DC-Build-Header: ruby-bio 1.4.1-2 / Sun Sep 11 12:09:56 +0200 2011 sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-122.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ ruby-bio 1.4.1-2 (amd64) 11 Sep 2011 12:09 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: ruby-bio Version: 1.4.1-2 Source Version: 1.4.1-2 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (63.4 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'ruby-bio' packaging is maintained in the 'Git' version control system at: git://git.debian.org/pkg-ruby-extras/ruby-bio.git Need to get 1371 kB of source archives. Get:1 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (dsc) [2053 B] Get:2 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (tar) [1360 kB] Get:3 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (diff) [9202 B] Fetched 1371 kB in 0s (4116 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/ruby-bio-f5XUcy/resolver-gPPBuB/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-0fe59ff1-ef8c-48ad-80f7-ac7df66ccf46/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), gem2deb (>= 0.2.4~), libxml-ruby1.8, libxml-ruby1.9.1, docbook-to-man, rdtool Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), gem2deb (>= 0.2.4~), libxml-ruby1.8, libxml-ruby1.9.1, docbook-to-man, rdtool dpkg-deb: building package `sbuild-build-depends-ruby-bio-dummy' in `/build/ruby-bio-f5XUcy/resolver-xaZY_z/apt_archive/sbuild-build-depends-ruby-bio-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install ruby-bio build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper devscripts docbook docbook-to-man file gem2deb gettext gettext-base groff-base html2text intltool-debian libcroco3 libdb4.8 libexpat1 libglib2.0-0 libmagic1 libpcre3 libpipeline1 librd-ruby1.8 libreadline5 libruby1.8 libruby1.9.1 libsp1c2 libsqlite3-0 libssl1.0.0 libunistring0 libxml-ruby1.8 libxml-ruby1.9.1 libxml2 libyaml-0-2 man-db mime-support po-debconf python python-minimal python2.6 python2.6-minimal rdtool ruby1.8 ruby1.8-dev ruby1.9.1 ruby1.9.1-dev rubygems rubygems1.8 sgml-base sgml-data sp xml-core Suggested packages: wamerican wordlist whois vacation dh-make bsd-mailx mailx cvs-buildpackage devscripts-el gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mutt ssh-client svn-buildpackage w3m psgml docbook-dsssl docbook-xml docbook-defguide gettext-doc groff www-browser libmail-box-perl python-doc python-tk python2.6-doc binfmt-support ruby1.8-examples ri1.8 ruby1.9.1-examples ri1.9.1 graphviz sgml-base-doc perlsgml doc-html-w3 opensp libxml2-utils doc-base Recommended packages: at curl wget dctrl-tools debian-keyring debian-maintainers dput dupload equivs libcrypt-ssleay-perl libjson-perl libparse-debcontrol-perl libsoap-lite-perl liburi-perl libwww-perl lintian patchutils python-debian python-magic strace unzip wdiff autopoint libglib2.0-data shared-mime-info libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper devscripts docbook docbook-to-man file gem2deb gettext gettext-base groff-base html2text intltool-debian libcroco3 libdb4.8 libexpat1 libglib2.0-0 libmagic1 libpcre3 libpipeline1 librd-ruby1.8 libreadline5 libruby1.8 libruby1.9.1 libsp1c2 libsqlite3-0 libssl1.0.0 libunistring0 libxml-ruby1.8 libxml-ruby1.9.1 libxml2 libyaml-0-2 man-db mime-support po-debconf python python-minimal python2.6 python2.6-minimal rdtool ruby1.8 ruby1.8-dev ruby1.9.1 ruby1.9.1-dev rubygems rubygems1.8 sbuild-build-depends-ruby-bio-dummy sgml-base sgml-data sp xml-core 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 30.5 MB/30.5 MB of archives. After this operation, 98.2 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 libpcre3 libreadline5 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 libxml2 mime-support python2.6-minimal libexpat1 python2.6 python-minimal python html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper devscripts sgml-base xml-core sgml-data docbook libsp1c2 sp docbook-to-man libruby1.8 ruby1.8 rubygems rubygems1.8 ruby1.8-dev libyaml-0-2 libruby1.9.1 ruby1.9.1 ruby1.9.1-dev gem2deb librd-ruby1.8 libxml-ruby1.8 libxml-ruby1.9.1 rdtool sbuild-build-depends-ruby-bio-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-2 [1143 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main libreadline5 amd64 5.2-10 [150 kB] Get:5 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-9 [694 kB] Get:6 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:7 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:8 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:9 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:10 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:11 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:12 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.7-2 [420 kB] Get:13 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:14 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:15 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:16 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7 [137 kB] Get:17 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:18 http://localhost/debian/ sid/main python-minimal all 2.6.7-3 [39.2 kB] Get:19 http://localhost/debian/ sid/main python all 2.6.7-3 [177 kB] Get:20 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:21 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:22 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:23 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:24 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:25 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:26 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:27 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:28 http://localhost/debian/ sid/main devscripts amd64 2.11.1 [696 kB] Get:29 http://localhost/debian/ sid/main sgml-base all 1.26+nmu1 [11.9 kB] Get:30 http://localhost/debian/ sid/main xml-core all 0.13 [23.4 kB] Get:31 http://localhost/debian/ sid/main sgml-data all 2.0.6 [284 kB] Get:32 http://localhost/debian/ sid/main docbook all 4.5-4 [450 kB] Get:33 http://localhost/debian/ sid/main libsp1c2 amd64 1.3.4-1.2.1-47.1 [1455 kB] Get:34 http://localhost/debian/ sid/main sp amd64 1.3.4-1.2.1-47.1 [175 kB] Get:35 http://localhost/debian/ sid/main docbook-to-man amd64 1:2.0.0-28 [76.9 kB] Get:36 http://localhost/debian/ sid/main libruby1.8 amd64 1.8.7.352-2 [2077 kB] Get:37 http://localhost/debian/ sid/main ruby1.8 amd64 1.8.7.352-2 [318 kB] Get:38 http://localhost/debian/ sid/main rubygems all 1.7.2-1 [446 kB] Get:39 http://localhost/debian/ sid/main rubygems1.8 all 1.7.2-1 [24.7 kB] Get:40 http://localhost/debian/ sid/main ruby1.8-dev amd64 1.8.7.352-2 [904 kB] Get:41 http://localhost/debian/ sid/main libyaml-0-2 amd64 0.1.4-1 [58.3 kB] Get:42 http://localhost/debian/ sid/main libruby1.9.1 amd64 1.9.2.290-2 [4565 kB] Get:43 http://localhost/debian/ sid/main ruby1.9.1 amd64 1.9.2.290-2 [776 kB] Get:44 http://localhost/debian/ sid/main ruby1.9.1-dev amd64 1.9.2.290-2 [1896 kB] Get:45 http://localhost/debian/ sid/main gem2deb all 0.2.7 [38.4 kB] Get:46 http://localhost/debian/ sid/main librd-ruby1.8 all 0.6.22-1 [36.3 kB] Get:47 http://localhost/debian/ sid/main libxml-ruby1.8 amd64 1.1.3-2 [78.4 kB] Get:48 http://localhost/debian/ sid/main libxml-ruby1.9.1 amd64 1.1.3-2 [77.2 kB] Get:49 http://localhost/debian/ sid/main rdtool all 0.6.22-1 [50.0 kB] Extracting templates from packages: 60% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 30.5 MB in 0s (51.0 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-2_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libreadline5. Unpacking libreadline5 (from .../libreadline5_5.2-10_amd64.deb) ... Selecting previously deselected package libdb4.8. Unpacking libdb4.8 (from .../libdb4.8_4.8.30-9_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. 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Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package devscripts. Unpacking devscripts (from .../devscripts_2.11.1_amd64.deb) ... Selecting previously deselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26+nmu1_all.deb) ... Selecting previously deselected package xml-core. Unpacking xml-core (from .../archives/xml-core_0.13_all.deb) ... Selecting previously deselected package sgml-data. Unpacking sgml-data (from .../sgml-data_2.0.6_all.deb) ... Selecting previously deselected package docbook. Unpacking docbook (from .../archives/docbook_4.5-4_all.deb) ... Selecting previously deselected package libsp1c2. Unpacking libsp1c2 (from .../libsp1c2_1.3.4-1.2.1-47.1_amd64.deb) ... Selecting previously deselected package sp. Unpacking sp (from .../sp_1.3.4-1.2.1-47.1_amd64.deb) ... Selecting previously deselected package docbook-to-man. Unpacking docbook-to-man (from .../docbook-to-man_1%3a2.0.0-28_amd64.deb) ... Selecting previously deselected package libruby1.8. Unpacking libruby1.8 (from .../libruby1.8_1.8.7.352-2_amd64.deb) ... Selecting previously deselected package ruby1.8. Unpacking ruby1.8 (from .../ruby1.8_1.8.7.352-2_amd64.deb) ... Selecting previously deselected package rubygems. Unpacking rubygems (from .../rubygems_1.7.2-1_all.deb) ... Selecting previously deselected package rubygems1.8. Unpacking rubygems1.8 (from .../rubygems1.8_1.7.2-1_all.deb) ... Selecting previously deselected package ruby1.8-dev. Unpacking ruby1.8-dev (from .../ruby1.8-dev_1.8.7.352-2_amd64.deb) ... Selecting previously deselected package libyaml-0-2. Unpacking libyaml-0-2 (from .../libyaml-0-2_0.1.4-1_amd64.deb) ... Selecting previously deselected package libruby1.9.1. Unpacking libruby1.9.1 (from .../libruby1.9.1_1.9.2.290-2_amd64.deb) ... Selecting previously deselected package ruby1.9.1. Unpacking ruby1.9.1 (from .../ruby1.9.1_1.9.2.290-2_amd64.deb) ... Selecting previously deselected package ruby1.9.1-dev. Unpacking ruby1.9.1-dev (from .../ruby1.9.1-dev_1.9.2.290-2_amd64.deb) ... Selecting previously deselected package gem2deb. Unpacking gem2deb (from .../archives/gem2deb_0.2.7_all.deb) ... Selecting previously deselected package librd-ruby1.8. Unpacking librd-ruby1.8 (from .../librd-ruby1.8_0.6.22-1_all.deb) ... Selecting previously deselected package libxml-ruby1.8. Unpacking libxml-ruby1.8 (from .../libxml-ruby1.8_1.1.3-2_amd64.deb) ... Selecting previously deselected package libxml-ruby1.9.1. Unpacking libxml-ruby1.9.1 (from .../libxml-ruby1.9.1_1.1.3-2_amd64.deb) ... Selecting previously deselected package rdtool. Unpacking rdtool (from .../rdtool_0.6.22-1_all.deb) ... Selecting previously deselected package sbuild-build-depends-ruby-bio-dummy. Unpacking sbuild-build-depends-ruby-bio-dummy (from .../sbuild-build-depends-ruby-bio-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libssl1.0.0 (1.0.0e-2) ... Setting up libpcre3 (8.12-4) ... Setting up libreadline5 (5.2-10) ... Setting up libdb4.8 (4.8.30-9) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libsqlite3-0 (3.7.7-2) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up mime-support (3.51-1) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up libexpat1 (2.0.1-7) ... Setting up python2.6 (2.6.7-4) ... Setting up python-minimal (2.6.7-3) ... Setting up python (2.6.7-3) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up devscripts (2.11.1) ... Setting up sgml-base (1.26+nmu1) ... Setting up xml-core (0.13) ... Setting up sgml-data (2.0.6) ... Setting up docbook (4.5-4) ... Setting up libsp1c2 (1.3.4-1.2.1-47.1) ... Setting up sp (1.3.4-1.2.1-47.1) ... Setting up docbook-to-man (1:2.0.0-28) ... Setting up libruby1.8 (1.8.7.352-2) ... Setting up ruby1.8 (1.8.7.352-2) ... update-alternatives: using /usr/bin/ruby1.8 to provide /usr/bin/ruby (ruby) in auto mode. Setting up rubygems (1.7.2-1) ... Setting up rubygems1.8 (1.7.2-1) ... Setting up ruby1.8-dev (1.8.7.352-2) ... Setting up libyaml-0-2 (0.1.4-1) ... Setting up libruby1.9.1 (1.9.2.290-2) ... Setting up ruby1.9.1 (1.9.2.290-2) ... Setting up ruby1.9.1-dev (1.9.2.290-2) ... Setting up gem2deb (0.2.7) ... Setting up librd-ruby1.8 (0.6.22-1) ... Setting up libxml-ruby1.8 (1.1.3-2) ... Setting up libxml-ruby1.9.1 (1.1.3-2) ... Setting up rdtool (0.6.22-1) ... Setting up sbuild-build-depends-ruby-bio-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 devscripts_2.11.1 diffutils_1:3.0-1 docbook_4.5-4 docbook-to-man_1:2.0.0-28 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gem2deb_0.2.7 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 librd-ruby1.8_0.6.22-1 libreadline5_5.2-10 libreadline6_6.2-4 libruby1.8_1.8.7.352-2 libruby1.9.1_1.9.2.290-2 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsp1c2_1.3.4-1.2.1-47.1 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml-ruby1.8_1.1.3-2 libxml-ruby1.9.1_1.1.3-2 libxml2_2.7.8.dfsg-4 libyaml-0-2_0.1.4-1 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 python_2.6.7-3 python-minimal_2.6.7-3 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 rdtool_0.6.22-1 readline-common_6.2-4 ruby1.8_1.8.7.352-2 ruby1.8-dev_1.8.7.352-2 ruby1.9.1_1.9.2.290-2 ruby1.9.1-dev_1.9.2.290-2 rubygems_1.7.2-1 rubygems1.8_1.7.2-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ruby-bio-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sp_1.3.4-1.2.1-47.1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jul 29 15:58:53 2011 CEST using RSA key ID F4DFBE99 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./ruby-bio_1.4.1-2.dsc dpkg-source: info: extracting ruby-bio in ruby-bio-1.4.1 dpkg-source: info: unpacking ruby-bio_1.4.1.orig.tar.gz dpkg-source: info: unpacking ruby-bio_1.4.1-2.debian.tar.gz dpkg-source: info: applying disable-test-soap.patch Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package ruby-bio dpkg-buildpackage: source version 1.4.1-2 dpkg-source --before-build ruby-bio-1.4.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby debian/rules override_dh_auto_clean make[1]: Entering directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' dh_auto_clean Entering dh_ruby --clean Leaving dh_ruby --clean rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' dh_clean -O--buildsystem=ruby dpkg-source -b ruby-bio-1.4.1 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building ruby-bio using existing ./ruby-bio_1.4.1.orig.tar.gz dpkg-source: info: building ruby-bio in ruby-bio_1.4.1-2.debian.tar.gz dpkg-source: info: building ruby-bio in ruby-bio_1.4.1-2.dsc debian/rules build dh build --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby debian/rules override_dh_auto_build make[1]: Entering directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' dh_auto_build docbook-to-man debian/br_biofetch.rb.sgml > br_biofetch.1 docbook-to-man debian/br_bioflat.rb.sgml > br_bioflat.1 docbook-to-man debian/br_biogetseq.rb.sgml > br_biogetseq.1 docbook-to-man debian/br_pmfetch.rb.sgml > br_pmfetch.1 make[1]: Leaving directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' dh_auto_test -O--buildsystem=ruby fakeroot debian/rules binary dh binary --buildsystem=ruby --with ruby dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby dh_installdirs -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' dh_auto_install Entering dh_ruby --install install -d /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin install -D -m755 bin/br_pmfetch.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_pmfetch.rb install -D -m755 bin/br_bioflat.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_bioflat.rb install -D -m755 bin/bioruby /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/bioruby install -D -m755 bin/br_biofetch.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_biofetch.rb install -D -m755 bin/br_biogetseq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_biogetseq.rb install -d /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 lib/bio/sequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 lib/bio/io/hinv.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 lib/bio/io/das.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 lib/bio/io/registry.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 lib/bio/io/fastacmd.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 lib/bio/io/ncbirest.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 lib/bio/io/soapwsdl.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/soapwsdl.rb install -D -m644 lib/bio/io/sql.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/sql.rb install -D -m644 lib/bio/io/keggapi.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/keggapi.rb install -D -m644 lib/bio/io/fetch.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 lib/bio/io/ddbjxml.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ddbjxml.rb install -D -m644 lib/bio/io/ensembl.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb install -D -m644 lib/bio/io/flatfile/splitter.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 lib/bio/io/flatfile/buffer.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 lib/bio/io/flatfile/index.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 lib/bio/io/flatfile/autodetection.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 lib/bio/io/flatfile/indexer.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 lib/bio/io/flatfile/bdb.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 lib/bio/io/pubmed.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 lib/bio/io/dbget.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/dbget.rb install -D -m644 lib/bio/io/higet.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/higet.rb install -D -m644 lib/bio/io/biosql/biosql.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/biosql.rb install -D -m644 lib/bio/io/biosql/config/database.yml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/config/database.yml install -D -m644 lib/bio/io/biosql/ar-biosql.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/ar-biosql.rb install -D -m644 lib/bio/io/ebisoap.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ebisoap.rb install -D -m644 lib/bio/io/togows.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 lib/bio/io/flatfile.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 lib/bio/io/ncbisoap.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbisoap.rb install -D -m644 lib/bio/appl/genscan/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 lib/bio/appl/hmmer.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 lib/bio/appl/emboss.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 lib/bio/appl/psort.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 lib/bio/appl/spidey/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 lib/bio/appl/tcoffee.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 lib/bio/appl/phylip/alignment.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 lib/bio/appl/phylip/distance_matrix.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 lib/bio/appl/hmmer/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 lib/bio/appl/targetp/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 lib/bio/appl/clustalw.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 lib/bio/appl/meme/motif.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 lib/bio/appl/meme/mast/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 lib/bio/appl/meme/mast.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 lib/bio/appl/iprscan/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 lib/bio/appl/fasta/format10.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 lib/bio/appl/pts1.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 lib/bio/appl/bl2seq/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 lib/bio/appl/clustalw/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 lib/bio/appl/gcg/msf.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 lib/bio/appl/gcg/seq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 lib/bio/appl/sosui/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 lib/bio/appl/muscle.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 lib/bio/appl/paml/codeml/rates.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 lib/bio/appl/paml/codeml/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 lib/bio/appl/paml/common_report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 lib/bio/appl/paml/yn00/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 lib/bio/appl/paml/baseml.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 lib/bio/appl/paml/baseml/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 lib/bio/appl/paml/yn00.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 lib/bio/appl/paml/common.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 lib/bio/appl/paml/codeml.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 lib/bio/appl/blat/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 lib/bio/appl/fasta.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 lib/bio/appl/blast/xmlparser.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/xmlparser.rb install -D -m644 lib/bio/appl/blast/remote.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 lib/bio/appl/blast/rexml.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 lib/bio/appl/blast/wublast.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 lib/bio/appl/blast/format0.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 lib/bio/appl/blast/ddbj.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ddbj.rb install -D -m644 lib/bio/appl/blast/rpsblast.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 lib/bio/appl/blast/format8.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 lib/bio/appl/blast/ncbioptions.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 lib/bio/appl/blast/genomenet.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 lib/bio/appl/blast/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 lib/bio/appl/tmhmm/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 lib/bio/appl/probcons.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 lib/bio/appl/sim4/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 lib/bio/appl/blast.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 lib/bio/appl/psort/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 lib/bio/appl/mafft.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 lib/bio/appl/sim4.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 lib/bio/appl/mafft/report.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 lib/bio/tree.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 lib/bio/version.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 lib/bio/db.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 lib/bio/compat/features.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 lib/bio/compat/references.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 lib/bio/alignment.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 lib/bio/db/aaindex.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 lib/bio/db/soft.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 lib/bio/db/genbank/genpept.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 lib/bio/db/genbank/ddbj.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 lib/bio/db/genbank/refseq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 lib/bio/db/genbank/common.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 lib/bio/db/genbank/genbank.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 lib/bio/db/genbank/genbank_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 lib/bio/db/genbank/format_genbank.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 lib/bio/db/nexus.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 lib/bio/db/pdb/chemicalcomponent.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 lib/bio/db/pdb/residue.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 lib/bio/db/pdb/utils.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 lib/bio/db/pdb/model.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 lib/bio/db/pdb/chain.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 lib/bio/db/pdb/pdb.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 lib/bio/db/pdb/atom.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 lib/bio/db/sanger_chromatogram/chromatogram.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 lib/bio/db/sanger_chromatogram/abif.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 lib/bio/db/sanger_chromatogram/scf.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 lib/bio/db/phyloxml/phyloxml.xsd /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml.xsd install -D -m644 lib/bio/db/phyloxml/phyloxml_writer.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_writer.rb install -D -m644 lib/bio/db/phyloxml/phyloxml_parser.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_parser.rb install -D -m644 lib/bio/db/phyloxml/phyloxml_elements.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_elements.rb install -D -m644 lib/bio/db/lasergene.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 lib/bio/db/transfac.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 lib/bio/db/litdb.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 lib/bio/db/fasta/qual_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 lib/bio/db/fasta/qual.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 lib/bio/db/fasta/format_qual.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 lib/bio/db/fasta/fasta_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 lib/bio/db/fasta/format_fasta.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 lib/bio/db/fasta/defline.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 lib/bio/db/prosite.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 lib/bio/db/newick.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 lib/bio/db/kegg/reaction.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 lib/bio/db/kegg/keggtab.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 lib/bio/db/kegg/orthology.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 lib/bio/db/kegg/module.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 lib/bio/db/kegg/kgml.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 lib/bio/db/kegg/glycan.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 lib/bio/db/kegg/enzyme.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 lib/bio/db/kegg/expression.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 lib/bio/db/kegg/taxonomy.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/taxonomy.rb install -D -m644 lib/bio/db/kegg/pathway.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 lib/bio/db/kegg/genes.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 lib/bio/db/kegg/compound.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 lib/bio/db/kegg/common.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 lib/bio/db/kegg/genome.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 lib/bio/db/kegg/drug.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 lib/bio/db/kegg/brite.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 lib/bio/db/gff.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 lib/bio/db/biosql/sequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/biosql/sequence.rb install -D -m644 lib/bio/db/biosql/biosql_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/biosql/biosql_to_biosequence.rb install -D -m644 lib/bio/db/fastq/fastq_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 lib/bio/db/fastq/format_fastq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 lib/bio/db/rebase.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 lib/bio/db/fantom.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 lib/bio/db/embl/trembl.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 lib/bio/db/embl/uniprot.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 lib/bio/db/embl/embl.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 lib/bio/db/embl/format_embl.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 lib/bio/db/embl/swissprot.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 lib/bio/db/embl/embl_to_biosequence.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 lib/bio/db/embl/sptr.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 lib/bio/db/embl/common.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 lib/bio/db/fasta.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 lib/bio/db/go.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 lib/bio/db/medline.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 lib/bio/db/pdb.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 lib/bio/db/fastq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 lib/bio/db/nbrf.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 lib/bio/reference.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 lib/bio/shell.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell.rb install -D -m644 lib/bio/pathway.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 lib/bio/feature.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 lib/bio/map.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 lib/bio/location.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 lib/bio/shell/object.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/object.rb install -D -m644 lib/bio/shell/demo.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/demo.rb install -D -m644 lib/bio/shell/plugin/das.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/das.rb install -D -m644 lib/bio/shell/plugin/emboss.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/emboss.rb install -D -m644 lib/bio/shell/plugin/psort.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/psort.rb install -D -m644 lib/bio/shell/plugin/ncbirest.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/ncbirest.rb install -D -m644 lib/bio/shell/plugin/keggapi.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/keggapi.rb install -D -m644 lib/bio/shell/plugin/soap.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/soap.rb install -D -m644 lib/bio/shell/plugin/seq.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/seq.rb install -D -m644 lib/bio/shell/plugin/codon.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/codon.rb install -D -m644 lib/bio/shell/plugin/obda.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/obda.rb install -D -m644 lib/bio/shell/plugin/entry.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/entry.rb install -D -m644 lib/bio/shell/plugin/blast.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/blast.rb install -D -m644 lib/bio/shell/plugin/togows.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/togows.rb install -D -m644 lib/bio/shell/plugin/flatfile.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/flatfile.rb install -D -m644 lib/bio/shell/plugin/midi.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/midi.rb install -D -m644 lib/bio/shell/interface.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/interface.rb install -D -m644 lib/bio/shell/core.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/core.rb install -D -m644 lib/bio/shell/irb.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/irb.rb install -D -m644 lib/bio/shell/web.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/web.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml install -D -m644 lib/bio/shell/setup.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/setup.rb install -D -m644 lib/bio/shell/script.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/script.rb install -D -m644 lib/bio/util/contingency_table.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 lib/bio/util/color_scheme/helix.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 lib/bio/util/color_scheme/buried.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 lib/bio/util/color_scheme/turn.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 lib/bio/util/color_scheme/zappo.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 lib/bio/util/color_scheme/hydropathy.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 lib/bio/util/color_scheme/nucleotide.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 lib/bio/util/color_scheme/strand.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 lib/bio/util/color_scheme/taylor.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 lib/bio/util/restriction_enzyme.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 lib/bio/util/restriction_enzyme/analysis_basic.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/enzymes.yaml /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 lib/bio/util/restriction_enzyme/string_formatting.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/cut_range.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 lib/bio/util/restriction_enzyme/cut_symbol.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 lib/bio/util/restriction_enzyme/analysis.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 lib/bio/util/color_scheme.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 lib/bio/util/sirna.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 lib/bio/command.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 lib/bio/sequence/quality_score.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 lib/bio/sequence/format_raw.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 lib/bio/sequence/adapter.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 lib/bio/sequence/generic.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 lib/bio/sequence/dblink.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 lib/bio/sequence/format.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 lib/bio/sequence/sequence_masker.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 lib/bio/sequence/na.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 lib/bio/sequence/compat.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 lib/bio/sequence/common.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 lib/bio/sequence/aa.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 lib/bio/data/codontable.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 lib/bio/data/na.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 lib/bio/data/aa.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 lib/bio.rb /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb /usr/bin/ruby1.8 -I/usr/lib/ruby/vendor_ruby /usr/lib/ruby/vendor_ruby/gem2deb/test_runner.rb Loaded suite debian/ruby-tests Started .......................F............EEEEEEEEEEEE.....EEEEEEEEEEEEEEEEEEEEEEEE..FFFFFFFFFFFFFFFFFFF..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Finished in 280.450352 seconds. 1) Failure: test_read_uri(Bio::FuncTestCommandNet) [./test/functional/bio/test_command.rb:337]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/open-uri.rb:242:in `open_http' /usr/lib/ruby/1.8/open-uri.rb:616:in `buffer_open' /usr/lib/ruby/1.8/open-uri.rb:164:in `open_loop' /usr/lib/ruby/1.8/open-uri.rb:162:in `catch' /usr/lib/ruby/1.8/open-uri.rb:162:in `open_loop' /usr/lib/ruby/1.8/open-uri.rb:132:in `open_uri' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:625:in `read_uri' ./test/functional/bio/test_command.rb:338:in `test_read_uri' ./test/functional/bio/test_command.rb:337:in `test_read_uri' --------------- 2) Error: test_fasta_exportview_with_hash_4th_params(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:59:in `test_fasta_exportview_with_hash_4th_params' 3) Error: test_fasta_exportview_with_named_args_and_hash_4th_params(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:73:in `test_fasta_exportview_with_named_args_and_hash_4th_params' 4) Error: test_fna_exportview(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:54:in `test_fna_exportview' 5) Error: test_fna_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:66:in `test_fna_exportview_with_named_args' 6) Error: test_gff_exportview(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:112:in `test_gff_exportview' 7) Error: test_gff_exportview_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:84:in `test_gff_exportview_for_empty_result' 8) Error: test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:148:in `test_gff_exportview_with_named_args' 9) Error: test_gff_exportview_with_named_args_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:117:in `test_gff_exportview_with_named_args_for_empty_result' 10) Error: test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:219:in `test_tab_exportview_with_named_args' 11) Error: test_tab_exportview_with_named_args_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:168:in `test_tab_exportview_with_named_args_for_empty_result' 12) Error: test_exec(Bio::FuncTestPTS1): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:62:in `test_exec' 13) Error: test_exec_with_faa(Bio::FuncTestPTS1): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:67:in `test_exec_with_faa' 14) Error: test_cterm(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 15) Error: test_entry_id(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 16) Error: test_fp(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 17) Error: test_prediction(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 18) Error: test_profile(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 19) Error: test_score(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 20) Error: test_sppta(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 21) Error: test_spptna(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 22) Error: test_efetch(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:80:in `test_efetch' 23) Error: test_efetch_multiple(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:89:in `test_efetch_multiple' 24) Error: test_efetch_multiple_xml(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:106:in `test_efetch_multiple_xml' 25) Error: test_efetch_single_xml(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:99:in `test_efetch_single_xml' 26) Error: test_efetch_str(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:84:in `test_efetch_str' 27) Error: test_esearch(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:26:in `test_esearch' 28) Error: test_esearch_count(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:282:in `esearch_count' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:253:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:38:in `test_esearch_count' 29) Error: test_esearch_retmax_retstart(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:46:in `test_esearch_retmax_retstart' 30) Error: test_efetch(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:80:in `test_efetch' 31) Error: test_efetch_multiple(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:89:in `test_efetch_multiple' 32) Error: test_efetch_multiple_xml(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:106:in `test_efetch_multiple_xml' 33) Error: test_efetch_single_xml(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:99:in `test_efetch_single_xml' 34) Error: test_efetch_str(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:84:in `test_efetch_str' 35) Error: test_esearch(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:26:in `test_esearch' 36) Error: test_esearch_count(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:282:in `esearch_count' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:253:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:38:in `test_esearch_count' 37) Error: test_esearch_retmax_retstart(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:46:in `test_esearch_retmax_retstart' 38) Failure: test_convert(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:120]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:702:in `http_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:414:in `post_data' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:305:in `convert' ./test/functional/bio/io/test_togows.rb:121:in `test_convert' ./test/functional/bio/io/test_togows.rb:120:in `test_convert' --------------- 39) Failure: test_entry(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:33]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:34:in `test_entry' ./test/functional/bio/io/test_togows.rb:33:in `test_entry' --------------- 40) Failure: test_entry_database_list(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:165]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:314:in `entry_database_list' ./test/functional/bio/io/test_togows.rb:166:in `test_entry_database_list' ./test/functional/bio/io/test_togows.rb:165:in `test_entry_database_list' --------------- 41) Failure: test_entry_multi(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:44]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:45:in `test_entry_multi' ./test/functional/bio/io/test_togows.rb:44:in `test_entry_multi' --------------- 42) Failure: test_entry_with_format(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:67]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:68:in `test_entry_with_format' ./test/functional/bio/io/test_togows.rb:67:in `test_entry_with_format' --------------- 43) Failure: test_entry_with_format_and_key(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:84]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:85:in `test_entry_with_format_and_key' ./test/functional/bio/io/test_togows.rb:84:in `test_entry_with_format_and_key' --------------- 44) Failure: test_entry_with_key(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:76]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:77:in `test_entry_with_key' ./test/functional/bio/io/test_togows.rb:76:in `test_entry_with_key' --------------- 45) Failure: test_retrieve(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:128]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:129:in `test_retrieve' ./test/functional/bio/io/test_togows.rb:128:in `test_retrieve' --------------- 46) Failure: test_retrieve_1id_1db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:136]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:205:in `retrieve' ./test/functional/bio/io/test_togows.rb:137:in `test_retrieve_1id_1db' ./test/functional/bio/io/test_togows.rb:136:in `test_retrieve_1id_1db' --------------- 47) Failure: test_retrieve_1id_2db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:147]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:148:in `test_retrieve_1id_2db' ./test/functional/bio/io/test_togows.rb:147:in `test_retrieve_1id_2db' --------------- 48) Failure: test_retrieve_2id_2db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:156]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:157:in `test_retrieve_2id_2db' ./test/functional/bio/io/test_togows.rb:156:in `test_retrieve_2id_2db' --------------- 49) Failure: test_search(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:92]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:93:in `test_search' ./test/functional/bio/io/test_togows.rb:92:in `test_search' --------------- 50) Failure: test_search_database_list(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:174]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:321:in `search_database_list' ./test/functional/bio/io/test_togows.rb:175:in `test_search_database_list' ./test/functional/bio/io/test_togows.rb:174:in `test_search_database_list' --------------- 51) Failure: test_search_with_offset_limit(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:100]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:101:in `test_search_with_offset_limit' ./test/functional/bio/io/test_togows.rb:100:in `test_search_with_offset_limit' --------------- 52) Failure: test_search_with_offset_limit_format(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:110]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:111:in `test_search_with_offset_limit_format' ./test/functional/bio/io/test_togows.rb:110:in `test_search_with_offset_limit_format' --------------- 53) Failure: test_database_list(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:245]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./test/functional/bio/io/test_togows.rb:247:in `test_database_list' ./test/functional/bio/io/test_togows.rb:246:in `instance_eval' ./test/functional/bio/io/test_togows.rb:246:in `test_database_list' ./test/functional/bio/io/test_togows.rb:245:in `test_database_list' --------------- 54) Failure: test_get(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:204]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./test/functional/bio/io/test_togows.rb:206:in `test_get' ./test/functional/bio/io/test_togows.rb:205:in `instance_eval' ./test/functional/bio/io/test_togows.rb:205:in `test_get' ./test/functional/bio/io/test_togows.rb:204:in `test_get' --------------- 55) Failure: test_get_dir(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:217]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./test/functional/bio/io/test_togows.rb:219:in `test_get_dir' ./test/functional/bio/io/test_togows.rb:218:in `instance_eval' ./test/functional/bio/io/test_togows.rb:218:in `test_get_dir' ./test/functional/bio/io/test_togows.rb:217:in `test_get_dir' --------------- 56) Failure: test_post_data(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:232]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:702:in `http_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:414:in `post_data' ./test/functional/bio/io/test_togows.rb:234:in `test_post_data' ./test/functional/bio/io/test_togows.rb:233:in `instance_eval' ./test/functional/bio/io/test_togows.rb:233:in `test_post_data' ./test/functional/bio/io/test_togows.rb:232:in `test_post_data' --------------- 3127 tests, 20292 assertions, 20 failures, 36 errors ERROR: Test "ruby1.8" failed. Exiting. dh_auto_install: dh_ruby --install /build/ruby-bio-f5XUcy/ruby-bio-1.4.1/debian/tmp returned exit code 1 make[1]: *** [override_dh_auto_install] Error 1 make[1]: Leaving directory `/build/ruby-bio-f5XUcy/ruby-bio-1.4.1' make: *** [binary] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1214 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-0fe59ff1-ef8c-48ad-80f7-ac7df66ccf46/build/ruby-bio-f5XUcy Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 9384 Build-Time: 283 Distribution: lsid64c Fail-Stage: build Install-Time: 8 Job: ruby-bio_1.4.1-2 Package: ruby-bio Package-Time: 302 Source-Version: 1.4.1-2 Space: 9384 Status: attempted Version: 1.4.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1214 Build needed 00:05:02, 9384k disc space DC-Message: Failed, but took only 303.194466. Retrying, you never know. Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-122.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ ruby-bio 1.4.1-2 (amd64) 11 Sep 2011 12:30 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: ruby-bio Version: 1.4.1-2 Source Version: 1.4.1-2 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (63.3 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'ruby-bio' packaging is maintained in the 'Git' version control system at: git://git.debian.org/pkg-ruby-extras/ruby-bio.git Need to get 1371 kB of source archives. Get:1 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (dsc) [2053 B] Get:2 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (tar) [1360 kB] Get:3 http://localhost/debian/ sid/main ruby-bio 1.4.1-2 (diff) [9202 B] Fetched 1371 kB in 0s (47.8 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/ruby-bio-auzhl7/resolver-YNcrLr/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-0bb257fe-1337-4c6f-a5a3-dbb81da6233c/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), gem2deb (>= 0.2.4~), libxml-ruby1.8, libxml-ruby1.9.1, docbook-to-man, rdtool Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 7.0.50~), gem2deb (>= 0.2.4~), libxml-ruby1.8, libxml-ruby1.9.1, docbook-to-man, rdtool dpkg-deb: building package `sbuild-build-depends-ruby-bio-dummy' in `/build/ruby-bio-auzhl7/resolver-lrOlVQ/apt_archive/sbuild-build-depends-ruby-bio-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install ruby-bio build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper devscripts docbook docbook-to-man file gem2deb gettext gettext-base groff-base html2text intltool-debian libcroco3 libdb4.8 libexpat1 libglib2.0-0 libmagic1 libpcre3 libpipeline1 librd-ruby1.8 libreadline5 libruby1.8 libruby1.9.1 libsp1c2 libsqlite3-0 libssl1.0.0 libunistring0 libxml-ruby1.8 libxml-ruby1.9.1 libxml2 libyaml-0-2 man-db mime-support po-debconf python python-minimal python2.6 python2.6-minimal rdtool ruby1.8 ruby1.8-dev ruby1.9.1 ruby1.9.1-dev rubygems rubygems1.8 sgml-base sgml-data sp xml-core Suggested packages: wamerican wordlist whois vacation dh-make bsd-mailx mailx cvs-buildpackage devscripts-el gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mutt ssh-client svn-buildpackage w3m psgml docbook-dsssl docbook-xml docbook-defguide gettext-doc groff www-browser libmail-box-perl python-doc python-tk python2.6-doc binfmt-support ruby1.8-examples ri1.8 ruby1.9.1-examples ri1.9.1 graphviz sgml-base-doc perlsgml doc-html-w3 opensp libxml2-utils doc-base Recommended packages: at curl wget dctrl-tools debian-keyring debian-maintainers dput dupload equivs libcrypt-ssleay-perl libjson-perl libparse-debcontrol-perl libsoap-lite-perl liburi-perl libwww-perl lintian patchutils python-debian python-magic strace unzip wdiff autopoint libglib2.0-data shared-mime-info libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper devscripts docbook docbook-to-man file gem2deb gettext gettext-base groff-base html2text intltool-debian libcroco3 libdb4.8 libexpat1 libglib2.0-0 libmagic1 libpcre3 libpipeline1 librd-ruby1.8 libreadline5 libruby1.8 libruby1.9.1 libsp1c2 libsqlite3-0 libssl1.0.0 libunistring0 libxml-ruby1.8 libxml-ruby1.9.1 libxml2 libyaml-0-2 man-db mime-support po-debconf python python-minimal python2.6 python2.6-minimal rdtool ruby1.8 ruby1.8-dev ruby1.9.1 ruby1.9.1-dev rubygems rubygems1.8 sbuild-build-depends-ruby-bio-dummy sgml-base sgml-data sp xml-core 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 30.5 MB/30.5 MB of archives. After this operation, 98.2 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 libpcre3 libreadline5 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 libxml2 mime-support python2.6-minimal libexpat1 python2.6 python-minimal python html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper devscripts sgml-base xml-core sgml-data docbook libsp1c2 sp docbook-to-man libruby1.8 ruby1.8 rubygems rubygems1.8 ruby1.8-dev libyaml-0-2 libruby1.9.1 ruby1.9.1 ruby1.9.1-dev gem2deb librd-ruby1.8 libxml-ruby1.8 libxml-ruby1.9.1 rdtool sbuild-build-depends-ruby-bio-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-2 [1143 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main libreadline5 amd64 5.2-10 [150 kB] Get:5 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-9 [694 kB] Get:6 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:7 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:8 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:9 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:10 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:11 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:12 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.7-2 [420 kB] Get:13 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:14 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:15 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:16 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7 [137 kB] Get:17 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:18 http://localhost/debian/ sid/main python-minimal all 2.6.7-3 [39.2 kB] Get:19 http://localhost/debian/ sid/main python all 2.6.7-3 [177 kB] Get:20 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:21 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:22 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:23 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:24 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:25 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:26 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:27 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:28 http://localhost/debian/ sid/main devscripts amd64 2.11.1 [696 kB] Get:29 http://localhost/debian/ sid/main sgml-base all 1.26+nmu1 [11.9 kB] Get:30 http://localhost/debian/ sid/main xml-core all 0.13 [23.4 kB] Get:31 http://localhost/debian/ sid/main sgml-data all 2.0.6 [284 kB] Get:32 http://localhost/debian/ sid/main docbook all 4.5-4 [450 kB] Get:33 http://localhost/debian/ sid/main libsp1c2 amd64 1.3.4-1.2.1-47.1 [1455 kB] Get:34 http://localhost/debian/ sid/main sp amd64 1.3.4-1.2.1-47.1 [175 kB] Get:35 http://localhost/debian/ sid/main docbook-to-man amd64 1:2.0.0-28 [76.9 kB] Get:36 http://localhost/debian/ sid/main libruby1.8 amd64 1.8.7.352-2 [2077 kB] Get:37 http://localhost/debian/ sid/main ruby1.8 amd64 1.8.7.352-2 [318 kB] Get:38 http://localhost/debian/ sid/main rubygems all 1.7.2-1 [446 kB] Get:39 http://localhost/debian/ sid/main rubygems1.8 all 1.7.2-1 [24.7 kB] Get:40 http://localhost/debian/ sid/main ruby1.8-dev amd64 1.8.7.352-2 [904 kB] Get:41 http://localhost/debian/ sid/main libyaml-0-2 amd64 0.1.4-1 [58.3 kB] Get:42 http://localhost/debian/ sid/main libruby1.9.1 amd64 1.9.2.290-2 [4565 kB] Get:43 http://localhost/debian/ sid/main ruby1.9.1 amd64 1.9.2.290-2 [776 kB] Get:44 http://localhost/debian/ sid/main ruby1.9.1-dev amd64 1.9.2.290-2 [1896 kB] Get:45 http://localhost/debian/ sid/main gem2deb all 0.2.7 [38.4 kB] Get:46 http://localhost/debian/ sid/main librd-ruby1.8 all 0.6.22-1 [36.3 kB] Get:47 http://localhost/debian/ sid/main libxml-ruby1.8 amd64 1.1.3-2 [78.4 kB] Get:48 http://localhost/debian/ sid/main libxml-ruby1.9.1 amd64 1.1.3-2 [77.2 kB] Get:49 http://localhost/debian/ sid/main rdtool all 0.6.22-1 [50.0 kB] Extracting templates from packages: 60% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 30.5 MB in 0s (60.8 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-2_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libreadline5. Unpacking libreadline5 (from .../libreadline5_5.2-10_amd64.deb) ... Selecting previously deselected package libdb4.8. Unpacking libdb4.8 (from .../libdb4.8_4.8.30-9_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. 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Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package devscripts. Unpacking devscripts (from .../devscripts_2.11.1_amd64.deb) ... Selecting previously deselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26+nmu1_all.deb) ... Selecting previously deselected package xml-core. Unpacking xml-core (from .../archives/xml-core_0.13_all.deb) ... Selecting previously deselected package sgml-data. Unpacking sgml-data (from .../sgml-data_2.0.6_all.deb) ... Selecting previously deselected package docbook. Unpacking docbook (from .../archives/docbook_4.5-4_all.deb) ... Selecting previously deselected package libsp1c2. 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Unpacking rdtool (from .../rdtool_0.6.22-1_all.deb) ... Selecting previously deselected package sbuild-build-depends-ruby-bio-dummy. Unpacking sbuild-build-depends-ruby-bio-dummy (from .../sbuild-build-depends-ruby-bio-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up libssl1.0.0 (1.0.0e-2) ... Setting up libpcre3 (8.12-4) ... Setting up libreadline5 (5.2-10) ... Setting up libdb4.8 (4.8.30-9) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libsqlite3-0 (3.7.7-2) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up mime-support (3.51-1) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up libexpat1 (2.0.1-7) ... Setting up python2.6 (2.6.7-4) ... Setting up python-minimal (2.6.7-3) ... Setting up python (2.6.7-3) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up devscripts (2.11.1) ... Setting up sgml-base (1.26+nmu1) ... Setting up xml-core (0.13) ... Setting up sgml-data (2.0.6) ... Setting up docbook (4.5-4) ... Setting up libsp1c2 (1.3.4-1.2.1-47.1) ... Setting up sp (1.3.4-1.2.1-47.1) ... Setting up docbook-to-man (1:2.0.0-28) ... Setting up libruby1.8 (1.8.7.352-2) ... Setting up ruby1.8 (1.8.7.352-2) ... update-alternatives: using /usr/bin/ruby1.8 to provide /usr/bin/ruby (ruby) in auto mode. Setting up rubygems (1.7.2-1) ... Setting up rubygems1.8 (1.7.2-1) ... Setting up ruby1.8-dev (1.8.7.352-2) ... Setting up libyaml-0-2 (0.1.4-1) ... Setting up libruby1.9.1 (1.9.2.290-2) ... Setting up ruby1.9.1 (1.9.2.290-2) ... Setting up ruby1.9.1-dev (1.9.2.290-2) ... Setting up gem2deb (0.2.7) ... Setting up librd-ruby1.8 (0.6.22-1) ... Setting up libxml-ruby1.8 (1.1.3-2) ... Setting up libxml-ruby1.9.1 (1.1.3-2) ... Setting up rdtool (0.6.22-1) ... Setting up sbuild-build-depends-ruby-bio-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 devscripts_2.11.1 diffutils_1:3.0-1 docbook_4.5-4 docbook-to-man_1:2.0.0-28 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gem2deb_0.2.7 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-10 librd-ruby1.8_0.6.22-1 libreadline5_5.2-10 libreadline6_6.2-4 libruby1.8_1.8.7.352-2 libruby1.9.1_1.9.2.290-2 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsp1c2_1.3.4-1.2.1-47.1 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml-ruby1.8_1.1.3-2 libxml-ruby1.9.1_1.1.3-2 libxml2_2.7.8.dfsg-4 libyaml-0-2_0.1.4-1 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 python_2.6.7-3 python-minimal_2.6.7-3 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 rdtool_0.6.22-1 readline-common_6.2-4 ruby1.8_1.8.7.352-2 ruby1.8-dev_1.8.7.352-2 ruby1.9.1_1.9.2.290-2 ruby1.9.1-dev_1.9.2.290-2 rubygems_1.7.2-1 rubygems1.8_1.7.2-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ruby-bio-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sp_1.3.4-1.2.1-47.1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jul 29 15:58:53 2011 CEST using RSA key ID F4DFBE99 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./ruby-bio_1.4.1-2.dsc dpkg-source: info: extracting ruby-bio in ruby-bio-1.4.1 dpkg-source: info: unpacking ruby-bio_1.4.1.orig.tar.gz dpkg-source: info: unpacking ruby-bio_1.4.1-2.debian.tar.gz dpkg-source: info: applying disable-test-soap.patch Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: source package ruby-bio dpkg-buildpackage: source version 1.4.1-2 dpkg-source --before-build ruby-bio-1.4.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby debian/rules override_dh_auto_clean make[1]: Entering directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' dh_auto_clean Entering dh_ruby --clean Leaving dh_ruby --clean rm -f br_biofetch.1 br_bioflat.1 br_biogetseq.1 br_pmfetch.1 make[1]: Leaving directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' dh_clean -O--buildsystem=ruby dpkg-source -b ruby-bio-1.4.1 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building ruby-bio using existing ./ruby-bio_1.4.1.orig.tar.gz dpkg-source: info: building ruby-bio in ruby-bio_1.4.1-2.debian.tar.gz dpkg-source: info: building ruby-bio in ruby-bio_1.4.1-2.dsc debian/rules build dh build --buildsystem=ruby --with ruby dh_testdir -O--buildsystem=ruby dh_auto_configure -O--buildsystem=ruby debian/rules override_dh_auto_build make[1]: Entering directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' dh_auto_build docbook-to-man debian/br_biofetch.rb.sgml > br_biofetch.1 docbook-to-man debian/br_bioflat.rb.sgml > br_bioflat.1 docbook-to-man debian/br_biogetseq.rb.sgml > br_biogetseq.1 docbook-to-man debian/br_pmfetch.rb.sgml > br_pmfetch.1 make[1]: Leaving directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' dh_auto_test -O--buildsystem=ruby fakeroot debian/rules binary dh binary --buildsystem=ruby --with ruby dh_testroot -O--buildsystem=ruby dh_prep -O--buildsystem=ruby dh_installdirs -O--buildsystem=ruby debian/rules override_dh_auto_install make[1]: Entering directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' dh_auto_install Entering dh_ruby --install install -d /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin install -D -m755 bin/br_pmfetch.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_pmfetch.rb install -D -m755 bin/br_bioflat.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_bioflat.rb install -D -m755 bin/bioruby /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/bioruby install -D -m755 bin/br_biofetch.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_biofetch.rb install -D -m755 bin/br_biogetseq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/bin/br_biogetseq.rb install -d /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby install -D -m644 lib/bio/sequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence.rb install -D -m644 lib/bio/io/hinv.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/hinv.rb install -D -m644 lib/bio/io/das.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/das.rb install -D -m644 lib/bio/io/registry.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/registry.rb install -D -m644 lib/bio/io/fastacmd.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fastacmd.rb install -D -m644 lib/bio/io/ncbirest.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb install -D -m644 lib/bio/io/soapwsdl.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/soapwsdl.rb install -D -m644 lib/bio/io/sql.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/sql.rb install -D -m644 lib/bio/io/keggapi.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/keggapi.rb install -D -m644 lib/bio/io/fetch.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/fetch.rb install -D -m644 lib/bio/io/ddbjxml.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ddbjxml.rb install -D -m644 lib/bio/io/ensembl.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb install -D -m644 lib/bio/io/flatfile/splitter.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/splitter.rb install -D -m644 lib/bio/io/flatfile/buffer.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/buffer.rb install -D -m644 lib/bio/io/flatfile/index.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/index.rb install -D -m644 lib/bio/io/flatfile/autodetection.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/autodetection.rb install -D -m644 lib/bio/io/flatfile/indexer.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/indexer.rb install -D -m644 lib/bio/io/flatfile/bdb.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile/bdb.rb install -D -m644 lib/bio/io/pubmed.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb install -D -m644 lib/bio/io/dbget.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/dbget.rb install -D -m644 lib/bio/io/higet.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/higet.rb install -D -m644 lib/bio/io/biosql/biosql.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/biosql.rb install -D -m644 lib/bio/io/biosql/config/database.yml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/config/database.yml install -D -m644 lib/bio/io/biosql/ar-biosql.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/biosql/ar-biosql.rb install -D -m644 lib/bio/io/ebisoap.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ebisoap.rb install -D -m644 lib/bio/io/togows.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/togows.rb install -D -m644 lib/bio/io/flatfile.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/flatfile.rb install -D -m644 lib/bio/io/ncbisoap.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/io/ncbisoap.rb install -D -m644 lib/bio/appl/genscan/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/genscan/report.rb install -D -m644 lib/bio/appl/hmmer.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer.rb install -D -m644 lib/bio/appl/emboss.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/emboss.rb install -D -m644 lib/bio/appl/psort.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort.rb install -D -m644 lib/bio/appl/spidey/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/spidey/report.rb install -D -m644 lib/bio/appl/tcoffee.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tcoffee.rb install -D -m644 lib/bio/appl/phylip/alignment.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/alignment.rb install -D -m644 lib/bio/appl/phylip/distance_matrix.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/phylip/distance_matrix.rb install -D -m644 lib/bio/appl/hmmer/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/hmmer/report.rb install -D -m644 lib/bio/appl/targetp/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/targetp/report.rb install -D -m644 lib/bio/appl/clustalw.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw.rb install -D -m644 lib/bio/appl/meme/motif.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/motif.rb install -D -m644 lib/bio/appl/meme/mast/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast/report.rb install -D -m644 lib/bio/appl/meme/mast.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/meme/mast.rb install -D -m644 lib/bio/appl/iprscan/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/iprscan/report.rb install -D -m644 lib/bio/appl/fasta/format10.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta/format10.rb install -D -m644 lib/bio/appl/pts1.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb install -D -m644 lib/bio/appl/bl2seq/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/bl2seq/report.rb install -D -m644 lib/bio/appl/clustalw/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/clustalw/report.rb install -D -m644 lib/bio/appl/gcg/msf.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/msf.rb install -D -m644 lib/bio/appl/gcg/seq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/gcg/seq.rb install -D -m644 lib/bio/appl/sosui/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sosui/report.rb install -D -m644 lib/bio/appl/muscle.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/muscle.rb install -D -m644 lib/bio/appl/paml/codeml/rates.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/rates.rb install -D -m644 lib/bio/appl/paml/codeml/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml/report.rb install -D -m644 lib/bio/appl/paml/common_report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common_report.rb install -D -m644 lib/bio/appl/paml/yn00/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00/report.rb install -D -m644 lib/bio/appl/paml/baseml.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml.rb install -D -m644 lib/bio/appl/paml/baseml/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/baseml/report.rb install -D -m644 lib/bio/appl/paml/yn00.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/yn00.rb install -D -m644 lib/bio/appl/paml/common.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/common.rb install -D -m644 lib/bio/appl/paml/codeml.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/paml/codeml.rb install -D -m644 lib/bio/appl/blat/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blat/report.rb install -D -m644 lib/bio/appl/fasta.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/fasta.rb install -D -m644 lib/bio/appl/blast/xmlparser.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/xmlparser.rb install -D -m644 lib/bio/appl/blast/remote.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/remote.rb install -D -m644 lib/bio/appl/blast/rexml.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rexml.rb install -D -m644 lib/bio/appl/blast/wublast.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/wublast.rb install -D -m644 lib/bio/appl/blast/format0.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format0.rb install -D -m644 lib/bio/appl/blast/ddbj.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ddbj.rb install -D -m644 lib/bio/appl/blast/rpsblast.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/rpsblast.rb install -D -m644 lib/bio/appl/blast/format8.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/format8.rb install -D -m644 lib/bio/appl/blast/ncbioptions.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/ncbioptions.rb install -D -m644 lib/bio/appl/blast/genomenet.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/genomenet.rb install -D -m644 lib/bio/appl/blast/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast/report.rb install -D -m644 lib/bio/appl/tmhmm/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/tmhmm/report.rb install -D -m644 lib/bio/appl/probcons.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/probcons.rb install -D -m644 lib/bio/appl/sim4/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4/report.rb install -D -m644 lib/bio/appl/blast.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/blast.rb install -D -m644 lib/bio/appl/psort/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/psort/report.rb install -D -m644 lib/bio/appl/mafft.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft.rb install -D -m644 lib/bio/appl/sim4.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/sim4.rb install -D -m644 lib/bio/appl/mafft/report.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/appl/mafft/report.rb install -D -m644 lib/bio/tree.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/tree.rb install -D -m644 lib/bio/version.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/version.rb install -D -m644 lib/bio/db.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db.rb install -D -m644 lib/bio/compat/features.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/features.rb install -D -m644 lib/bio/compat/references.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/compat/references.rb install -D -m644 lib/bio/alignment.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/alignment.rb install -D -m644 lib/bio/db/aaindex.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/aaindex.rb install -D -m644 lib/bio/db/soft.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/soft.rb install -D -m644 lib/bio/db/genbank/genpept.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genpept.rb install -D -m644 lib/bio/db/genbank/ddbj.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/ddbj.rb install -D -m644 lib/bio/db/genbank/refseq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/refseq.rb install -D -m644 lib/bio/db/genbank/common.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/common.rb install -D -m644 lib/bio/db/genbank/genbank.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank.rb install -D -m644 lib/bio/db/genbank/genbank_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/genbank_to_biosequence.rb install -D -m644 lib/bio/db/genbank/format_genbank.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/genbank/format_genbank.rb install -D -m644 lib/bio/db/nexus.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nexus.rb install -D -m644 lib/bio/db/pdb/chemicalcomponent.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chemicalcomponent.rb install -D -m644 lib/bio/db/pdb/residue.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/residue.rb install -D -m644 lib/bio/db/pdb/utils.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/utils.rb install -D -m644 lib/bio/db/pdb/model.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/model.rb install -D -m644 lib/bio/db/pdb/chain.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/chain.rb install -D -m644 lib/bio/db/pdb/pdb.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/pdb.rb install -D -m644 lib/bio/db/pdb/atom.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb/atom.rb install -D -m644 lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb install -D -m644 lib/bio/db/sanger_chromatogram/chromatogram.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/chromatogram.rb install -D -m644 lib/bio/db/sanger_chromatogram/abif.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/abif.rb install -D -m644 lib/bio/db/sanger_chromatogram/scf.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/sanger_chromatogram/scf.rb install -D -m644 lib/bio/db/phyloxml/phyloxml.xsd /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml.xsd install -D -m644 lib/bio/db/phyloxml/phyloxml_writer.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_writer.rb install -D -m644 lib/bio/db/phyloxml/phyloxml_parser.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_parser.rb install -D -m644 lib/bio/db/phyloxml/phyloxml_elements.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/phyloxml/phyloxml_elements.rb install -D -m644 lib/bio/db/lasergene.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/lasergene.rb install -D -m644 lib/bio/db/transfac.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/transfac.rb install -D -m644 lib/bio/db/litdb.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/litdb.rb install -D -m644 lib/bio/db/fasta/qual_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual_to_biosequence.rb install -D -m644 lib/bio/db/fasta/qual.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/qual.rb install -D -m644 lib/bio/db/fasta/format_qual.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_qual.rb install -D -m644 lib/bio/db/fasta/fasta_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/fasta_to_biosequence.rb install -D -m644 lib/bio/db/fasta/format_fasta.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/format_fasta.rb install -D -m644 lib/bio/db/fasta/defline.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta/defline.rb install -D -m644 lib/bio/db/prosite.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/prosite.rb install -D -m644 lib/bio/db/newick.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/newick.rb install -D -m644 lib/bio/db/kegg/reaction.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/reaction.rb install -D -m644 lib/bio/db/kegg/keggtab.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/keggtab.rb install -D -m644 lib/bio/db/kegg/orthology.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/orthology.rb install -D -m644 lib/bio/db/kegg/module.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/module.rb install -D -m644 lib/bio/db/kegg/kgml.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/kgml.rb install -D -m644 lib/bio/db/kegg/glycan.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/glycan.rb install -D -m644 lib/bio/db/kegg/enzyme.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/enzyme.rb install -D -m644 lib/bio/db/kegg/expression.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/expression.rb install -D -m644 lib/bio/db/kegg/taxonomy.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/taxonomy.rb install -D -m644 lib/bio/db/kegg/pathway.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/pathway.rb install -D -m644 lib/bio/db/kegg/genes.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genes.rb install -D -m644 lib/bio/db/kegg/compound.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/compound.rb install -D -m644 lib/bio/db/kegg/common.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/common.rb install -D -m644 lib/bio/db/kegg/genome.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/genome.rb install -D -m644 lib/bio/db/kegg/drug.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/drug.rb install -D -m644 lib/bio/db/kegg/brite.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/kegg/brite.rb install -D -m644 lib/bio/db/gff.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/gff.rb install -D -m644 lib/bio/db/biosql/sequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/biosql/sequence.rb install -D -m644 lib/bio/db/biosql/biosql_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/biosql/biosql_to_biosequence.rb install -D -m644 lib/bio/db/fastq/fastq_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/fastq_to_biosequence.rb install -D -m644 lib/bio/db/fastq/format_fastq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq/format_fastq.rb install -D -m644 lib/bio/db/rebase.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/rebase.rb install -D -m644 lib/bio/db/fantom.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fantom.rb install -D -m644 lib/bio/db/embl/trembl.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/trembl.rb install -D -m644 lib/bio/db/embl/uniprot.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/uniprot.rb install -D -m644 lib/bio/db/embl/embl.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl.rb install -D -m644 lib/bio/db/embl/format_embl.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/format_embl.rb install -D -m644 lib/bio/db/embl/swissprot.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/swissprot.rb install -D -m644 lib/bio/db/embl/embl_to_biosequence.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/embl_to_biosequence.rb install -D -m644 lib/bio/db/embl/sptr.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/sptr.rb install -D -m644 lib/bio/db/embl/common.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/embl/common.rb install -D -m644 lib/bio/db/fasta.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fasta.rb install -D -m644 lib/bio/db/go.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/go.rb install -D -m644 lib/bio/db/medline.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/medline.rb install -D -m644 lib/bio/db/pdb.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/pdb.rb install -D -m644 lib/bio/db/fastq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/fastq.rb install -D -m644 lib/bio/db/nbrf.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/db/nbrf.rb install -D -m644 lib/bio/reference.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/reference.rb install -D -m644 lib/bio/shell.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell.rb install -D -m644 lib/bio/pathway.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/pathway.rb install -D -m644 lib/bio/feature.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/feature.rb install -D -m644 lib/bio/map.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/map.rb install -D -m644 lib/bio/location.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/location.rb install -D -m644 lib/bio/shell/object.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/object.rb install -D -m644 lib/bio/shell/demo.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/demo.rb install -D -m644 lib/bio/shell/plugin/das.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/das.rb install -D -m644 lib/bio/shell/plugin/emboss.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/emboss.rb install -D -m644 lib/bio/shell/plugin/psort.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/psort.rb install -D -m644 lib/bio/shell/plugin/ncbirest.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/ncbirest.rb install -D -m644 lib/bio/shell/plugin/keggapi.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/keggapi.rb install -D -m644 lib/bio/shell/plugin/soap.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/soap.rb install -D -m644 lib/bio/shell/plugin/seq.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/seq.rb install -D -m644 lib/bio/shell/plugin/codon.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/codon.rb install -D -m644 lib/bio/shell/plugin/obda.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/obda.rb install -D -m644 lib/bio/shell/plugin/entry.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/entry.rb install -D -m644 lib/bio/shell/plugin/blast.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/blast.rb install -D -m644 lib/bio/shell/plugin/togows.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/togows.rb install -D -m644 lib/bio/shell/plugin/flatfile.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/flatfile.rb install -D -m644 lib/bio/shell/plugin/midi.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/plugin/midi.rb install -D -m644 lib/bio/shell/interface.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/interface.rb install -D -m644 lib/bio/shell/core.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/core.rb install -D -m644 lib/bio/shell/irb.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/irb.rb install -D -m644 lib/bio/shell/web.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/web.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif install -D -m644 lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml install -D -m644 lib/bio/shell/setup.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/setup.rb install -D -m644 lib/bio/shell/script.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/shell/script.rb install -D -m644 lib/bio/util/contingency_table.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/contingency_table.rb install -D -m644 lib/bio/util/color_scheme/helix.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/helix.rb install -D -m644 lib/bio/util/color_scheme/buried.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/buried.rb install -D -m644 lib/bio/util/color_scheme/turn.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/turn.rb install -D -m644 lib/bio/util/color_scheme/zappo.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/zappo.rb install -D -m644 lib/bio/util/color_scheme/hydropathy.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/hydropathy.rb install -D -m644 lib/bio/util/color_scheme/nucleotide.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/nucleotide.rb install -D -m644 lib/bio/util/color_scheme/strand.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/strand.rb install -D -m644 lib/bio/util/color_scheme/taylor.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme/taylor.rb install -D -m644 lib/bio/util/restriction_enzyme.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand.rb install -D -m644 lib/bio/util/restriction_enzyme/analysis_basic.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis_basic.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded/cut_locations.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb install -D -m644 lib/bio/util/restriction_enzyme/enzymes.yaml /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/enzymes.yaml install -D -m644 lib/bio/util/restriction_enzyme/string_formatting.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/string_formatting.rb install -D -m644 lib/bio/util/restriction_enzyme/double_stranded.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/double_stranded.rb install -D -m644 lib/bio/util/restriction_enzyme/single_strand_complement.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/single_strand_complement.rb install -D -m644 lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/horizontal_cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/cut_range.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/vertical_cut_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range.rb install -D -m644 lib/bio/util/restriction_enzyme/range/cut_ranges.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/cut_ranges.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragment.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/fragments.rb install -D -m644 lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb install -D -m644 lib/bio/util/restriction_enzyme/cut_symbol.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/cut_symbol.rb install -D -m644 lib/bio/util/restriction_enzyme/analysis.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/restriction_enzyme/analysis.rb install -D -m644 lib/bio/util/color_scheme.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/color_scheme.rb install -D -m644 lib/bio/util/sirna.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/util/sirna.rb install -D -m644 lib/bio/command.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/command.rb install -D -m644 lib/bio/sequence/quality_score.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/quality_score.rb install -D -m644 lib/bio/sequence/format_raw.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format_raw.rb install -D -m644 lib/bio/sequence/adapter.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/adapter.rb install -D -m644 lib/bio/sequence/generic.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/generic.rb install -D -m644 lib/bio/sequence/dblink.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/dblink.rb install -D -m644 lib/bio/sequence/format.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/format.rb install -D -m644 lib/bio/sequence/sequence_masker.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/sequence_masker.rb install -D -m644 lib/bio/sequence/na.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/na.rb install -D -m644 lib/bio/sequence/compat.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/compat.rb install -D -m644 lib/bio/sequence/common.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/common.rb install -D -m644 lib/bio/sequence/aa.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/sequence/aa.rb install -D -m644 lib/bio/data/codontable.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/codontable.rb install -D -m644 lib/bio/data/na.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/na.rb install -D -m644 lib/bio/data/aa.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio/data/aa.rb install -D -m644 lib/bio.rb /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/ruby-bio/usr/lib/ruby/vendor_ruby/bio.rb /usr/bin/ruby1.8 -I/usr/lib/ruby/vendor_ruby /usr/lib/ruby/vendor_ruby/gem2deb/test_runner.rb Loaded suite debian/ruby-tests Started .......................F............EEEEEEEEEEEE.....EEEEEEEEEEEEEEEEEEEEEEEE..FFFFFFFFFFFFFFFFFFF..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Finished in 299.335503 seconds. 1) Failure: test_read_uri(Bio::FuncTestCommandNet) [./test/functional/bio/test_command.rb:337]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/open-uri.rb:242:in `open_http' /usr/lib/ruby/1.8/open-uri.rb:616:in `buffer_open' /usr/lib/ruby/1.8/open-uri.rb:164:in `open_loop' /usr/lib/ruby/1.8/open-uri.rb:162:in `catch' /usr/lib/ruby/1.8/open-uri.rb:162:in `open_loop' /usr/lib/ruby/1.8/open-uri.rb:132:in `open_uri' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:625:in `read_uri' ./test/functional/bio/test_command.rb:338:in `test_read_uri' ./test/functional/bio/test_command.rb:337:in `test_read_uri' --------------- 2) Error: test_fasta_exportview_with_hash_4th_params(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:59:in `test_fasta_exportview_with_hash_4th_params' 3) Error: test_fasta_exportview_with_named_args_and_hash_4th_params(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:73:in `test_fasta_exportview_with_named_args_and_hash_4th_params' 4) Error: test_fna_exportview(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:54:in `test_fna_exportview' 5) Error: test_fna_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:66:in `test_fna_exportview_with_named_args' 6) Error: test_gff_exportview(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:112:in `test_gff_exportview' 7) Error: test_gff_exportview_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:84:in `test_gff_exportview_for_empty_result' 8) Error: test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:148:in `test_gff_exportview_with_named_args' 9) Error: test_gff_exportview_with_named_args_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:117:in `test_gff_exportview_with_named_args_for_empty_result' 10) Error: test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:219:in `test_tab_exportview_with_named_args' 11) Error: test_tab_exportview_with_named_args_for_empty_result(Bio::FuncTestEnsemblHumanExportView): Errno::ENETUNREACH: Network is unreachable - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ensembl.rb:188:in `exportview' ./test/functional/bio/io/test_ensembl.rb:168:in `test_tab_exportview_with_named_args_for_empty_result' 12) Error: test_exec(Bio::FuncTestPTS1): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:62:in `test_exec' 13) Error: test_exec_with_faa(Bio::FuncTestPTS1): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:67:in `test_exec_with_faa' 14) Error: test_cterm(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 15) Error: test_entry_id(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 16) Error: test_fp(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 17) Error: test_prediction(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 18) Error: test_profile(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 19) Error: test_score(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 20) Error: test_sppta(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 21) Error: test_spptna(Bio::FuncTestPTS1Report): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/appl/pts1.rb:148:in `exec' ./test/functional/bio/appl/test_pts1.rb:77:in `setup' 22) Error: test_efetch(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:80:in `test_efetch' 23) Error: test_efetch_multiple(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:89:in `test_efetch_multiple' 24) Error: test_efetch_multiple_xml(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:106:in `test_efetch_multiple_xml' 25) Error: test_efetch_single_xml(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:99:in `test_efetch_single_xml' 26) Error: test_efetch_str(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:84:in `test_efetch_str' 27) Error: test_esearch(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:26:in `test_esearch' 28) Error: test_esearch_count(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:282:in `esearch_count' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:253:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:38:in `test_esearch_count' 29) Error: test_esearch_retmax_retstart(Bio::FuncTestPubmed): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./test/functional/bio/io/test_pubmed.rb:46:in `test_esearch_retmax_retstart' 30) Error: test_efetch(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:80:in `test_efetch' 31) Error: test_efetch_multiple(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:89:in `test_efetch_multiple' 32) Error: test_efetch_multiple_xml(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:106:in `test_efetch_multiple_xml' 33) Error: test_efetch_single_xml(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:99:in `test_efetch_single_xml' 34) Error: test_efetch_str(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:331:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:328:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:120:in `efetch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:205:in `efetch' ./test/functional/bio/io/test_pubmed.rb:72:in `do_efetch_single' ./test/functional/bio/io/test_pubmed.rb:84:in `test_efetch_str' 35) Error: test_esearch(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:26:in `test_esearch' 36) Error: test_esearch_count(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:282:in `esearch_count' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:253:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:38:in `test_esearch_count' 37) Error: test_esearch_retmax_retstart(Bio::FuncTestPubmedClassMethod): Errno::ECONNREFUSED: Connection refused - connect(2) /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:440:in `start' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:649:in `start_http' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:735:in `post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:130:in `ncbi_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:267:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `step' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/ncbirest.rb:264:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:96:in `esearch' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/pubmed.rb:201:in `esearch' ./test/functional/bio/io/test_pubmed.rb:46:in `test_esearch_retmax_retstart' 38) Failure: test_convert(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:120]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:702:in `http_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:414:in `post_data' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:305:in `convert' ./test/functional/bio/io/test_togows.rb:121:in `test_convert' ./test/functional/bio/io/test_togows.rb:120:in `test_convert' --------------- 39) Failure: test_entry(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:33]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:34:in `test_entry' ./test/functional/bio/io/test_togows.rb:33:in `test_entry' --------------- 40) Failure: test_entry_database_list(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:165]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:314:in `entry_database_list' ./test/functional/bio/io/test_togows.rb:166:in `test_entry_database_list' ./test/functional/bio/io/test_togows.rb:165:in `test_entry_database_list' --------------- 41) Failure: test_entry_multi(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:44]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:45:in `test_entry_multi' ./test/functional/bio/io/test_togows.rb:44:in `test_entry_multi' --------------- 42) Failure: test_entry_with_format(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:67]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:68:in `test_entry_with_format' ./test/functional/bio/io/test_togows.rb:67:in `test_entry_with_format' --------------- 43) Failure: test_entry_with_format_and_key(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:84]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:85:in `test_entry_with_format_and_key' ./test/functional/bio/io/test_togows.rb:84:in `test_entry_with_format_and_key' --------------- 44) Failure: test_entry_with_key(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:76]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./test/functional/bio/io/test_togows.rb:77:in `test_entry_with_key' ./test/functional/bio/io/test_togows.rb:76:in `test_entry_with_key' --------------- 45) Failure: test_retrieve(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:128]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:129:in `test_retrieve' ./test/functional/bio/io/test_togows.rb:128:in `test_retrieve' --------------- 46) Failure: test_retrieve_1id_1db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:136]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:205:in `retrieve' ./test/functional/bio/io/test_togows.rb:137:in `test_retrieve_1id_1db' ./test/functional/bio/io/test_togows.rb:136:in `test_retrieve_1id_1db' --------------- 47) Failure: test_retrieve_1id_2db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:147]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:148:in `test_retrieve_1id_2db' ./test/functional/bio/io/test_togows.rb:147:in `test_retrieve_1id_2db' --------------- 48) Failure: test_retrieve_2id_2db(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:156]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:253:in `entry' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:211:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:210:in `retrieve' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `each' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:209:in `retrieve' ./test/functional/bio/io/test_togows.rb:157:in `test_retrieve_2id_2db' ./test/functional/bio/io/test_togows.rb:156:in `test_retrieve_2id_2db' --------------- 49) Failure: test_search(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:92]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:93:in `test_search' ./test/functional/bio/io/test_togows.rb:92:in `test_search' --------------- 50) Failure: test_search_database_list(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:174]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:321:in `search_database_list' ./test/functional/bio/io/test_togows.rb:175:in `test_search_database_list' ./test/functional/bio/io/test_togows.rb:174:in `test_search_database_list' --------------- 51) Failure: test_search_with_offset_limit(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:100]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:101:in `test_search_with_offset_limit' ./test/functional/bio/io/test_togows.rb:100:in `test_search_with_offset_limit' --------------- 52) Failure: test_search_with_offset_limit_format(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:110]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:286:in `search' ./test/functional/bio/io/test_togows.rb:111:in `test_search_with_offset_limit_format' ./test/functional/bio/io/test_togows.rb:110:in `test_search_with_offset_limit_format' --------------- 53) Failure: test_database_list(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:245]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:445:in `database_list' ./test/functional/bio/io/test_togows.rb:247:in `test_database_list' ./test/functional/bio/io/test_togows.rb:246:in `instance_eval' ./test/functional/bio/io/test_togows.rb:246:in `test_database_list' ./test/functional/bio/io/test_togows.rb:245:in `test_database_list' --------------- 54) Failure: test_get(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:204]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:377:in `get' ./test/functional/bio/io/test_togows.rb:206:in `test_get' ./test/functional/bio/io/test_togows.rb:205:in `instance_eval' ./test/functional/bio/io/test_togows.rb:205:in `test_get' ./test/functional/bio/io/test_togows.rb:204:in `test_get' --------------- 55) Failure: test_get_dir(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:217]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:772:in `get' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:397:in `get_dir' ./test/functional/bio/io/test_togows.rb:219:in `test_get_dir' ./test/functional/bio/io/test_togows.rb:218:in `instance_eval' ./test/functional/bio/io/test_togows.rb:218:in `test_get_dir' ./test/functional/bio/io/test_togows.rb:217:in `test_get_dir' --------------- 56) Failure: test_post_data(Bio::FuncTestTogoWSRESTprivate) [./test/functional/bio/io/test_togows.rb:232]: Exception raised: Class: Message: <"Connection refused - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/command.rb:702:in `http_post_form' ./debian/ruby-bio//usr/lib/ruby/vendor_ruby/bio/io/togows.rb:414:in `post_data' ./test/functional/bio/io/test_togows.rb:234:in `test_post_data' ./test/functional/bio/io/test_togows.rb:233:in `instance_eval' ./test/functional/bio/io/test_togows.rb:233:in `test_post_data' ./test/functional/bio/io/test_togows.rb:232:in `test_post_data' --------------- 3127 tests, 20292 assertions, 20 failures, 36 errors ERROR: Test "ruby1.8" failed. Exiting. dh_auto_install: dh_ruby --install /build/ruby-bio-auzhl7/ruby-bio-1.4.1/debian/tmp returned exit code 1 make[1]: *** [override_dh_auto_install] Error 1 make[1]: Leaving directory `/build/ruby-bio-auzhl7/ruby-bio-1.4.1' make: *** [binary] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1235 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-0bb257fe-1337-4c6f-a5a3-dbb81da6233c/build/ruby-bio-auzhl7 Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 9384 Build-Time: 304 Distribution: lsid64c Fail-Stage: build Install-Time: 9 Job: ruby-bio_1.4.1-2 Package: ruby-bio Package-Time: 333 Source-Version: 1.4.1-2 Space: 9384 Status: attempted Version: 1.4.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1235 Build needed 00:05:33, 9384k disc space DC-Build-Status: Failed 1538.337846s ### Content of /var/log/daemon.log ### Sep 11 10:47:42 talc-122 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:47:53 talc-122 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:24 talc-122 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:31 talc-122 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:48:35 talc-122 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:55 talc-122 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:06 talc-122 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:10 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:21 talc-122 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:29 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:47 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:47 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Sep 11 10:49:58 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:09 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:20 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:37 talc-122 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:50:39 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:48 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Sep 11 10:51:05 talc-122 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:51:15 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long Sep 11 10:51:22 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Sep 11 10:51:26 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long Sep 11 10:51:28 talc-122 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 1538.337846 versus expected 32000 (r/m: 19.8016724565457 ; m: 1538.337846) DC-Build-Network: USED. See /tmp/rulesafter.tLXHVt ! ************************************************************ # Generated by iptables-save v1.4.8 on Sun Sep 11 12:35:34 2011 *filter :INPUT ACCEPT [2817371:16287010539] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [1121144:14396609581] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [619845:59020570] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [3526:339600] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [270:16200] -A OUTPUT -j LD [270:16200] -A LD -j LOG [270:16200] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Sun Sep 11 12:35:34 2011 ************************************************************ --- /tmp/rulesbefore.fsfGRb 2011-09-11 12:09:56.322149920 +0200 +++ /tmp/rulesafter.tLXHVt 2011-09-11 12:35:34.666150870 +0200 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Sun Sep 11 12:09:56 2011 +# Generated by iptables-save v1.4.8 on Sun Sep 11 12:35:34 2011 *filter -:INPUT ACCEPT [2270084:12530202675] +:INPUT ACCEPT [2817371:16287010539] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[855304:10918862635] -A OUTPUT -o lo -j ACCEPT +[1121144:14396609581] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,10 +16,10 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[530828:50546269] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT -[2808:271752] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT -[0:0] -A OUTPUT -j LD -[0:0] -A LD -j LOG -[0:0] -A LD -j REJECT --reject-with icmp-port-unreachable +[619845:59020570] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[3526:339600] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[270:16200] -A OUTPUT -j LD +[270:16200] -A LD -j LOG +[270:16200] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Sun Sep 11 12:09:56 2011 +# Completed on Sun Sep 11 12:35:34 2011 ************************************************************ [ 7018.025599] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37096 DF PROTO=TCP SPT=46068 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7021.116025] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37097 DF PROTO=TCP SPT=46068 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7021.208915] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33838 DF PROTO=TCP SPT=46069 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7024.300029] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=33839 DF PROTO=TCP SPT=46069 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7024.392908] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61804 DF PROTO=TCP SPT=46070 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7027.481542] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61805 DF PROTO=TCP SPT=46070 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7027.574497] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8656 DF PROTO=TCP SPT=46071 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7030.661524] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8657 DF PROTO=TCP SPT=46071 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7030.753588] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26147 DF PROTO=TCP SPT=46072 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7033.841530] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26148 DF PROTO=TCP SPT=46072 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7033.934106] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=42118 DF PROTO=TCP SPT=46073 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7037.021533] IN= OUT=eth0 SRC=172.16.66.122 DST=130.14.29.110 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=42119 DF PROTO=TCP SPT=46073 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7037.144284] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8748 DF PROTO=TCP SPT=49423 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7040.233532] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8749 DF PROTO=TCP SPT=49423 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7040.329600] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61843 DF PROTO=TCP SPT=49424 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7043.417538] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=61844 DF PROTO=TCP SPT=49424 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7043.512549] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=24791 DF PROTO=TCP SPT=49425 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7046.601532] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=24792 DF PROTO=TCP SPT=49425 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7046.698819] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=46307 DF PROTO=TCP SPT=49455 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7049.789526] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=46308 DF PROTO=TCP SPT=49455 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7049.884159] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=57771 DF PROTO=TCP SPT=49457 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7052.973528] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=57772 DF PROTO=TCP SPT=49457 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7053.068513] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=51418 DF PROTO=TCP SPT=49458 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7056.157529] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=51419 DF PROTO=TCP SPT=49458 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7056.252579] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40043 DF PROTO=TCP SPT=49463 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7059.341529] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=40044 DF PROTO=TCP SPT=49463 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7059.453647] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=35244 DF PROTO=TCP SPT=49468 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7062.544033] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=35245 DF PROTO=TCP SPT=49468 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7062.643218] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=47698 DF PROTO=TCP SPT=49469 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7065.736044] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=47699 DF PROTO=TCP SPT=49469 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7065.831359] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5018 DF PROTO=TCP SPT=49471 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7068.924036] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=5019 DF PROTO=TCP SPT=49471 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7069.018781] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13547 DF PROTO=TCP SPT=49474 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7072.112039] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=13548 DF PROTO=TCP SPT=49474 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7072.206778] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=53805 DF PROTO=TCP SPT=49482 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7075.300030] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=53806 DF PROTO=TCP SPT=49482 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7075.395146] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=18719 DF PROTO=TCP SPT=49483 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7078.488030] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=18720 DF PROTO=TCP SPT=49483 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7078.582574] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=29284 DF PROTO=TCP SPT=49484 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7081.676043] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=29285 DF PROTO=TCP SPT=49484 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7081.773977] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26116 DF PROTO=TCP SPT=49485 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7084.864023] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=26117 DF PROTO=TCP SPT=49485 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7084.958279] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=59098 DF PROTO=TCP SPT=49486 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7088.052045] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=59099 DF PROTO=TCP SPT=49486 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7088.147143] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1232 DF PROTO=TCP SPT=49487 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7091.240029] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=1233 DF PROTO=TCP SPT=49487 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7091.334093] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=4109 DF PROTO=TCP SPT=49488 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7094.424030] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=4110 DF PROTO=TCP SPT=49488 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7094.519119] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=9392 DF PROTO=TCP SPT=49489 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7097.612029] IN= OUT=eth0 SRC=172.16.66.122 DST=133.11.132.131 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=9393 DF PROTO=TCP SPT=49489 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 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