (0.028447) test_cc_mass_spectrometry: .: (0.003901) test_de: .: (0.001800) test_dr: .: (0.002752) test_dr_with_key: .: (0.002532) test_dr_with_key_empty: .: (0.002298) test_dt: .: (0.001382) test_dt_annotation: .: (0.001408) test_dt_created: .: (0.001339) test_dt_sequence: .: (0.001437) test_entry: .: (0.001321) test_ft: .: (0.007124) test_gene_name: .: (0.002755) test_gene_names: .: (0.002355) test_gn: .: (0.001791) test_gn_old_parser: .: (0.001642) test_gn_uniprot_parser: .: (0.001497) test_id_line: .: (0.001466) test_id_line_data_class: .: (0.001409) test_id_line_entry_name: .: (0.001384) test_id_line_molecule_type: .: (0.001421) test_id_line_sequence_length: .: (0.001511) test_kw: .: (0.001431) test_molecule: .: (0.001978) test_oc: .: (0.001251) test_og_1: .: (0.001274) test_og_2: .: (0.001315) test_og_3: .: (0.001311) test_og_4: .: (0.001339) test_og_5: .: (0.001355) test_og_6: .: (0.001409) test_os: .: (0.004604) test_os_access: .: (0.001994) test_os_access2: .: (0.002427) test_ox: .: (0.001836) test_protein_name: .: (0.002021) test_ref: .: (0.004014) test_seq: .: (0.001401) test_sequence_length: .: (0.001437) test_sq: .: (0.001411) test_sq_crc64: .: (0.002191) test_sq_len: .: (0.001208) test_sq_mw: .: (0.001216) test_synonyms: .: (0.001298) Bio::TestUniProtKB_CC: test_allergen: .: (0.000186) test_alternative_products_access_as_hash: .: (0.000112) test_alternative_products_ai: .: (0.000139) test_alternative_products_apu: .: (0.000232) test_alternative_products_as: .: (0.000136) test_alternative_products_rf: .: (0.000041) test_biophysicochemical_properties: .: (0.000201) test_biotechnology: .: (0.000104) test_catalytic_activity: .: (0.000096) test_caution: .: (0.000100) test_cofactor: .: (0.000085) test_developmental_stage: .: (0.000092) test_disease: .: (0.000141) test_domain: .: (0.000163) test_enzyme_regulation: .: (0.000088) test_function: .: (0.000103) test_induction: .: (0.000074) test_interaction: .: (0.000114) test_mass_spectrometry: .: (0.000124) test_miscellaneous: .: (0.000077) test_pathway: .: (0.000097) test_pharmaceutical: .: (0.000089) test_polymorphism: .: (0.000130) test_ptm: .: (0.000079) test_rna_editing: .: (0.000111) test_similarity: .: (0.000077) test_subcellular_location: .: (0.000098) test_subunit: .: (0.000066) test_tissue_specificity: .: (0.000091) test_toxic_dose: .: (0.000070) test_web_resource: .: (0.000128) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: test_cc_web_resource: .: (0.000194) Bio::TestUniProtKB_DE_since_rel14_0: test_private_parse_DE_line_rel14: .: (0.000223) test_protein_name: .: (0.000139) test_synonyms: .: (0.000167) Bio::TestUniProtKB_ID_since_rel9_0: test_aalen: .: (0.000101) test_entry: .: (0.000050) test_entry_id: .: (0.000045) test_entry_name: .: (0.000042) test_id_line: .: (0.000060) test_molecule: .: (0.000046) test_sequence_length: .: (0.000044) Bio::TestUniProtKB_P03589: test_ac: .: (0.000270) test_accession: .: (0.000212) test_cc: .: (0.000331) test_cc_alternative_products: .: (0.000317) test_cc_database: .: (0.000320) test_cc_mass_spectrometry: .: (0.000316) test_de: .: (0.000205) test_dr: .: (0.000339) test_dr_with_key: .: (0.000339) test_dr_with_key_empty: .: (0.000311) test_dt: .: (0.000187) test_dt_annotation: .: (0.000186) test_dt_created: .: (0.000202) test_dt_sequence: .: (0.000181) test_entry: .: (0.000193) test_ft: .: (0.000319) test_gene_name: .: (0.000229) test_gene_names: .: (0.000211) test_gn: .: (0.000203) test_gn_old_parser: .: (0.000223) test_gn_uniprot_parser: .: (0.000214) test_id_line: .: (0.000193) test_id_line_data_class: .: (0.000185) test_id_line_entry_name: .: (0.000181) test_id_line_sequence_length: .: (0.000176) test_kw: .: (0.000223) test_oc: .: (0.000216) test_oh: .: (0.002622) test_os: .: (0.000236) test_os_access: .: (0.000206) test_os_access2: .: (0.000201) test_ox: .: (0.000211) test_protein_name: .: (0.000231) test_protein_name_after_calling_de: .: (0.000851) test_ref: .: (0.000234) test_seq: .: (0.000374) test_sequence_length: .: (0.000187) test_sq: .: (0.000200) test_sq_crc64: .: (0.000731) test_sq_len: .: (0.000204) test_sq_mw: .: (0.000194) test_synonyms: .: (0.000203) Bio::TestUniProtKB_P28907: test_ac: .: (0.001212) test_accession: .: (0.000570) test_cc: .: (0.001485) test_cc_alternative_products: .: (0.000894) test_cc_database: .: (0.001359) test_cc_mass_spectrometry: .: (0.000852) test_de: .: (0.001000) test_dr: .: (0.001921) test_dr_with_key: .: (0.001600) test_dr_with_key_empty: .: (0.001696) test_dt: .: (0.000556) test_dt_annotation: .: (0.002390) test_dt_created: .: (0.000490) test_dt_sequence: .: (0.000472) test_entry: .: (0.000512) test_ft: .: (0.001076) test_gene_name: .: (0.000513) test_gene_names: .: (0.000493) test_gn: .: (0.000511) test_gn_old_parser: .: (0.000566) test_gn_uniprot_parser: .: (0.000577) test_id_line: .: (0.000538) test_id_line_data_class: .: (0.000509) test_id_line_entry_name: .: (0.000511) test_id_line_sequence_length: .: (0.000512) test_kw: .: (0.000557) test_oc: .: (0.000549) test_os: .: (0.000542) test_os_access: .: (0.000535) test_os_access2: .: (0.000545) test_ox: .: (0.000530) test_protein_name: .: (0.000590) test_protein_name_after_calling_de: .: (0.002977) test_ref: .: (0.001527) test_seq: .: (0.001223) test_sequence_length: .: (0.000551) test_sq: .: (0.001092) test_sq_crc64: .: (0.000527) test_sq_len: .: (0.001151) test_sq_mw: .: (0.000565) test_synonyms: .: (0.001037) test_synonyms_after_calling_de: .: (0.000997) Bio::TestUniProtKB_P49144: test_ac: .: (0.000380) test_accession: .: (0.000284) test_cc: .: (0.000877) test_cc_alternative_products: .: (0.000535) test_cc_database: .: (0.000511) test_cc_mass_spectrometry: .: (0.000503) test_de: .: (0.000279) test_dr: .: (0.000615) test_dr_with_key: .: (0.000540) test_dr_with_key_empty: .: (0.000514) test_dt: .: (0.000426) test_dt_annotation: .: (0.000257) test_dt_created: .: (0.000276) test_dt_sequence: .: (0.000262) test_entry: .: (0.000398) test_ft: .: (0.000748) test_gene_name: .: (0.000306) test_gene_names: .: (0.000291) test_gn: .: (0.000336) test_gn_old_parser: .: (0.000295) test_gn_uniprot_parser: .: (0.000299) test_id_line: .: (0.000407) test_id_line_data_class: .: (0.000277) test_id_line_entry_name: .: (0.000269) test_id_line_sequence_length: .: (0.000266) test_kw: .: (0.000311) test_oc: .: (0.000403) test_os: .: (0.000265) test_os_access: .: (0.000276) test_os_access2: .: (0.000287) test_ox: .: (0.000283) test_protein_name: .: (0.000290) test_protein_name_after_calling_de: .: (0.000300) test_ref: .: (0.000387) test_seq: .: (0.000449) test_sequence_length: .: (0.000276) test_sq: .: (0.000282) test_sq_crc64: .: (0.000958) test_sq_len: .: (0.000284) test_sq_mw: .: (0.000270) test_synonyms: .: (0.000295) test_synonyms_after_calling_de: .: (0.000293) Bio::TestUniProtKB_Ref: test_RA: .: (0.000206) test_RC: .: (0.000117) test_RG: .: (0.000108) test_RL: .: (0.000106) test_RN: .: (0.000104) test_RP: .: (0.000115) test_RT: .: (0.000105) test_RX: .: (0.000108) test_ref: .: (0.000112) Bio::TestUniProtKB_SwissProtRel41_0: test_multiple_RP_lines: .: (0.000124) Bio::TestUniProtKB_SwissProtRel41_1: test_alternative_products: .: (0.000254) test_alternative_products_with_ft: .: (0.000358) Bio::TestUniProtKB_SwissProtRel41_10: test_RC_lines: .: (0.000168) Bio::TestUniProtKB_SwissProtRel41_20: test_CC_allergen: .: (0.000140) test_RL_lines: .: (0.000060) Bio::TestUniProtKB_SwissProtRel42_6: test_CC_rna_editing: .: (0.000257) Bio::TestUniProtKB_UniProtRel1_12: test_DOI_in_RX_line: .: (0.000112) test_RG_line: .: (0.000064) Bio::TestUniProtKB_UniProtRel2_0: test_GN_line: .: (0.000246) Bio::TestUniProtKB_UniProtRel2_1: test_CC_mass_spectrometry: .: (0.000141) Bio::TestUniProtKB_UniProtRel2_3: test_DR_PDB: .: (0.000097) test_RL_line: .: (0.000060) Bio::TestUniProtKB_UniProtRel3_4: test_CC_biophysiochemical_properties: .: (0.000350) test_RP_line: .: (0.000111) Bio::TestUniProtKB_UniProtRel3_5: test_entry_name_format: .: (0.000071) Bio::TestUniProtKB_UniProtRel4_0: test_CC_interaction: .: (0.000142) test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000101) test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000085) test_CC_interaction_isoform: .: (0.000079) test_CC_interaction_no_gene_name: .: (0.000078) test_CC_interaction_self_association: .: (0.000089) Bio::TestUniProtKB_UniProtRel5_0: test_DR_line: .: (0.000118) Bio::TestUniProtKB_UniProtRel5_4: test_multiple_cofactors: .: (0.000133) Bio::TestUniProtKB_UniProtRel6_0: test_OG_line: .: (0.000179) Bio::TestUniProtKB_UniProtRel6_1: test_FT_metal: .: (0.000144) Bio::TestUniProtKB_UniProtRel6_5: test_HI_line: .: (0.000130) Bio::TestUniProtKB_UniProtRel7_0: test_CC_copyright_statement: .: (0.000113) test_DT_line: .: (0.000070) Bio::TestUniProtKB_UniProtRel7_6: test_10000aa: .: (0.001890) Bio::TestUniProtKB_UniProtRel8_0: test_CC_alternative_products: .: (0.000338) test_CC_web_resource: .: (0.000041) test_FT_VER_SEQ: .: (0.000085) test_OH_line_exception: .: (0.000126) test_OH_lines: .: (0.000155) Bio::TestUtils: test_centreOfGravity: .: (0.000263) test_dihedral_angle: .: (0.000173) test_distance: .: (0.000160) test_geometricCentre: .: (0.000116) test_rad2deg: .: (0.000077) Bio::TestWeightedGraph: test_bellman_ford_on_negative_weighted_graph: .: (0.000160) test_dijkstra_on_weighted_graph: .: (0.000067) Finished in 8.231574695 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- 478.77 tests/s, 2624.16 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/reproducible-path/ruby-bio-2.0.6' 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_2.0.6-1+rebuild1766571925_all.deb'. dpkg-genbuildinfo --build=binary -O../ruby-bio_2.0.6-1+rebuild1766571925_amd64.buildinfo dpkg-genchanges --build=binary -mAutomated rebuild -O../ruby-bio_2.0.6-1+rebuild1766571925_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-12-24T10:26:19Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 24 Dec 2025 10:26:19 +0000 | +------------------------------------------------------------------------------+ ruby-bio_2.0.6-1+rebuild1766571925_amd64.changes: ------------------------------------------------- Format: 1.8 Date: Wed, 24 Dec 2025 10:25:25 +0000 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1+rebuild1766571925 Distribution: unstable Urgency: medium Maintainer: Automated rebuild Changed-By: mass-rebuild Description: ruby-bio - Ruby tools for computational molecular biology Changes: ruby-bio (2.0.6-1+rebuild1766571925) UNRELEASED; urgency=medium . * Rebuild with mass-rebuild Checksums-Sha1: 98f1b7ef4427c1ca7ce660365e4daeb0c5c1b6eb 705928 ruby-bio_2.0.6-1+rebuild1766571925_all.deb e35d08ff19909f452b9fa1cb180729e8f6bfc3d5 5690 ruby-bio_2.0.6-1+rebuild1766571925_amd64.buildinfo Checksums-Sha256: 1a16f2ab6580b18449856b85c28b3d029cfe0d2272ca9c85e91c6a0dfc5057e8 705928 ruby-bio_2.0.6-1+rebuild1766571925_all.deb 17406c981954837a4f2823d075fe50cc7d8ad1f2726fa9ad09cbaad6e9e5a846 5690 ruby-bio_2.0.6-1+rebuild1766571925_amd64.buildinfo Files: 997693d9e83dd560eb1a069aec86ad9c 705928 ruby optional ruby-bio_2.0.6-1+rebuild1766571925_all.deb 6fbd27ad8305c741d3de9022812220fc 5690 ruby optional ruby-bio_2.0.6-1+rebuild1766571925_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Wed, 24 Dec 2025 10:26:20 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: ruby-bio Binary: ruby-bio Architecture: all Version: 2.0.6-1+rebuild1766571925 Checksums-Md5: 997693d9e83dd560eb1a069aec86ad9c 705928 ruby-bio_2.0.6-1+rebuild1766571925_all.deb Checksums-Sha1: 98f1b7ef4427c1ca7ce660365e4daeb0c5c1b6eb 705928 ruby-bio_2.0.6-1+rebuild1766571925_all.deb Checksums-Sha256: 1a16f2ab6580b18449856b85c28b3d029cfe0d2272ca9c85e91c6a0dfc5057e8 705928 ruby-bio_2.0.6-1+rebuild1766571925_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 24 Dec 2025 10:26:19 +0000 Build-Path: /build/reproducible-path/ruby-bio-2.0.6 Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-1), binutils (= 2.45.50.20251209-1), binutils-common (= 2.45.50.20251209-1), binutils-x86-64-linux-gnu (= 2.45.50.20251209-1), bsdextrautils (= 2.41.3-2), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20250419), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-15 (= 15.2.0-12), cpp-15-x86-64-linux-gnu (= 15.2.0-12), cpp-x86-64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.29), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), docbook (= 4.5-11), docbook-to-man (= 1:2.0.0-50), dpkg (= 1.23.3), dpkg-dev (= 1.23.3), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-12), g++-15-x86-64-linux-gnu (= 15.2.0-12), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-15 (= 15.2.0-12), gcc-15-base (= 15.2.0-12), gcc-15-x86-64-linux-gnu (= 15.2.0-12), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gem2deb (= 2.2.6), gem2deb-test-runner (= 2.2.6), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-12), libatomic1 (= 15.2.0-12), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.45.50.20251209-1), libblkid1 (= 2.41.3-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.42-6), libc-dev-bin (= 2.42-6), libc-gconv-modules-extra (= 2.42-6), libc6 (= 2.42-6), libc6-dev (= 2.42-6), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-12), libcrypt-dev (= 1:4.5.1-1), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.45.50.20251209-1), libctf0 (= 2.45.50.20251209-1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.29), libdpkg-perl (= 1.23.3), libelf1t64 (= 0.194-1), libffi8 (= 3.5.2-3), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-12), libgcc-s1 (= 15.2.0-12), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgmp-dev (= 2:6.3.0+dfsg-5), libgmp10 (= 2:6.3.0+dfsg-5), libgmpxx4ldbl (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-12), libgprofng0 (= 2.45.50.20251209-1), libhwasan0 (= 15.2.0-12), libisl23 (= 0.27-1), libitm1 (= 15.2.0-12), libjansson4 (= 2.14-2+b4), liblsan0 (= 15.2.0-12), liblzma5 (= 5.8.1-2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.3-2), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libosp5 (= 1.5.2-15.2), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.46-1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libquadmath0 (= 15.2.0-12), libruby (= 1:3.3+b1), libruby3.3 (= 3.3.8-2), libruby3.4 (= 3.4.5-1~exp1), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+rebuild1766544377), libsframe2 (= 2.45.50.20251209-1), libsmartcols1 (= 2.41.3-2), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-12), libstdc++6 (= 15.2.0-12), libsystemd0 (= 259-1), libtinfo6 (= 6.5+20251123-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-12), libubsan1 (= 15.2.0-12), libuchardet0 (= 0.0.8-2), libudev1 (= 259-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.3-2), libxml2-16 (= 2.15.1+dfsg-2+b1), libyaml-0-2 (= 0.2.5-2+b1), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.13-1), m4 (= 1.4.20-2), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-2), ncurses-base (= 6.5+20251123-1), ncurses-bin (= 6.5+20251123-1), opensp (= 1.5.2-15.2), openssl (= 3.5.4-1), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), rake (= 13.2.1-1), rdtool (= 0.6.38-5), rpcsvc-proto (= 1.4.3-1), ruby (= 1:3.3+b1), ruby-all-dev (= 1:3.3+support3.4~0), ruby-csv (= 3.3.4-1), ruby-did-you-mean (= 1.6.3-2), ruby-libxml (= 5.0.5-2+rebuild1766548530), ruby-minitest (= 5.26.1-1), ruby-net-telnet (= 0.2.0-1), ruby-power-assert (= 2.0.5-1), ruby-rd (= 0.6.38-5), ruby-ruby2-keywords (= 0.0.5-1), ruby-rubygems (= 3.6.7-2), ruby-test-unit (= 3.6.2-1), ruby-webrick (= 1.9.1-1), ruby-xmlrpc (= 0.3.3-2), ruby3.3 (= 3.3.8-2), ruby3.3-dev (= 3.3.8-2), ruby3.4 (= 3.4.5-1~exp1), ruby3.4-dev (= 3.4.5-1~exp1), rubygems-integration (= 1.19), sed (= 4.9-2), sensible-utils (= 0.0.26), sgml-base (= 1.31+nmu1), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.3-2), xml-core (= 0.19), xz-utils (= 5.8.1-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b2) Environment: DEB_BUILD_OPTIONS="parallel=8" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1766571925" +------------------------------------------------------------------------------+ | Package contents Wed, 24 Dec 2025 10:26:20 +0000 | +------------------------------------------------------------------------------+ ruby-bio_2.0.6-1+rebuild1766571925_all.deb ------------------------------------------ new Debian package, version 2.0. size 705928 bytes: control archive=8316 bytes. 860 bytes, 18 lines control 25124 bytes, 296 lines md5sums Package: ruby-bio Version: 2.0.6-1+rebuild1766571925 Architecture: all Maintainer: Debian Ruby Team Installed-Size: 2855 Recommends: ncbi-blast+-legacy, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Breaks: ruby-crb-blast (<< 0.6.9-4) Section: ruby Priority: optional Homepage: https://bioruby.org/ Description: Ruby tools for computational molecular biology BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation. drwxr-xr-x root/root 0 2025-12-24 10:25 ./ drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/ drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ruby/ drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/ -rw-r--r-- root/root 8467 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio.rb drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio/ -rw-r--r-- root/root 75097 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio/alignment.rb drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio/appl/ drwxr-xr-x root/root 0 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/ -rw-r--r-- root/root 4515 2025-12-24 10:25 ./usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb -rw-r--r-- root/root 15469 2025-12-24 10:25 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+------------------------------------------------------------------------------+ | Post Build Wed, 24 Dec 2025 10:26:20 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 24 Dec 2025 10:26:20 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 24 Dec 2025 10:26:21 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 11032 Build-Time: 23 Distribution: unstable Host Architecture: amd64 Install-Time: 8 Job: /home/admin/mass-rebuild/builds/3/ruby-bio/ruby-bio_2.0.6-1+rebuild1766571925.dsc Machine Architecture: amd64 Package: ruby-bio Package-Time: 53 Source-Version: 2.0.6-1+rebuild1766571925 Space: 11032 Status: successful Version: 2.0.6-1+rebuild1766571925 -------------------------------------------------------------------------------- Finished at 2025-12-24T10:26:19Z Build needed 00:00:53, 11032k disk space