RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-018 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:30:44 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_157 python-lpbuildd_157 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.3 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 10 Jan 21:29:10 ntpdate[1846]: adjust time server 10.211.37.1 offset -0.019313 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 /home/buildd/filecache-default/78cf3583c71e53d2c7312b9d7596a64d82c6adad Creating target for build PACKAGEBUILD-14051892 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Starting target for build PACKAGEBUILD-14051892 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic main' 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-14051892 RUN: /usr/share/launchpad-buildd/slavebin/in-target add-trusted-keys --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Adding trusted keys to build-PACKAGEBUILD-14051892 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Updating target for build PACKAGEBUILD-14051892 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic InRelease [15.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main arm64 Packages [973 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [518 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main arm64 Packages [3416 B] Get:8 http://ftpmaster.internal/ubuntu bionic/restricted Translation-en [2384 B] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main Translation-en [3684 B] Get:10 http://ftpmaster.internal/ubuntu bionic/universe arm64 Packages [8163 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4931 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/multiverse arm64 Packages [127 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/multiverse Translation-en [109 kB] Fetched 15.2 MB in 5s (2617 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: liblsan0 libnghttp2-14 libtsan0 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd binutils binutils-aarch64-linux-gnu binutils-common bsdutils build-essential coreutils cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv init init-system-helpers libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libitm1 libkeyutils1 libkrb5-26-heimdal liblockfile-bin liblockfile1 libmount1 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libroken18-heimdal libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev lsb-base mount multiarch-support openssl optipng perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 107 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 53.1 MB of archives. After this operation, 5692 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main arm64 perl-modules-5.26 all 5.26.1-3 [2761 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main arm64 libbinutils arm64 2.29.51.20180110-1ubuntu1 [429 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main arm64 binutils arm64 2.29.51.20180110-1ubuntu1 [3368 B] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main arm64 binutils-common arm64 2.29.51.20180110-1ubuntu1 [193 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/binutils/ubuntu bionic/main arm64 binutils-aarch64-linux-gnu arm64 2.29.51.20180110-1ubuntu1 [2171 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main arm64 libperl5.26 arm64 5.26.1-3 [3300 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main arm64 perl arm64 5.26.1-3 [201 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main arm64 perl-base arm64 5.26.1-3 [1234 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main arm64 libc6-dev arm64 2.26-0ubuntu2 [2013 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main arm64 libc-dev-bin arm64 2.26-0ubuntu2 [59.1 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main arm64 linux-libc-dev arm64 4.13.0-25.29 [939 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main arm64 libgomp1 arm64 7.2.0-18ubuntu2 [62.0 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main arm64 libitm1 arm64 7.2.0-18ubuntu2 [25.6 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main arm64 gcc-7-base arm64 7.2.0-18ubuntu2 [19.1 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcc1 arm64 1:7.2.0-18ubuntu2 [33.4 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main arm64 libatomic1 arm64 7.2.0-18ubuntu2 [6636 B] Get:17 http://ftpmaster.internal/ubuntu bionic/main arm64 libasan4 arm64 7.2.0-18ubuntu2 [336 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main arm64 liblsan0 arm64 7.2.0-18ubuntu2 [123 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main arm64 libtsan0 arm64 7.2.0-18ubuntu2 [265 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main arm64 libubsan0 arm64 7.2.0-18ubuntu2 [117 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main arm64 cpp-7 arm64 7.2.0-18ubuntu2 [5320 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main arm64 libcc1-0 arm64 7.2.0-18ubuntu2 [35.4 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main arm64 g++-7 arm64 7.2.0-18ubuntu2 [6128 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main arm64 gcc-7 arm64 7.2.0-18ubuntu2 [5969 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcc-7-dev arm64 7.2.0-18ubuntu2 [835 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main arm64 libstdc++-7-dev arm64 7.2.0-18ubuntu2 [1456 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main arm64 libstdc++6 arm64 7.2.0-18ubuntu2 [377 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main arm64 libc6 arm64 2.26-0ubuntu2 [2246 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main arm64 init-system-helpers all 1.51 [37.3 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main arm64 base-files arm64 10ubuntu1 [55.9 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main arm64 bsdutils arm64 1:2.30.2-0.1ubuntu1 [54.6 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main arm64 coreutils arm64 8.26-3ubuntu4 [1059 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main arm64 debianutils arm64 4.8.4 [84.7 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main arm64 dpkg arm64 1.19.0.4ubuntu1 [1100 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main arm64 e2fslibs arm64 1.43.8-1ubuntu1 [138 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main arm64 e2fsprogs arm64 1.43.8-1ubuntu1 [455 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main arm64 findutils arm64 4.6.0+git+20170828-2 [278 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main arm64 libuuid1 arm64 2.30.2-0.1ubuntu1 [14.1 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main arm64 libblkid1 arm64 2.30.2-0.1ubuntu1 [100 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main arm64 libsmartcols1 arm64 2.30.2-0.1ubuntu1 [67.0 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main arm64 libfdisk1 arm64 2.30.2-0.1ubuntu1 [132 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main arm64 libpcre3 arm64 2:8.39-8 [203 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main arm64 libselinux1 arm64 2.7-2 [57.4 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main arm64 libmount1 arm64 2.30.2-0.1ubuntu1 [111 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main arm64 fdisk arm64 2.30.2-0.1ubuntu1 [93.9 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main arm64 util-linux arm64 2.30.2-0.1ubuntu1 [796 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main arm64 base-passwd arm64 3.5.44 [45.6 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main arm64 libc-bin arm64 2.26-0ubuntu2 [475 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main arm64 sysvinit-utils arm64 2.88dsf-59.10ubuntu1 [17.7 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main arm64 libudev1 arm64 235-3ubuntu3 [46.3 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main arm64 libapt-pkg5.0 arm64 1.6~alpha5 [740 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main arm64 debconf all 1.5.65 [124 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main arm64 adduser all 3.116ubuntu1 [163 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main arm64 libgpg-error0 arm64 1.27-5 [32.8 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcrypt20 arm64 1.8.1-4 [325 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main arm64 gpgv arm64 2.1.15-1ubuntu8 [156 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main arm64 libseccomp2 arm64 2.3.1-2.1ubuntu3 [33.9 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main arm64 apt arm64 1.6~alpha5 [1112 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main arm64 libapparmor1 arm64 2.11.0-2ubuntu18 [25.8 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main arm64 libcap2 arm64 1:2.25-1.2 [12.2 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main arm64 libidn11 arm64 1.33-2.1 [43.0 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main arm64 libip4tc0 arm64 1.6.1-2ubuntu2 [18.3 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main arm64 mount arm64 2.30.2-0.1ubuntu1 [102 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main arm64 systemd arm64 235-3ubuntu3 [2487 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main arm64 libsystemd0 arm64 235-3ubuntu3 [165 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main arm64 init arm64 1.51 [5864 B] Get:67 http://ftpmaster.internal/ubuntu bionic/main arm64 systemd-sysv arm64 235-3ubuntu3 [13.1 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main arm64 libcap-ng0 arm64 0.7.7-3.1 [10.0 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main arm64 libcomerr2 arm64 1.43.8-1ubuntu1 [10.7 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main arm64 libsemanage-common all 2.7-2 [6916 B] Get:71 http://ftpmaster.internal/ubuntu bionic/main arm64 libsemanage1 arm64 2.7-2 [70.1 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main arm64 libss2 arm64 1.43.8-1ubuntu1 [9892 B] Get:73 http://ftpmaster.internal/ubuntu bionic/main arm64 libnettle6 arm64 3.3-2 [96.3 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main arm64 libhogweed4 arm64 3.3-2 [128 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main arm64 libp11-kit0 arm64 0.23.9-2 [138 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main arm64 libtasn1-6 arm64 4.12-3 [32.1 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main arm64 lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main arm64 sensible-utils all 0.0.11 [14.8 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main arm64 libassuan0 arm64 2.5.1-1 [28.8 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main arm64 pinentry-curses arm64 1.0.0-3 [31.3 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main arm64 libnpth0 arm64 1.5-3 [6844 B] Get:82 http://ftpmaster.internal/ubuntu bionic/main arm64 gnupg arm64 2.1.15-1ubuntu8 [706 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main arm64 gnupg-agent arm64 2.1.15-1ubuntu8 [213 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main arm64 libsqlite3-0 arm64 3.21.0-1 [422 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main arm64 libroken18-heimdal arm64 7.5.0+dfsg-1 [35.4 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main arm64 libasn1-8-heimdal arm64 7.5.0+dfsg-1 [130 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main arm64 libheimbase1-heimdal arm64 7.5.0+dfsg-1 [24.9 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main arm64 libhcrypto4-heimdal arm64 7.5.0+dfsg-1 [76.4 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main arm64 libwind0-heimdal arm64 7.5.0+dfsg-1 [47.0 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main arm64 libhx509-5-heimdal arm64 7.5.0+dfsg-1 [88.5 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main arm64 libkrb5-26-heimdal arm64 7.5.0+dfsg-1 [170 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main arm64 libheimntlm0-heimdal arm64 7.5.0+dfsg-1 [13.3 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main arm64 libgssapi3-heimdal arm64 7.5.0+dfsg-1 [79.1 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main arm64 libssl1.0.0 arm64 1.0.2g-1ubuntu14 [717 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main arm64 multiarch-support arm64 2.26-0ubuntu2 [6832 B] Get:96 http://ftpmaster.internal/ubuntu bionic/main arm64 openssl arm64 1.0.2g-1ubuntu14 [466 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main arm64 tzdata all 2017c-1 [188 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main arm64 libidn2-0 arm64 2.0.4-1 [89.1 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/main arm64 libkeyutils1 arm64 1.5.9-9.2ubuntu1 [8708 B] Get:100 http://ftpmaster.internal/ubuntu bionic/main arm64 libpng16-16 arm64 1.6.34-1 [161 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/universe arm64 apt-transport-https all 1.6~alpha5 [1692 B] Get:102 http://ftpmaster.internal/ubuntu bionic/main arm64 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main arm64 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main arm64 build-essential arm64 12.4ubuntu1 [4754 B] Get:105 http://ftpmaster.internal/ubuntu bionic/main arm64 libnghttp2-14 arm64 1.29.0-1 [68.7 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main arm64 libpsl5 arm64 0.19.1-4 [40.3 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main arm64 libcurl3-gnutls arm64 7.57.0-1ubuntu1 [177 kB] Get:108 http://ftpmaster.internal/ubuntu bionic/main arm64 liblockfile-bin arm64 1.14-1.1 [11.1 kB] Get:109 http://ftpmaster.internal/ubuntu bionic/main arm64 liblockfile1 arm64 1.14-1.1 [6192 B] Get:110 http://ftpmaster.internal/ubuntu bionic/main arm64 optipng arm64 0.7.6-1.1 [78.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.1 MB in 2s (24.2 MB/s) (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../perl_5.26.1-3_arm64.deb ... Unpacking perl (5.26.1-3) over (5.26.0-8ubuntu1) ... Preparing to unpack .../perl-modules-5.26_5.26.1-3_all.deb ... Unpacking perl-modules-5.26 (5.26.1-3) over (5.26.0-8ubuntu1) ... Preparing to unpack .../libperl5.26_5.26.1-3_arm64.deb ... Unpacking libperl5.26:arm64 (5.26.1-3) over (5.26.0-8ubuntu1) ... Preparing to unpack .../perl-base_5.26.1-3_arm64.deb ... Unpacking perl-base (5.26.1-3) over (5.26.0-8ubuntu1) ... Setting up perl-base (5.26.1-3) ... (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.26-0ubuntu2_arm64.deb ... Unpacking libc6-dev:arm64 (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../1-libc-dev-bin_2.26-0ubuntu2_arm64.deb ... Unpacking libc-dev-bin (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../2-linux-libc-dev_4.13.0-25.29_arm64.deb ... Unpacking linux-libc-dev:arm64 (4.13.0-25.29) over (4.13.0-11.12) ... 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Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 10 21:30:24 UTC 2018. Universal Time is now: Wed Jan 10 21:30:24 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (235-3ubuntu3) ... Setting up libubsan0:arm64 (7.2.0-18ubuntu2) ... Setting up libtsan0:arm64 (7.2.0-18ubuntu2) ... Setting up liblockfile1:arm64 (1.14-1.1) ... Setting up linux-libc-dev:arm64 (4.13.0-25.29) ... Setting up libroken18-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up perl-modules-5.26 (5.26.1-3) ... Setting up optipng (0.7.6-1.1) ... Setting up cpp-7 (7.2.0-18ubuntu2) ... Setting up lsb-base (9.20170808ubuntu1) ... Setting up liblsan0:arm64 (7.2.0-18ubuntu2) ... Setting up binutils-common:arm64 (2.29.51.20180110-1ubuntu1) ... Setting up sensible-utils (0.0.11) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libperl5.26:arm64 (5.26.1-3) ... Setting up libheimbase1-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up openssl (1.0.2g-1ubuntu14) ... Setting up libsqlite3-0:arm64 (3.21.0-1) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:arm64 (1.5.9-9.2ubuntu1) ... Setting up libc6-dev:arm64 (2.26-0ubuntu2) ... Setting up libassuan0:arm64 (2.5.1-1) ... Setting up libitm1:arm64 (7.2.0-18ubuntu2) ... Setting up libwind0-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up libbinutils:arm64 (2.29.51.20180110-1ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.57.0-1ubuntu1) ... Setting up init (1.51) ... Setting up libasn1-8-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up libhcrypto4-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up libhx509-5-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up libgcc-7-dev:arm64 (7.2.0-18ubuntu2) ... Setting up libstdc++-7-dev:arm64 (7.2.0-18ubuntu2) ... Setting up perl (5.26.1-3) ... Setting up binutils-aarch64-linux-gnu (2.29.51.20180110-1ubuntu1) ... Setting up pinentry-curses (1.0.0-3) ... Setting up binutils (2.29.51.20180110-1ubuntu1) ... Setting up libkrb5-26-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up gnupg-agent (2.1.15-1ubuntu8) ... Setting up libheimntlm0-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up gcc-7 (7.2.0-18ubuntu2) ... Setting up g++-7 (7.2.0-18ubuntu2) ... Setting up gnupg (2.1.15-1ubuntu8) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up libgssapi3-heimdal:arm64 (7.5.0+dfsg-1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14051892 arm64 bionic -c chroot:build-PACKAGEBUILD-14051892 --arch=arm64 --dist=bionic --nolog python-biopython_1.70+dfsg-4.dsc Initiating build PACKAGEBUILD-14051892 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:30:44 UTC 2017 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-018.buildd +==============================================================================+ | python-biopython 1.70+dfsg-4 (arm64) 10 Jan 2018 21:30 | +==============================================================================+ Package: python-biopython Version: 1.70+dfsg-4 Source Version: 1.70+dfsg-4 Distribution: bionic Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/python-biopython-0eU8Kq/python-biopython-1.70+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-biopython-0eU8Kq' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14051892/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-biopython_1.70+dfsg-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-SOuHiQ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-SOuHiQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SOuHiQ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-SOuHiQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SOuHiQ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-SOuHiQ/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (58.2 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'apt autoremove' to remove them. 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-SOuHiQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (64.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12579 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), python-all-dev, python3-all-dev, python-numpy, python3-numpy, flex, python-reportlab, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, phyml, prank, probcons, python-mysqldb, python3-mysqldb, python-matplotlib, python3-matplotlib, python-pil, python3-pil, python-rdflib (>= 4), python3-rdflib, python-renderpm, python3-renderpm, python-psycopg2, python3-psycopg2, python-scipy, python3-scipy, python-setuptools, python3-setuptools, t-coffee, wise (>= 2.4.1-16) Filtered Build-Depends: debhelper (>= 10), python-all-dev, python3-all-dev, python-numpy, python3-numpy, flex, python-reportlab, python3-reportlab, hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended, clustalo, clustalw, dialign, dssp, emboss, fasttree, mafft, muscle, ncbi-blast+, phylip, phyml, prank, probcons, python-mysqldb, python3-mysqldb, python-matplotlib, python3-matplotlib, python-pil, python3-pil, python-rdflib (>= 4), python3-rdflib, python-renderpm, python3-renderpm, python-psycopg2, python3-psycopg2, python-scipy, python3-scipy, python-setuptools, python3-setuptools, t-coffee, wise (>= 2.4.1-16) dpkg-deb: building package 'sbuild-build-depends-python-biopython-dummy' in '/<>/resolver-kZ7gIG/apt_archive/sbuild-build-depends-python-biopython-dummy.deb'. Ign:1 copy:/<>/resolver-kZ7gIG/apt_archive ./ InRelease Get:2 copy:/<>/resolver-kZ7gIG/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-kZ7gIG/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-kZ7gIG/apt_archive ./ Sources [486 B] Get:5 copy:/<>/resolver-kZ7gIG/apt_archive ./ Packages [771 B] Fetched 3376 B in 0s (65.2 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install python-biopython build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libcurl3-gnutls libidn2-0 libnghttp2-14 libpsl5 librtmp1 Use 'apt autoremove' to remove them. The following additional packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bsdmainutils clustalo clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp emboss emboss-data emboss-lib fasttree file flex fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx gettext gettext-base ghostscript groff-base gsfonts gtk-update-icon-cache hevea hicolor-icon-theme humanity-icon-theme intltool-debian libarchive-zip-perl libargtable2-0 libart-2.0-2 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.65.1 libboost-system1.65.1 libboost-thread1.65.1 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdatrie1 libdbus-1-3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran4 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-icu0 libharfbuzz0b libhpdf-2.2.1 libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu-le-hb0 libicu60 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libkpathsea6 liblapack3 liblcms2-2 libltdl7 libmagic-mgc libmagic1 libmpdec2 libmysqlclient20 libnetpbm10 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenmpi2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpipeline1 libpixman-1-0 libpoppler68 libpotrace0 libpq5 libptexenc1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib librsvg2-2 librsvg2-common libsigsegv2 libsm6 libsynctex1 libtexlua52 libthai-data libthai0 libtiff5 libtimedate-perl libtool libwebp6 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxmu6 libxpm4 libxrandr2 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm ocaml-base-nox ocl-icd-libopencl1 openmpi-bin openmpi-common phylip phyml po-debconf poppler-data prank preview-latex-style probcons python python-all python-all-dev python-cycler python-dateutil python-decorator python-dev python-functools32 python-isodate python-matplotlib python-matplotlib-data python-minimal python-mysqldb python-numpy python-olefile python-pil python-pkg-resources python-psycopg2 python-pyparsing python-rdflib python-renderpm python-reportlab python-reportlab-accel python-scipy python-setuptools python-six python-subprocess32 python-tz python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-matplotlib python3-minimal python3-mysqldb python3-numpy python3-olefile python3-pil python3-pkg-resources python3-psycopg2 python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3.6 python3.6-2to3 python3.6-dev python3.6-minimal shared-mime-info t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ubuntu-mono ucf wise wise-data x11-common xdg-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation clustalx seaview dh-make dwz emboss-doc emboss-test embassy bison gettext-doc libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc cups-common libgd-tools gvfs libhwloc-contrib-plugins libjs-jquery-ui-docs liblcms2-utils pciutils librsvg2-bin libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor opencl-icd gfortran phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra python-doc python-tk python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 inkscape ipython python-cairocffi python-configobj python-excelerator python-gobject python-gtk2 python-matplotlib-doc python-nose python-qt4 python-sip python-tornado python-traits python-wxgtk3.0 texlive-extra-utils ttf-staypuft default-mysql-server | virtual-mysql-server python-egenix-mxdatetime python-mysqldb-dbg python-numpy-dbg python-numpy-doc python-pil-doc python-pil-dbg python-psycopg2-doc python-pyparsing-doc python-rdflib-doc python-rdflib-tools python-renderpm-dbg pdf-viewer python-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv ipython3 python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt4 python3-sip python3-tornado python3-mysqldb-dbg python3-numpy-dbg python3-pil-dbg python3-renderpm-dbg python3-egenix-mxtexttools python3.6-venv python3.6-doc boxshade t-coffee-examples perl-tk xpdf-reader | pdf-viewer python-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby wise-doc libglib2.0-bin Recommended packages: primer3 libfl-dev curl | wget | lynx libcupsfilters1 dbus libarchive-cpio-perl libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs fonts-droid-fallback libgail-common libgtk2.0-bin javascript-common libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python-glade2 python-imaging python-tk python-egenix-mxdatetime python-sparqlwrapper python-html5lib python3-tk python3-sparqlwrapper python3-html5lib amap-align dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl mustang poa proda tm-align lmodern wish tex-gyre texlive-fonts-recommended-doc tipa texlive-latex-base-doc texlive-latex-extra-doc texlive-plain-generic texlive-latex-recommended-doc ruby | ruby-interpreter texlive-pictures-doc tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bsdmainutils clustalo clustalw debhelper dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp emboss emboss-data emboss-lib fasttree file flex fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern fonts-lyx gettext gettext-base ghostscript groff-base gsfonts gtk-update-icon-cache hevea hicolor-icon-theme humanity-icon-theme intltool-debian libarchive-zip-perl libargtable2-0 libart-2.0-2 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-program-options1.65.1 libboost-system1.65.1 libboost-thread1.65.1 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libdatrie1 libdbus-1-3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran4 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-icu0 libharfbuzz0b libhpdf-2.2.1 libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu-le-hb0 libicu60 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libkpathsea6 liblapack3 liblcms2-2 libltdl7 libmagic-mgc libmagic1 libmpdec2 libmysqlclient20 libnetpbm10 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenmpi2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpipeline1 libpixman-1-0 libpoppler68 libpotrace0 libpq5 libptexenc1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib librsvg2-2 librsvg2-common libsigsegv2 libsm6 libsynctex1 libtexlua52 libthai-data libthai0 libtiff5 libtimedate-perl libtool libwebp6 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxi6 libxinerama1 libxml2 libxmu6 libxpm4 libxrandr2 libxrender1 libxt6 libzzip-0-13 m4 mafft man-db mime-support muscle mysql-common ncbi-blast+ ncbi-data netpbm ocaml-base-nox ocl-icd-libopencl1 openmpi-bin openmpi-common phylip phyml po-debconf poppler-data prank preview-latex-style probcons python python-all python-all-dev python-cycler python-dateutil python-decorator python-dev python-functools32 python-isodate python-matplotlib python-matplotlib-data python-minimal python-mysqldb python-numpy python-olefile python-pil python-pkg-resources python-psycopg2 python-pyparsing python-rdflib python-renderpm python-reportlab python-reportlab-accel python-scipy python-setuptools python-six python-subprocess32 python-tz python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-isodate python3-matplotlib python3-minimal python3-mysqldb python3-numpy python3-olefile python3-pil python3-pkg-resources python3-psycopg2 python3-pyparsing python3-rdflib python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3.6 python3.6-2to3 python3.6-dev python3.6-minimal sbuild-build-depends-python-biopython-dummy shared-mime-info t-coffee t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ttf-bitstream-vera ubuntu-mono ucf wise wise-data x11-common xdg-utils 0 upgraded, 261 newly installed, 1 to remove and 0 not upgraded. Need to get 273 MB of archives. After this operation, 1269 MB of additional disk space will be used. Get:1 copy:/<>/resolver-kZ7gIG/apt_archive ./ sbuild-build-depends-python-biopython-dummy 0.invalid.0 [1096 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3.6-minimal arm64 3.6.4-2 [524 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main arm64 libexpat1 arm64 2.2.5-3 [69.2 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main arm64 python3.6-minimal arm64 3.6.4-2 [1286 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-minimal arm64 3.6.3-0ubuntu2 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main arm64 mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main arm64 libmpdec2 arm64 2.4.2-1 [74.3 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3.6-stdlib arm64 3.6.4-2 [1598 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main arm64 python3.6-2to3 all 3.6.4-2 [13.9 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-distutils all 3.6.4~rc1-6 [145 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main arm64 python3.6 arm64 3.6.4-2 [181 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3-stdlib arm64 3.6.3-0ubuntu2 [6820 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-python all 2.20170125 [83.7 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main arm64 python3 arm64 3.6.3-0ubuntu2 [8712 B] Get:15 http://ftpmaster.internal/ubuntu bionic/main arm64 libxau6 arm64 1:1.0.8-1 [7590 B] Get:16 http://ftpmaster.internal/ubuntu bionic/main arm64 libbsd0 arm64 0.8.6-3 [36.6 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main arm64 libxdmcp6 arm64 1:1.1.2-3 [9694 B] Get:18 http://ftpmaster.internal/ubuntu bionic/main arm64 libxcb1 arm64 1.12-1ubuntu1 [37.0 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main arm64 libx11-data all 2:1.6.4-3 [114 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main arm64 libx11-6 arm64 2:1.6.4-3 [515 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main arm64 libxext6 arm64 2:1.3.3-1 [25.4 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main arm64 groff-base arm64 1.22.3-9 [1129 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main arm64 bsdmainutils arm64 9.0.14ubuntu1 [173 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main arm64 libpipeline1 arm64 1.5.0-1 [22.0 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main arm64 man-db arm64 2.7.6.1-4 [873 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main arm64 libsigsegv2 arm64 2.11-1 [12.5 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main arm64 m4 arm64 1.4.18-1 [185 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main arm64 flex arm64 2.6.1-1.3 [283 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main arm64 libfreetype6 arm64 2.8-0.2ubuntu2 [289 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main arm64 ucf all 3.0036 [52.9 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main arm64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/universe arm64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main arm64 fontconfig-config all 2.12.6-0ubuntu1 [55.5 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main arm64 libfontconfig1 arm64 2.12.6-0ubuntu1 [125 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main arm64 fontconfig arm64 2.12.6-0ubuntu1 [167 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main arm64 libjpeg-turbo8 arm64 1.5.2-0ubuntu5 [91.1 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main arm64 x11-common all 1:7.7+19ubuntu3 [22.0 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main arm64 libice6 arm64 2:1.0.9-2 [33.7 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main arm64 libsm6 arm64 2:1.2.2-1 [13.7 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main arm64 libxinerama1 arm64 2:1.1.3-1 [7438 B] Get:41 http://ftpmaster.internal/ubuntu bionic/main arm64 poppler-data all 0.4.8-2 [1479 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython2.7-minimal arm64 2.7.14-4 [337 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main arm64 python2.7-minimal arm64 2.7.14-4 [1139 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main arm64 python-minimal arm64 2.7.14-2ubuntu1 [28.1 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython2.7-stdlib arm64 2.7.14-4 [1851 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main arm64 python2.7 arm64 2.7.14-4 [233 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython-stdlib arm64 2.7.14-2ubuntu1 [7576 B] Get:48 http://ftpmaster.internal/ubuntu bionic/main arm64 python arm64 2.7.14-2ubuntu1 [140 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main arm64 tex-common all 6.09 [33.0 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main arm64 libjbig0 arm64 2.1-3.1 [23.8 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main arm64 libmagic-mgc arm64 1:5.32-1 [184 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main arm64 libmagic1 arm64 1:5.32-1 [61.7 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main arm64 file arm64 1:5.32-1 [21.6 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main arm64 libdbus-1-3 arm64 1.12.2-1ubuntu1 [152 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main arm64 libglib2.0-0 arm64 2.54.1-1ubuntu1 [980 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main arm64 libgraphite2-3 arm64 1.3.10-8 [65.7 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main arm64 libharfbuzz0b arm64 1.7.2-1 [207 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main arm64 libicu-le-hb0 arm64 1.0.3+git161113-4 [14.4 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main arm64 libicu60 arm64 60.2-1ubuntu1 [7998 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main arm64 libxml2 arm64 2.9.4+dfsg1-5.2ubuntu1 [553 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main arm64 shared-mime-info arm64 1.9-2 [423 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main arm64 gettext-base arm64 0.19.8.1-4ubuntu2 [46.4 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main arm64 libnuma1 arm64 2.0.11-2.1 [19.1 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main arm64 hicolor-icon-theme all 0.17-1 [10.3 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:66 http://ftpmaster.internal/ubuntu bionic/main arm64 libtiff5 arm64 4.0.9-3 [129 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main arm64 libgdk-pixbuf2.0-common all 2.36.11-1 [4260 B] Get:68 http://ftpmaster.internal/ubuntu bionic/main arm64 libgdk-pixbuf2.0-0 arm64 2.36.11-1 [142 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main arm64 gtk-update-icon-cache arm64 3.22.26-2ubuntu1 [26.6 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main arm64 libpixman-1-0 arm64 0.34.0-2 [115 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main arm64 libxcb-render0 arm64 1.12-1ubuntu1 [12.5 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main arm64 libxcb-shm0 arm64 1.12-1ubuntu1 [5180 B] Get:73 http://ftpmaster.internal/ubuntu bionic/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main arm64 libcairo2 arm64 1.15.8-3 [485 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main arm64 libcroco3 arm64 0.6.12-2 [68.2 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main arm64 libthai-data all 0.1.27-1 [133 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main arm64 libdatrie1 arm64 0.2.10-6 [15.2 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main arm64 libthai0 arm64 0.1.27-1 [15.3 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main arm64 libpango-1.0-0 arm64 1.40.14-1 [137 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main arm64 libpangoft2-1.0-0 arm64 1.40.14-1 [27.6 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main arm64 libpangocairo-1.0-0 arm64 1.40.14-1 [17.4 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main arm64 librsvg2-2 arm64 2.40.18-2 [78.7 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main arm64 librsvg2-common arm64 2.40.18-2 [4908 B] Get:84 http://ftpmaster.internal/ubuntu bionic/main arm64 humanity-icon-theme all 0.6.14 [1250 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main arm64 ubuntu-mono all 16.10+18.04.20171224.1-0ubuntu1 [149 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main arm64 adwaita-icon-theme all 3.26.1-1ubuntu1 [3447 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main arm64 autoconf all 2.69-11 [322 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main arm64 autotools-dev all 20171216.1 [39.7 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main arm64 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main arm64 autopoint all 0.19.8.1-4ubuntu2 [412 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/universe arm64 libargtable2-0 arm64 13-1 [12.1 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/universe arm64 clustalo arm64 1.2.4-1 [223 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/universe arm64 clustalw arm64 2.1+lgpl-5 [248 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main arm64 libtool all 2.4.6-2 [194 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-autoreconf all 15 [15.8 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main arm64 libarchive-zip-perl all 1.60-1 [83.9 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main arm64 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:100 http://ftpmaster.internal/ubuntu bionic/main arm64 gettext arm64 0.19.8.1-4ubuntu2 [1027 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main arm64 po-debconf all 1.0.20 [232 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main arm64 debhelper all 11ubuntu1 [887 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/universe arm64 dialign arm64 2.2.1-9 [138 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main arm64 libboost-program-options1.65.1 arm64 1.65.1+dfsg-0ubuntu4 [128 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main arm64 libboost-system1.65.1 arm64 1.65.1+dfsg-0ubuntu4 [10.5 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main arm64 libboost-thread1.65.1 arm64 1.65.1+dfsg-0ubuntu4 [42.4 kB] Get:108 http://ftpmaster.internal/ubuntu bionic/universe arm64 dssp arm64 3.0.0-1ubuntu1 [243 kB] Get:109 http://ftpmaster.internal/ubuntu bionic/main arm64 libwebp6 arm64 0.6.0-4 [166 kB] Get:110 http://ftpmaster.internal/ubuntu bionic/main arm64 libxpm4 arm64 1:3.5.12-1 [28.8 kB] Get:111 http://ftpmaster.internal/ubuntu bionic/main arm64 libgd3 arm64 2.2.5-4 [99.3 kB] Get:112 http://ftpmaster.internal/ubuntu bionic/universe arm64 libhpdf-2.2.1 arm64 2.2.1-1.1build1 [327 kB] Get:113 http://ftpmaster.internal/ubuntu bionic/main arm64 mysql-common all 5.8+1.0.3 [5936 B] Get:114 http://ftpmaster.internal/ubuntu bionic/main arm64 libmysqlclient20 arm64 5.7.20-1ubuntu1 [778 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main arm64 libpq5 arm64 10.1-2 [90.3 kB] Get:116 http://ftpmaster.internal/ubuntu bionic/universe arm64 emboss-lib arm64 6.6.0+dfsg-6 [2314 kB] Get:117 http://ftpmaster.internal/ubuntu bionic/universe arm64 emboss-data all 6.6.0+dfsg-6 [60.6 MB] Get:118 http://ftpmaster.internal/ubuntu bionic/universe arm64 emboss arm64 6.6.0+dfsg-6 [922 kB] Get:119 http://ftpmaster.internal/ubuntu bionic/main arm64 fonts-lmodern all 2.004.5-3 [4551 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/universe arm64 fonts-lyx all 2.2.3-2 [155 kB] Get:121 http://ftpmaster.internal/ubuntu bionic/main arm64 libavahi-common-data arm64 0.7-3ubuntu1 [22.7 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main arm64 libavahi-common3 arm64 0.7-3ubuntu1 [18.4 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main arm64 libavahi-client3 arm64 0.7-3ubuntu1 [21.8 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/main arm64 libcups2 arm64 2.2.6-4 [180 kB] Get:125 http://ftpmaster.internal/ubuntu bionic/main arm64 libcupsimage2 arm64 2.2.6-4 [16.7 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/main arm64 libijs-0.35 arm64 0.35-12 [14.1 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/main arm64 libjbig2dec0 arm64 0.13-5 [50.0 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/main arm64 liblcms2-2 arm64 2.9-1 [115 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main arm64 libpaper1 arm64 1.1.24+nmu5ubuntu1 [13.0 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/main arm64 libgs9-common all 9.21~dfsg+1-0ubuntu3 [5121 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/main arm64 libgs9 arm64 9.21~dfsg+1-0ubuntu3 [1882 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main arm64 ghostscript arm64 9.21~dfsg+1-0ubuntu3 [49.6 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main arm64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.4 [3120 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/main arm64 libnetpbm10 arm64 2:10.0-15.3build1 [50.7 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/main arm64 netpbm arm64 2:10.0-15.3build1 [927 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/main arm64 libpaper-utils arm64 1.1.24+nmu5ubuntu1 [8178 B] Get:137 http://ftpmaster.internal/ubuntu bionic/main arm64 libkpathsea6 arm64 2017.20170613.44572-6ubuntu1 [49.1 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main arm64 libptexenc1 arm64 2017.20170613.44572-6ubuntu1 [32.9 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/main arm64 libsynctex1 arm64 2017.20170613.44572-6ubuntu1 [37.5 kB] Get:140 http://ftpmaster.internal/ubuntu bionic/main arm64 libtexlua52 arm64 2017.20170613.44572-6ubuntu1 [76.1 kB] Get:141 http://ftpmaster.internal/ubuntu bionic/main arm64 t1utils arm64 1.41-2 [48.9 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main arm64 libharfbuzz-icu0 arm64 1.7.2-1 [5356 B] Get:143 http://ftpmaster.internal/ubuntu bionic/main arm64 libnspr4 arm64 2:4.16-1ubuntu2 [93.3 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main arm64 libnss3 arm64 2:3.32-1ubuntu3 [966 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main arm64 libpoppler68 arm64 0.57.0-2ubuntu5 [671 kB] Get:146 http://ftpmaster.internal/ubuntu bionic/main arm64 libpotrace0 arm64 1.14-2 [14.9 kB] Get:147 http://ftpmaster.internal/ubuntu bionic/main arm64 libxt6 arm64 1:1.1.5-1 [128 kB] Get:148 http://ftpmaster.internal/ubuntu bionic/main arm64 libxmu6 arm64 2:1.1.2-2 [38.8 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/main arm64 libxaw7 arm64 2:1.0.13-1 [137 kB] Get:150 http://ftpmaster.internal/ubuntu bionic/main arm64 libxi6 arm64 2:1.7.9-1 [25.4 kB] Get:151 http://ftpmaster.internal/ubuntu bionic/main arm64 libzzip-0-13 arm64 0.13.62-3.1 [22.5 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/main arm64 texlive-binaries arm64 2017.20170613.44572-6ubuntu1 [6623 kB] Get:153 http://ftpmaster.internal/ubuntu bionic/main arm64 xdg-utils all 1.1.1-1ubuntu3 [59.4 kB] Get:154 http://ftpmaster.internal/ubuntu bionic/main arm64 texlive-base all 2017.20171128-1 [18.6 MB] Get:155 http://ftpmaster.internal/ubuntu bionic/universe arm64 ocaml-base-nox arm64 4.05.0-10ubuntu1 [535 kB] Get:156 http://ftpmaster.internal/ubuntu bionic/universe arm64 hevea all 2.30-1 [883 kB] Get:157 http://ftpmaster.internal/ubuntu bionic/main arm64 libart-2.0-2 arm64 2.3.21-3 [40.4 kB] Get:158 http://ftpmaster.internal/ubuntu bionic/main arm64 libatk1.0-data all 2.26.1-2 [3008 B] Get:159 http://ftpmaster.internal/ubuntu bionic/main arm64 libatk1.0-0 arm64 2.26.1-2 [37.3 kB] Get:160 http://ftpmaster.internal/ubuntu bionic/main arm64 libblas3 arm64 3.7.1-4ubuntu1 [83.1 kB] Get:161 http://ftpmaster.internal/ubuntu bionic/main arm64 libexpat1-dev arm64 2.2.5-3 [110 kB] Get:162 http://ftpmaster.internal/ubuntu bionic/main arm64 libgfortran4 arm64 7.2.0-18ubuntu2 [248 kB] Get:163 http://ftpmaster.internal/ubuntu bionic/main arm64 libgtk2.0-common all 2.24.31-4ubuntu1 [124 kB] Get:164 http://ftpmaster.internal/ubuntu bionic/main arm64 libxcomposite1 arm64 1:0.4.4-2 [6646 B] Get:165 http://ftpmaster.internal/ubuntu bionic/main arm64 libxfixes3 arm64 1:5.0.3-1 [9844 B] Get:166 http://ftpmaster.internal/ubuntu bionic/main arm64 libxcursor1 arm64 1:1.1.15-1 [17.4 kB] Get:167 http://ftpmaster.internal/ubuntu bionic/main arm64 libxdamage1 arm64 1:1.1.4-3 [6668 B] Get:168 http://ftpmaster.internal/ubuntu bionic/main arm64 libxrandr2 arm64 2:1.5.1-1 [16.0 kB] Get:169 http://ftpmaster.internal/ubuntu bionic/main arm64 libgtk2.0-0 arm64 2.24.31-4ubuntu1 [1453 kB] Get:170 http://ftpmaster.internal/ubuntu bionic/main arm64 libjs-jquery all 3.2.1-1 [152 kB] Get:171 http://ftpmaster.internal/ubuntu bionic/universe arm64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:172 http://ftpmaster.internal/ubuntu bionic/main arm64 liblapack3 arm64 3.7.1-4ubuntu1 [1371 kB] Get:173 http://ftpmaster.internal/ubuntu bionic/main arm64 libltdl7 arm64 2.4.6-2 [35.9 kB] Get:174 http://ftpmaster.internal/ubuntu bionic/main arm64 libnl-3-200 arm64 3.2.29-0ubuntu3 [44.4 kB] Get:175 http://ftpmaster.internal/ubuntu bionic/main arm64 libnl-route-3-200 arm64 3.2.29-0ubuntu3 [116 kB] Get:176 http://ftpmaster.internal/ubuntu bionic/main arm64 libpciaccess0 arm64 0.13.4-1ubuntu1 [15.1 kB] Get:177 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython2.7 arm64 2.7.14-4 [902 kB] Get:178 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython2.7-dev arm64 2.7.14-4 [28.0 MB] Get:179 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython-dev arm64 2.7.14-2ubuntu1 [7644 B] Get:180 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython-all-dev arm64 2.7.14-2ubuntu1 [1006 B] Get:181 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3.6 arm64 3.6.4-2 [1283 kB] Get:182 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3.6-dev arm64 3.6.4-2 [2267 kB] Get:183 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3-dev arm64 3.6.3-0ubuntu2 [6914 B] Get:184 http://ftpmaster.internal/ubuntu bionic/main arm64 libpython3-all-dev arm64 3.6.3-0ubuntu2 [1010 B] Get:185 http://ftpmaster.internal/ubuntu bionic/main arm64 libwebpmux3 arm64 0.6.0-4 [17.2 kB] Get:186 http://ftpmaster.internal/ubuntu bionic/universe arm64 mafft arm64 7.310-1 [701 kB] Get:187 http://ftpmaster.internal/ubuntu bionic/universe arm64 muscle arm64 1:3.8.31+dfsg-3 [150 kB] Get:188 http://ftpmaster.internal/ubuntu bionic/universe arm64 ncbi-data all 6.1.20170106-2 [3645 kB] Get:189 http://ftpmaster.internal/ubuntu bionic/universe arm64 ncbi-blast+ arm64 2.6.0-1 [8425 kB] Get:190 http://ftpmaster.internal/ubuntu bionic/universe arm64 libhwloc5 arm64 1.11.8-1 [84.4 kB] Get:191 http://ftpmaster.internal/ubuntu bionic/main arm64 libibverbs1 arm64 1.2.1-2ubuntu1 [26.7 kB] Get:192 http://ftpmaster.internal/ubuntu bionic/main arm64 ocl-icd-libopencl1 arm64 2.2.11-1ubuntu1 [29.2 kB] Get:193 http://ftpmaster.internal/ubuntu bionic/universe arm64 libhwloc-plugins arm64 1.11.8-1 [11.1 kB] Get:194 http://ftpmaster.internal/ubuntu bionic/universe arm64 libopenmpi2 arm64 2.1.1-7 [1751 kB] Get:195 http://ftpmaster.internal/ubuntu bionic/universe arm64 openmpi-common all 2.1.1-7 [140 kB] Get:196 http://ftpmaster.internal/ubuntu bionic/universe arm64 openmpi-bin arm64 2.1.1-7 [81.3 kB] Get:197 http://ftpmaster.internal/ubuntu bionic/universe arm64 phylip arm64 1:3.696+dfsg-5 [798 kB] Get:198 http://ftpmaster.internal/ubuntu bionic/universe arm64 phyml arm64 3:3.3.20170530+dfsg-2 [1458 kB] Get:199 http://ftpmaster.internal/ubuntu bionic/universe arm64 prank arm64 0.0.170427+dfsg-1 [327 kB] Get:200 http://ftpmaster.internal/ubuntu bionic/main arm64 preview-latex-style all 11.91-1ubuntu1 [185 kB] Get:201 http://ftpmaster.internal/ubuntu bionic/universe arm64 probcons arm64 1.12-11 [102 kB] Get:202 http://ftpmaster.internal/ubuntu bionic/main arm64 python-all arm64 2.7.14-2ubuntu1 [994 B] Get:203 http://ftpmaster.internal/ubuntu bionic/main arm64 python2.7-dev arm64 2.7.14-4 [282 kB] Get:204 http://ftpmaster.internal/ubuntu bionic/main arm64 python-dev arm64 2.7.14-2ubuntu1 [1172 B] Get:205 http://ftpmaster.internal/ubuntu bionic/main arm64 python-all-dev arm64 2.7.14-2ubuntu1 [1014 B] Get:206 http://ftpmaster.internal/ubuntu bionic/main arm64 python-six all 1.11.0-1 [11.1 kB] Get:207 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-cycler all 0.10.0-1 [7520 B] Get:208 http://ftpmaster.internal/ubuntu bionic/main arm64 python-dateutil all 2.6.1-1 [60.6 kB] Get:209 http://ftpmaster.internal/ubuntu bionic/main arm64 python-decorator all 4.1.2-1 [9300 B] Get:210 http://ftpmaster.internal/ubuntu bionic/main arm64 python-functools32 all 3.2.3.2-3 [10.8 kB] Get:211 http://ftpmaster.internal/ubuntu 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[288 kB] Get:221 http://ftpmaster.internal/ubuntu bionic/main arm64 python-pkg-resources all 36.2.7-2 [128 kB] Get:222 http://ftpmaster.internal/ubuntu bionic/main arm64 python-psycopg2 arm64 2.7.3-1ubuntu1 [144 kB] Get:223 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-rdflib all 4.2.1-2 [237 kB] Get:224 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-renderpm arm64 3.4.0-3build1 [29.3 kB] Get:225 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-reportlab-accel arm64 3.4.0-3build1 [21.2 kB] Get:226 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-reportlab all 3.4.0-3build1 [476 kB] Get:227 http://ftpmaster.internal/ubuntu bionic/main arm64 python-setuptools all 36.2.7-2 [260 kB] Get:228 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-all arm64 3.6.3-0ubuntu2 [984 B] Get:229 http://ftpmaster.internal/ubuntu bionic/main arm64 python3.6-dev arm64 3.6.4-2 [524 kB] Get:230 http://ftpmaster.internal/ubuntu bionic/main arm64 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bionic/universe arm64 python3-matplotlib arm64 2.0.0+dfsg1-2ubuntu3 [1444 kB] Get:241 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-mysqldb arm64 1.3.10-1build1 [43.6 kB] Get:242 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-olefile all 0.44-1 [36.3 kB] Get:243 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-pil arm64 4.3.0-2ubuntu1 [297 kB] Get:244 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-pkg-resources all 36.2.7-2 [98.7 kB] Get:245 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-psycopg2 arm64 2.7.3-1ubuntu1 [142 kB] Get:246 http://ftpmaster.internal/ubuntu bionic/universe arm64 python3-rdflib all 4.2.1-2 [236 kB] Get:247 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-renderpm arm64 3.4.0-3build1 [29.7 kB] Get:248 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-reportlab-accel arm64 3.4.0-3build1 [17.0 kB] Get:249 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-reportlab all 3.4.0-3build1 [473 kB] Get:250 http://ftpmaster.internal/ubuntu bionic/main arm64 python3-setuptools all 36.2.7-2 [178 kB] Get:251 http://ftpmaster.internal/ubuntu bionic/universe arm64 t-coffee arm64 11.00.8cbe486-6 [1840 kB] Get:252 http://ftpmaster.internal/ubuntu bionic/universe arm64 texlive-fonts-recommended all 2017.20171128-1 [5263 kB] Get:253 http://ftpmaster.internal/ubuntu bionic/main arm64 texlive-latex-base all 2017.20171128-1 [948 kB] Get:254 http://ftpmaster.internal/ubuntu bionic/main arm64 texlive-latex-recommended all 2017.20171128-1 [14.9 MB] Get:255 http://ftpmaster.internal/ubuntu bionic/universe arm64 texlive-pictures all 2017.20171128-1 [3997 kB] Get:256 http://ftpmaster.internal/ubuntu bionic/universe arm64 texlive-latex-extra all 2017.20171128-1 [10.5 MB] Get:257 http://ftpmaster.internal/ubuntu bionic/universe arm64 wise-data all 2.4.1-20 [107 kB] Get:258 http://ftpmaster.internal/ubuntu bionic/universe arm64 wise arm64 2.4.1-20 [797 kB] Get:259 http://ftpmaster.internal/ubuntu bionic/universe arm64 fasttree arm64 2.1.10-1 [153 kB] Get:260 http://ftpmaster.internal/ubuntu bionic/universe arm64 python-scipy arm64 0.19.1-1ubuntu1 [8656 kB] Get:261 http://ftpmaster.internal/ubuntu bionic/universe arm64 python3-scipy arm64 0.19.1-1ubuntu1 [8635 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 273 MB in 13s (20.3 MB/s) (Reading database ... 12579 files and directories currently installed.) 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Setting up mime-support (3.60ubuntu1) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Setting up libgfortran4:arm64 (7.2.0-18ubuntu2) ... Setting up t-coffee (11.00.8cbe486-6) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:arm64 (2.9-1) ... Setting up libjbig0:arm64 (2.1-3.1) ... Setting up libsigsegv2:arm64 (2.11-1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.8-2) ... Setting up libnuma1:arm64 (2.0.11-2.1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:arm64 (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up mysql-common (5.8+1.0.3) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libnetpbm10 (2:10.0-15.3build1) ... Setting up ocaml-base-nox (4.05.0-10ubuntu1) ... Setting up probcons (1.12-11) ... Setting up dialign (2.2.1-9) ... Setting up libgdk-pixbuf2.0-common (2.36.11-1) ... Setting up libdatrie1:arm64 (0.2.10-6) ... Setting up gettext-base (0.19.8.1-4ubuntu2) ... Setting up libjpeg-turbo8:arm64 (1.5.2-0ubuntu5) ... Setting up libpipeline1:arm64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:arm64 (0.8.6-3) ... Setting up libnspr4:arm64 (2:4.16-1ubuntu2) ... Setting up ucf (3.0036) ... Setting up libfreetype6:arm64 (2.8-0.2ubuntu2) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:arm64 (1:5.32-1) ... Setting up libgraphite2-3:arm64 (1.3.10-8) ... Setting up libboost-system1.65.1:arm64 (1.65.1+dfsg-0ubuntu4) ... Setting up libatk1.0-data (2.26.1-2) ... Setting up libjbig2dec0:arm64 (0.13-5) ... Setting up ncbi-data (6.1.20170106-2) ... Setting up libpixman-1-0:arm64 (0.34.0-2) ... Setting up libblas3:arm64 (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpq5:arm64 (10.1-2) ... Setting up openmpi-common (2.1.1-7) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up wise-data (2.4.1-20) ... Setting up fasttree (2.1.10-1) ... Setting up autotools-dev (20171216.1) ... Setting up t1utils (1.41-2) ... Setting up libatk1.0-0:arm64 (2.26.1-2) ... Setting up libboost-thread1.65.1:arm64 (1.65.1+dfsg-0ubuntu4) ... Setting up wise (2.4.1-20) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Processing triggers for systemd (235-3ubuntu3) ... Setting up libltdl7:arm64 (2.4.6-2) ... Setting up libijs-0.35:arm64 (0.35-12) ... Setting up emboss-data (6.6.0+dfsg-6) ... Setting up libexpat1-dev:arm64 (2.2.5-3) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up libpciaccess0:arm64 (0.13.4-1ubuntu1) ... Setting up libpotrace0 (1.14-2) ... Setting up libmysqlclient20:arm64 (5.7.20-1ubuntu1) ... Setting up muscle (1:3.8.31+dfsg-3) ... Setting up libthai-data (0.1.27-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up ocl-icd-libopencl1:arm64 (2.2.11-1ubuntu1) ... Setting up libboost-program-options1.65.1:arm64 (1.65.1+dfsg-0ubuntu4) ... Setting up bsdmainutils (9.0.14ubuntu1) ... 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 libnl-3-200:arm64 (3.2.29-0ubuntu3) ... Setting up libzzip-0-13:arm64 (0.13.62-3.1) ... Setting up x11-common (1:7.7+19ubuntu3) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up clustalw (2.1+lgpl-5) ... Setting up xdg-utils (1.1.1-1ubuntu3) ... Setting up hicolor-icon-theme (0.17-1) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:arm64 (2.7.14-4) ... Setting up libxau6:arm64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-4ubuntu2) ... Setting up libmpdec2:arm64 (2.4.2-1) ... Setting up libdbus-1-3:arm64 (1.12.2-1ubuntu1) ... Setting up fonts-lmodern (2.004.5-3) ... Setting up libavahi-common-data:arm64 (0.7-3ubuntu1) ... Setting up fonts-lyx (2.2.3-2) ... Setting up libwebp6:arm64 (0.6.0-4) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up libjpeg8:arm64 (8c-2ubuntu8) ... Setting up libpaper1:arm64 (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up libpython3.6-stdlib:arm64 (3.6.4-2) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up fontconfig-config (2.12.6-0ubuntu1) ... Setting up tex-common (6.09) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python-matplotlib-data (2.0.0+dfsg1-2ubuntu3) ... Setting up flex (2.6.1-1.3) ... Setting up liblapack3:arm64 (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up python2.7 (2.7.14-4) ... Setting up libnss3:arm64 (2:3.32-1ubuntu3) ... Setting up libharfbuzz0b:arm64 (1.7.2-1) ... Setting up libtiff5:arm64 (4.0.9-3) ... Setting up libnl-route-3-200:arm64 (3.2.29-0ubuntu3) ... Setting up preview-latex-style (11.91-1ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up libthai0:arm64 (0.1.27-1) ... Setting up file (1:5.32-1) ... Setting up libhwloc5:arm64 (1.11.8-1) ... Setting up dssp (3.0.0-1ubuntu1) ... Setting up libpython-stdlib:arm64 (2.7.14-2ubuntu1) ... Setting up libwebpmux3:arm64 (0.6.0-4) ... Setting up libpython2.7:arm64 (2.7.14-4) ... Setting up automake (1:1.15.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up netpbm (2:10.0-15.3build1) ... Setting up libice6:arm64 (2:1.0.9-2) ... Setting up man-db (2.7.6.1-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:arm64 (2.7.14-4) ... Setting up libavahi-common3:arm64 (0.7-3ubuntu1) ... Setting up python2.7-dev (2.7.14-4) ... Setting up libxcb1:arm64 (1.12-1ubuntu1) ... Setting up python (2.7.14-2ubuntu1) ... Setting up libpython3.6:arm64 (3.6.4-2) ... Setting up python-pyparsing (2.1.10+dfsg1-1) ... Setting up libtool (2.4.6-2) ... Setting up libpython3-stdlib:arm64 (3.6.3-0ubuntu2) ... Setting up libibverbs1 (1.2.1-2ubuntu1) ... Setting up libpython-dev:arm64 (2.7.14-2ubuntu1) ... Setting up libfontconfig1:arm64 (2.12.6-0ubuntu1) ... Setting up libsm6:arm64 (2:1.2.2-1) ... Setting up python-functools32 (3.2.3.2-3) ... Setting up libxcb-render0:arm64 (1.12-1ubuntu1) ... Setting up python-reportlab-accel:arm64 (3.4.0-3build1) ... Setting up python-psycopg2 (2.7.3-1ubuntu1) ... Setting up python-dev (2.7.14-2ubuntu1) ... Setting up python-tz (2017.2-2) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up libx11-6:arm64 (2:1.6.4-3) ... Setting up libpython-all-dev:arm64 (2.7.14-2ubuntu1) ... Setting up python-pkg-resources (36.2.7-2) ... Setting up libpython3.6-dev:arm64 (3.6.4-2) ... Setting up python-numpy (1:1.13.3-2ubuntu1) ... Setting up python-six (1.11.0-1) ... Setting up python-mysqldb (1.3.10-1build1) ... Setting up python-isodate (0.5.4-1) ... Setting up python-renderpm:arm64 (3.4.0-3build1) ... Setting up libxcomposite1:arm64 (1:0.4.4-2) ... Setting up libxcb-shm0:arm64 (1.12-1ubuntu1) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up libxt6:arm64 (1:1.1.5-1) ... Setting up python-olefile (0.44-1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libavahi-client3:arm64 (0.7-3ubuntu1) ... Setting up python-decorator (4.1.2-1) ... Setting up python-subprocess32 (3.2.7-2) ... Setting up libpoppler68:arm64 (0.57.0-2ubuntu5) ... Setting up python-all (2.7.14-2ubuntu1) ... Setting up python-pil:arm64 (4.3.0-2ubuntu1) ... Setting up fontconfig (2.12.6-0ubuntu1) ... Regenerating fonts cache... done. Setting up libcups2:arm64 (2.2.6-4) ... Setting up libpython3-dev:arm64 (3.6.3-0ubuntu2) ... Setting up python-setuptools (36.2.7-2) ... Setting up libxdamage1:arm64 (1:1.1.4-3) ... Setting up libxext6:arm64 (2:1.3.3-1) ... Setting up libxfixes3:arm64 (1:5.0.3-1) ... Setting up python-scipy (0.19.1-1ubuntu1) ... Setting up python-reportlab (3.4.0-3build1) ... Setting up python-rdflib (4.2.1-2) ... Setting up libgd3:arm64 (2.2.5-4) ... Setting up python-cycler (0.10.0-1) ... Setting up libxmu6:arm64 (2:1.1.2-2) ... Setting up python-dateutil (2.6.1-1) ... Setting up libcupsimage2:arm64 (2.2.6-4) ... Setting up libxcursor1:arm64 (1:1.1.15-1) ... Setting up python-all-dev (2.7.14-2ubuntu1) ... Setting up libpython3-all-dev:arm64 (3.6.3-0ubuntu2) ... Setting up libpango-1.0-0:arm64 (1.40.14-1) ... Setting up emboss-lib (6.6.0+dfsg-6) ... Setting up libgs9:arm64 (9.21~dfsg+1-0ubuntu3) ... Setting up libxrandr2:arm64 (2:1.5.1-1) ... Setting up libxi6:arm64 (2:1.7.9-1) ... Setting up libxaw7:arm64 (2:1.0.13-1) ... Setting up libcairo2:arm64 (1.15.8-3) ... Setting up libxinerama1:arm64 (2:1.1.3-1) ... Setting up ghostscript (9.21~dfsg+1-0ubuntu3) ... Setting up libpangoft2-1.0-0:arm64 (1.40.14-1) ... Setting up emboss (6.6.0+dfsg-6) ... Setting up libpangocairo-1.0-0:arm64 (1.40.14-1) ... Setting up python3.6 (3.6.4-2) ... Setting up dh-autoreconf (15) ... Setting up python3 (3.6.3-0ubuntu2) ... Setting up python3-olefile (0.44-1) ... Setting up python3-numpy (1:1.13.3-2ubuntu1) ... Setting up libicu-le-hb0:arm64 (1.0.3+git161113-4) ... Setting up python3-six (1.11.0-1) ... Setting up python3.6-2to3 (3.6.4-2) ... python3.6: can't get files for byte-compilation Setting up python3-pyparsing (2.1.10+dfsg1-1) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-mysqldb (1.3.10-1build1) ... Setting up python3-pkg-resources (36.2.7-2) ... Setting up python3-psycopg2 (2.7.3-1ubuntu1) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up python3-all (3.6.3-0ubuntu2) ... Setting up python3-reportlab-accel:arm64 (3.4.0-3build1) ... Setting up python3-setuptools (36.2.7-2) ... Setting up python3.6-dev (3.6.4-2) ... Setting up dh-python (2.20170125) ... Setting up python3-decorator (4.1.2-1) ... Setting up python3-tz (2017.2-2) ... Setting up python3-distutils (3.6.4~rc1-6) ... Setting up python3-dateutil (2.6.1-1) ... Setting up python3-renderpm:arm64 (3.4.0-3build1) ... Setting up python3-isodate (0.5.4-1) ... Setting up libicu60:arm64 (60.2-1ubuntu1) ... Setting up python3-pil:arm64 (4.3.0-2ubuntu1) ... Setting up python3-scipy (0.19.1-1ubuntu1) ... Setting up libharfbuzz-icu0:arm64 (1.7.2-1) ... Setting up python3-dev (3.6.3-0ubuntu2) ... Setting up texlive-binaries (2017.20170613.44572-6ubuntu1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libxml2:arm64 (2.9.4+dfsg1-5.2ubuntu1) ... Setting up libcroco3:arm64 (0.6.12-2) ... Setting up python3-reportlab (3.4.0-3build1) ... Setting up libhwloc-plugins (1.11.8-1) ... Setting up texlive-base (2017.20171128-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up shared-mime-info (1.9-2) ... Setting up libopenmpi2:arm64 (2.1.1-7) ... Setting up texlive-fonts-recommended (2017.20171128-1) ... Setting up python3-matplotlib (2.0.0+dfsg1-2ubuntu3) ... Setting up texlive-latex-base (2017.20171128-1) ... Setting up python3-rdflib (4.2.1-2) ... Setting up texlive-latex-recommended (2017.20171128-1) ... Setting up gettext (0.19.8.1-4ubuntu2) ... Setting up python3-all-dev (3.6.3-0ubuntu2) ... Setting up texlive-pictures (2017.20171128-1) ... Setting up libgdk-pixbuf2.0-0:arm64 (2.36.11-1) ... Setting up hevea (2.30-1) ... Setting up openmpi-bin (2.1.1-7) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up intltool-debian (0.35.0+20060710.4) ... Setting up gtk-update-icon-cache (3.22.26-2ubuntu1) ... Setting up phyml (3:3.3.20170530+dfsg-2) ... Setting up librsvg2-2:arm64 (2.40.18-2) ... Setting up texlive-latex-extra (2017.20171128-1) ... Setting up po-debconf (1.0.20) ... Setting up librsvg2-common:arm64 (2.40.18-2) ... Setting up adwaita-icon-theme (3.26.1-1ubuntu1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up debhelper (11ubuntu1) ... Setting up libgtk2.0-0:arm64 (2.24.31-4ubuntu1) ... Setting up python-matplotlib (2.0.0+dfsg1-2ubuntu3) ... Setting up humanity-icon-theme (0.6.14) ... Setting up sbuild-build-depends-python-biopython-dummy (0.invalid.0) ... Setting up ubuntu-mono (16.10+18.04.20171224.1-0ubuntu1) ... (Reading database ... 56569 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for tex-common (6.09) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Processing triggers for libgdk-pixbuf2.0-0:arm64 (2.36.11-1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Processing triggers for systemd (235-3ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-101-generic arm64 (aarch64) Toolchain package versions: binutils_2.29.51.20180110-1ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-18ubuntu2 gcc-7_7.2.0-18ubuntu2 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-18ubuntu2 libstdc++6_7.2.0-18ubuntu2 linux-libc-dev_4.13.0-25.29 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 adwaita-icon-theme_3.26.1-1ubuntu1 apt_1.6~alpha5 apt-transport-https_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu2 autotools-dev_20171216.1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.51.20180110-1ubuntu1 binutils-aarch64-linux-gnu_2.29.51.20180110-1ubuntu1 binutils-common_2.29.51.20180110-1ubuntu1 bsdmainutils_9.0.14ubuntu1 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libgdbm3_1.8.3-14 libgdk-pixbuf2.0-0_2.36.11-1 libgdk-pixbuf2.0-common_2.36.11-1 libgfortran4_7.2.0-18ubuntu2 libglib2.0-0_2.54.1-1ubuntu1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-18ubuntu2 libgpg-error0_1.27-5 libgraphite2-3_1.3.10-8 libgs9_9.21~dfsg+1-0ubuntu3 libgs9-common_9.21~dfsg+1-0ubuntu3 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.5.0+dfsg-1 libgtk2.0-0_2.24.31-4ubuntu1 libgtk2.0-common_2.24.31-4ubuntu1 libharfbuzz-icu0_1.7.2-1 libharfbuzz0b_1.7.2-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.3-2 libhpdf-2.2.1_2.2.1-1.1build1 libhwloc-plugins_1.11.8-1 libhwloc5_1.11.8-1 libhx509-5-heimdal_7.5.0+dfsg-1 libibverbs1_1.2.1-2ubuntu1 libice6_2:1.0.9-2 libicu-le-hb0_1.0.3+git161113-4 libicu60_60.2-1ubuntu1 libidn11_1.33-2.1 libidn2-0_2.0.4-1 libijs-0.35_0.35-12 libip4tc0_1.6.1-2ubuntu2 libisl15_0.18-1 libitm1_7.2.0-18ubuntu2 libjbig0_2.1-3.1 libjbig2dec0_0.13-5 libjpeg-turbo8_1.5.2-0ubuntu5 libjpeg8_8c-2ubuntu8 libjs-jquery_3.2.1-1 libjs-jquery-ui_1.12.1+dfsg-5 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9.2ubuntu1 libkmod2_24-1ubuntu2 libkpathsea6_2017.20170613.44572-6ubuntu1 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 liblapack3_3.7.1-4ubuntu1 liblcms2-2_2.9-1 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_7.2.0-18ubuntu2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1ubuntu1 libmpc3_1.0.3-2 libmpdec2_2.4.2-1 libmpfr4_3.1.6-1 libmysqlclient20_5.7.20-1ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnetpbm10_2:10.0-15.3build1 libnettle6_3.3-2 libnghttp2-14_1.29.0-1 libnl-3-200_3.2.29-0ubuntu3 libnl-route-3-200_3.2.29-0ubuntu3 libnpth0_1.5-3 libnspr4_2:4.16-1ubuntu2 libnss3_2:3.32-1ubuntu3 libnuma1_2.0.11-2.1 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python3-reportlab_3.4.0-3build1 python3-reportlab-accel_3.4.0-3build1 python3-scipy_0.19.1-1ubuntu1 python3-setuptools_36.2.7-2 python3-six_1.11.0-1 python3-tz_2017.2-2 python3.6_3.6.4-2 python3.6-2to3_3.6.4-2 python3.6-dev_3.6.4-2 python3.6-minimal_3.6.4-2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-biopython-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 shared-mime-info_1.9-2 systemd_235-3ubuntu3 systemd-sysv_235-3ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 t-coffee_11.00.8cbe486-6 t1utils_1.41-2 tar_1.29b-2 tex-common_6.09 texlive-base_2017.20171128-1 texlive-binaries_2017.20170613.44572-6ubuntu1 texlive-fonts-recommended_2017.20171128-1 texlive-latex-base_2017.20171128-1 texlive-latex-extra_2017.20171128-1 texlive-latex-recommended_2017.20171128-1 texlive-pictures_2017.20171128-1 ttf-bitstream-vera_1.10-8 tzdata_2017c-1 ubuntu-keyring_2016.10.27 ubuntu-mono_16.10+18.04.20171224.1-0ubuntu1 ucf_3.0036 util-linux_2.30.2-0.1ubuntu1 wise_2.4.1-20 wise-data_2.4.1-20 x11-common_1:7.7+19ubuntu3 xdg-utils_1.1.1-1ubuntu3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 19 11:00:18 2017 UTC gpgv: using RSA key gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-biopython_1.70+dfsg-4.dsc dpkg-source: info: extracting python-biopython in python-biopython-1.70+dfsg dpkg-source: info: unpacking python-biopython_1.70+dfsg.orig.tar.xz dpkg-source: info: unpacking python-biopython_1.70+dfsg-4.debian.tar.xz dpkg-source: info: applying remove_mathml-qname.patch dpkg-source: info: applying privacy_breach.patch dpkg-source: info: applying 0dbcdbaa00b2749f82bd7936128d1fd45c82deca.patch dpkg-source: info: applying 24aba217c82522eb4cfbfc0d73197a6c3f96fb8a.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-14051892 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14051892 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14051892 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.70+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build python-biopython-1.70+dfsg dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/python-biopython-1.70+dfsg' dh_auto_clean pybuild --clean -i python{version} -p 2.7 I: pybuild base:184: python2.7 setup.py clean running clean removing '/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it pybuild --clean -i python{version} -p 3.6 I: pybuild base:184: python3.6 setup.py clean running clean removing '/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd Doc && make distclean make[2]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc' make -C install make[3]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc/install' pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. No file Installation.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) LaTeX Warning: Reference `sec:windows_install' on page 1 undefined on input lin e 108. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] LaTeX Warning: Reference `sec:is_working' on page 7 undefined on input line 460 . [7] LaTeX Warning: Reference `sec:unix_install' on page 8 undefined on input line 5 37. Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . LaTeX Warning: Reference `sec:is_working' on page 8 undefined on input line 558 . Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' [8] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) Package rerunfilecheck Warning: File `Installation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 144363 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150116 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 52. (./Installation.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150261 bytes). Transcript written on Installation.log. hevea -fix Installation.tex Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:108: Warning: Undefined label: 'sec:windows_install' ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:460: Warning: Undefined label: 'sec:is_working' ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:537: Warning: Undefined label: 'sec:unix_install' ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:558: Warning: Undefined label: 'sec:is_working' ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element Fixpoint reached in 2 step(s) hevea -fix -text Installation.tex Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) make[3]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc/install' ( for f in install ; do make clean -C $f ; done ) make[3]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc/install' rm -f Installation.aux rm -f Installation.log rm -f Installation.out rm -f Installation.toc rm -f Installation.haux rm -f Installation.htoc make[3]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc/install' rm -f Tutorial.aux rm -f Tutorial.toc rm -f Tutorial.log rm -f Tutorial.out rm -f Tutorial.haux rm -f Tutorial.htoc rm -f biopdb_faq.aux rm -f biopdb_faq.log rm -f biopdb_faq.out ( for f in install ; do make distclean -C $f ; done ) make[3]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc/install' rm -f Installation.aux rm -f Installation.log rm -f Installation.out rm -f Installation.toc rm -f Installation.haux rm -f Installation.htoc rm -f Installation.pdf rm -f Installation.txt rm -f Installation.html make[3]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc/install' rm -f biopdb_faq.pdf rm -f Tutorial.pdf rm -f Tutorial.html rm -f Tutorial.txt rm -f *_motif.gif #output from hacha make[2]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc' rm -f Doc/install/Installation.pdf rm -f Doc/install/Installation.txt rm -f Doc/install/Installation.html rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf rm -f Doc/Tutorial/*.aux rm -rf biopython.egg-info dh_auto_clean pybuild --clean -i python{version} -p 2.7 I: pybuild base:184: python2.7 setup.py clean running clean removing '/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it pybuild --clean -i python{version} -p 3.6 I: pybuild base:184: python3.6 setup.py clean running clean removing '/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; if [ -d Tests_avoid ] ; then \ mv Tests_avoid/* Tests ; \ rmdir Tests_avoid ; \ fi rm -rf debian/tmp_tests make[1]: Leaving directory '/<>/python-biopython-1.70+dfsg' dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python-biopython.substvars debian/python3-biopython.substvars debian/python-biopython-doc.substvars debian/python-biopython-sql.substvars debian/python3-biopython-sql.substvars debian/files rm -fr -- debian/python-biopython/ debian/tmp/ debian/python3-biopython/ debian/python-biopython-doc/ debian/python-biopython-sql/ debian/python3-biopython-sql/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild pybuild --configure -i python{version} -p 2.7 I: pybuild base:184: python2.7 setup.py config running config pybuild --configure -i python{version} -p 3.6 I: pybuild base:184: python3.6 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/python-biopython-1.70+dfsg' dh_auto_build pybuild --build -i python{version} -p 2.7 I: pybuild base:184: /usr/bin/python setup.py build running build running build_py creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/ParserSupport.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/File.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/DocSQL.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/AlignIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Alphabet creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/NCBIStandalone.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Blast creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/CAPS creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/codonalign creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Compass creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Crystal creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Data creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Emboss creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/ExPASy creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/FSSP creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA copying Bio/GA/Evolver.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA copying Bio/GA/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA copying Bio/GA/Organism.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/Uniform.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/GeneralPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/General.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/Point.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover copying Bio/GA/Crossover/TwoPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Crossover creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Mutation copying Bio/GA/Mutation/Simple.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Mutation copying Bio/GA/Mutation/General.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Mutation copying Bio/GA/Mutation/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Mutation creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Repair copying Bio/GA/Repair/Stabilizing.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Repair copying Bio/GA/Repair/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Repair creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection copying Bio/GA/Selection/Diversity.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection copying Bio/GA/Selection/RouletteWheel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection copying Bio/GA/Selection/Abstract.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection copying Bio/GA/Selection/Tournament.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection copying Bio/GA/Selection/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GA/Selection creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/GenBank creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Geo creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/HMM creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Compound creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/Map creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/mmtf creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KEGG/KGML creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Medline creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/jaspar creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/Training.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/StopTraining.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Layer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Network.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/BackPropagation creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Schema.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Motif.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Signature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Pattern.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NeuralNetwork/Gene creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/NMR creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Pathway/Rep copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Vector.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction copying Bio/Restriction/RanaConfig.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Restriction creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SCOP creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/_model creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Statistics creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SubsMat creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SwissProt creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/TogoWS creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/PAML creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/UniGene creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/UniProt creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Wise creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/_py3k creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/BioSQL creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Affy creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Cluster creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KDTree creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/phenotype creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd 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/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Entrez/DTDs running build_ext building 'Bio.cpairwise2' extension creating build creating build/temp.linux-arm64-2.7 creating build/temp.linux-arm64-2.7/Bio aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.linux-arm64-2.7/Bio/cpairwise2module.o In file included from /usr/include/python2.7/Python.h:100:0, from Bio/cpairwise2module.c:14: Bio/cpairwise2module.c: In function ‘cpairwise2__make_score_matrix_fast’: /usr/include/python2.7/listobject.h:62:58: warning: ‘py_trace_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v)) ^~ Bio/cpairwise2module.c:343:34: note: ‘py_trace_row’ was declared here PyObject *py_score_row, *py_trace_row; ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/cpairwise2module.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/cpairwise2.so building 'Bio.trie' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python2.7 -c Bio/triemodule.c -o build/temp.linux-arm64-2.7/Bio/triemodule.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python2.7 -c Bio/trie.c -o build/temp.linux-arm64-2.7/Bio/trie.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/triemodule.o build/temp.linux-arm64-2.7/Bio/trie.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/trie.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-arm64-2.7/Bio/Nexus aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c Bio/Nexus/cnexus.c -o build/temp.linux-arm64-2.7/Bio/Nexus/cnexus.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Nexus/cnexus.so building 'Bio.Cluster.cluster' extension creating build/temp.linux-arm64-2.7/Bio/Cluster aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-arm64-2.7/Bio/Cluster/clustermodule.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/cluster.c -o build/temp.linux-arm64-2.7/Bio/Cluster/cluster.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/Cluster/clustermodule.o build/temp.linux-arm64-2.7/Bio/Cluster/cluster.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Cluster/cluster.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-arm64-2.7/Bio/KDTree aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTree.c -o build/temp.linux-arm64-2.7/Bio/KDTree/KDTree.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-arm64-2.7/Bio/KDTree/KDTreemodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/KDTree/KDTree.o build/temp.linux-arm64-2.7/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/KDTree/_CKDTree.so building 'Bio.motifs._pwm' extension creating build/temp.linux-arm64-2.7/Bio/motifs aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/motifs/_pwm.c -o build/temp.linux-arm64-2.7/Bio/motifs/_pwm.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/motifs/_pwm.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/_pwm.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-arm64-2.7/Bio/PDB creating build/temp.linux-arm64-2.7/Bio/PDB/QCPSuperimposer aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-arm64-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-t6iTr2/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/QCPSuperimposer/qcprotmodule.so pybuild --build -i python{version} -p 3.6 I: pybuild base:184: /usr/bin/python3 setup.py build running build running build_py creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/triefind.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/SeqRecord.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/LogisticRegression.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/MarkovModel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/bgzf.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/kNN.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/ParserSupport.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/File.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/pairwise2.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/Index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/MaxEntropy.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/Seq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/DocSQL.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/SeqFeature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio copying Bio/NaiveBayes.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align copying Bio/Align/AlignInfo.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align copying Bio/Align/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Align/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/AlignIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Alphabet copying Bio/Alphabet/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Alphabet copying Bio/Alphabet/Reduced.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Alphabet creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Application copying Bio/Application/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Application creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/Applications.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/NCBIStandalone.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/NCBIXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast copying Bio/Blast/NCBIWWW.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Blast creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/CAPS copying Bio/CAPS/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/CAPS creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign copying Bio/codonalign/chisq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign copying Bio/codonalign/codonalphabet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign copying Bio/codonalign/codonalignment.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign copying Bio/codonalign/codonseq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign copying Bio/codonalign/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/codonalign creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Compass copying Bio/Compass/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Compass creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Crystal copying Bio/Crystal/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Crystal creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Data copying Bio/Data/IUPACData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Data copying Bio/Data/SCOPData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Data copying Bio/Data/CodonTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Data copying Bio/Data/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Data creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Emboss copying Bio/Emboss/Applications.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Emboss copying Bio/Emboss/Primer3.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Emboss copying Bio/Emboss/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Emboss creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez copying Bio/Entrez/Parser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez copying Bio/Entrez/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy copying Bio/ExPASy/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/ExPASy creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/FSSP copying Bio/FSSP/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/FSSP creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA copying Bio/GA/Evolver.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA copying Bio/GA/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA copying Bio/GA/Organism.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/Uniform.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/GeneralPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/General.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/Point.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover copying Bio/GA/Crossover/TwoPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Crossover creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Mutation copying Bio/GA/Mutation/Simple.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Mutation copying Bio/GA/Mutation/General.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Mutation copying Bio/GA/Mutation/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Mutation creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Repair copying Bio/GA/Repair/Stabilizing.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Repair copying Bio/GA/Repair/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Repair creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection copying Bio/GA/Selection/Diversity.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection copying Bio/GA/Selection/RouletteWheel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection copying Bio/GA/Selection/Abstract.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection copying Bio/GA/Selection/Tournament.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection copying Bio/GA/Selection/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GA/Selection creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank copying Bio/GenBank/Scanner.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank copying Bio/GenBank/utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank copying Bio/GenBank/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank copying Bio/GenBank/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Geo copying Bio/Geo/Record.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Geo copying Bio/Geo/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Geo creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/Comparative.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/Distribution.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics copying Bio/Graphics/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Graphics/GenomeDiagram creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM copying Bio/HMM/MarkovModel.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM copying Bio/HMM/Trainer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM copying Bio/HMM/Utilities.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM copying Bio/HMM/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/HMM creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG copying Bio/KEGG/REST.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG copying Bio/KEGG/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Compound creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Enzyme creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/Map creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/mmtf creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KEGG/KGML creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Medline copying Bio/Medline/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Medline creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/meme.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/transfac.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/alignace.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/matrix.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/thresholds.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs copying Bio/motifs/mast.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/jaspar creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/Training.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork copying Bio/NeuralNetwork/StopTraining.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Layer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Network.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/BackPropagation creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Schema.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Motif.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Signature.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Pattern.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NeuralNetwork/Gene creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus copying Bio/Nexus/Trees.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus copying Bio/Nexus/Nodes.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus copying Bio/Nexus/StandardData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus copying Bio/Nexus/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus copying Bio/Nexus/Nexus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NMR copying Bio/NMR/xpktools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NMR copying Bio/NMR/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NMR copying Bio/NMR/NOEtools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/NMR creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway copying Bio/Pathway/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Pathway/Rep copying Bio/PDB/ResidueDepth.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Model.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/PDBParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/FragmentMapper.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Chain.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Polypeptide.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/StructureBuilder.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/PDBExceptions.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Structure.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Vector.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Dice.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/HSExposure.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Selection.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/StructureAlignment.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/NeighborSearch.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/NACCESS.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Superimposer.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Atom.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/PDBList.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/MMCIFParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/PDBIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Entity.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/Residue.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/PSEA.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB copying Bio/PDB/DSSP.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen copying Bio/PopGen/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PopGen/GenePop creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction copying Bio/Restriction/Restriction.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction copying Bio/Restriction/RanaConfig.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction copying Bio/Restriction/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Restriction creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Raf.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Cla.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Des.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Residues.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Hie.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP copying Bio/SCOP/Dom.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SCOP creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO copying Bio/SearchIO/_index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO copying Bio/SearchIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO copying Bio/SearchIO/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/_model creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/BlastIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/HmmerIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SearchIO/ExonerateIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/_convert.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/_index.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqIO creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SeqUtils creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing copying Bio/Sequencing/Phd.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing copying Bio/Sequencing/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing copying Bio/Sequencing/Ace.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Sequencing/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Statistics copying Bio/Statistics/lowess.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Statistics copying Bio/Statistics/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Statistics creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SubsMat copying Bio/SubsMat/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SubsMat creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SVDSuperimposer creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/QCPSuperimposer creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SwissProt copying Bio/SwissProt/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/SwissProt creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/TogoWS copying Bio/TogoWS/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/TogoWS creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/NexusIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/BaseTree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/_io.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/CDAO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/Consensus.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/Newick.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/NewickIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/NeXML.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/_utils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/Applications creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Phylo/PAML creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/UniGene copying Bio/UniGene/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/UniGene creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/UniProt copying Bio/UniProt/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/UniProt copying Bio/UniProt/GOA.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/UniProt creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Wise copying Bio/Wise/dnal.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Wise copying Bio/Wise/psw.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Wise copying Bio/Wise/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Wise creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/_py3k copying Bio/_py3k/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/_py3k creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL copying BioSQL/BioSeq.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL copying BioSQL/Loader.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL copying BioSQL/DBUtils.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL copying BioSQL/BioSeqDatabase.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL copying BioSQL/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/BioSQL creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Affy copying Bio/Affy/CelFile.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Affy copying Bio/Affy/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Affy creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Cluster copying Bio/Cluster/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Cluster creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KDTree copying Bio/KDTree/KDTree.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KDTree copying Bio/KDTree/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KDTree creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/phenotype copying Bio/phenotype/phen_micro.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/phenotype copying Bio/phenotype/__init__.py -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/phenotype creating /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> 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/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Entrez/DTDs running build_ext building 'Bio.cpairwise2' extension creating build/temp.linux-arm64-3.6 creating build/temp.linux-arm64-3.6/Bio aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c Bio/cpairwise2module.c -o build/temp.linux-arm64-3.6/Bio/cpairwise2module.o In file included from /usr/include/python3.6m/Python.h:86:0, from Bio/cpairwise2module.c:14: Bio/cpairwise2module.c: In function ‘cpairwise2__make_score_matrix_fast’: /usr/include/python3.6m/listobject.h:73:58: warning: ‘py_trace_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v)) ^~ Bio/cpairwise2module.c:343:34: note: ‘py_trace_row’ was declared here PyObject *py_score_row, *py_trace_row; ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/cpairwise2module.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/cpairwise2.cpython-36m-aarch64-linux-gnu.so building 'Bio.trie' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.6m -c Bio/triemodule.c -o build/temp.linux-arm64-3.6/Bio/triemodule.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.6m -c Bio/trie.c -o build/temp.linux-arm64-3.6/Bio/trie.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/triemodule.o build/temp.linux-arm64-3.6/Bio/trie.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/trie.cpython-36m-aarch64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-arm64-3.6/Bio/Nexus aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c Bio/Nexus/cnexus.c -o build/temp.linux-arm64-3.6/Bio/Nexus/cnexus.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/Nexus/cnexus.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Nexus/cnexus.cpython-36m-aarch64-linux-gnu.so building 'Bio.Cluster.cluster' extension creating build/temp.linux-arm64-3.6/Bio/Cluster aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/Cluster/clustermodule.c -o build/temp.linux-arm64-3.6/Bio/Cluster/clustermodule.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/Cluster/cluster.c -o build/temp.linux-arm64-3.6/Bio/Cluster/cluster.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/Cluster/clustermodule.o build/temp.linux-arm64-3.6/Bio/Cluster/cluster.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/Cluster/cluster.cpython-36m-aarch64-linux-gnu.so building 'Bio.KDTree._CKDTree' extension creating build/temp.linux-arm64-3.6/Bio/KDTree aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/KDTree/KDTree.c -o build/temp.linux-arm64-3.6/Bio/KDTree/KDTree.o aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-arm64-3.6/Bio/KDTree/KDTreemodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/KDTree/KDTree.o build/temp.linux-arm64-3.6/Bio/KDTree/KDTreemodule.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/KDTree/_CKDTree.cpython-36m-aarch64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-arm64-3.6/Bio/motifs aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/motifs/_pwm.c -o build/temp.linux-arm64-3.6/Bio/motifs/_pwm.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/motifs/_pwm.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/motifs/_pwm.cpython-36m-aarch64-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-arm64-3.6/Bio/PDB creating build/temp.linux-arm64-3.6/Bio/PDB/QCPSuperimposer aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-arm64-3.6/Bio/PDB/QCPSuperimposer/qcprotmodule.o aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/python-biopython-1.70+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.6/Bio/PDB/QCPSuperimposer/qcprotmodule.o -o /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-36m-aarch64-linux-gnu.so cd Doc && make make[2]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc' hevea -fix Tutorial.tex Exclude comment 'comment' ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:250: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:converting-alignments' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:35: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_quick_start.tex:154: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:162: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:163: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:173: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:207: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:209: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:376: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:449: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:564: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:570: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:810: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:871: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:48: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:131: Warning: Undefined label: 'chapter:quick-start' ./Tutorial/chapter_seq_annot.tex:133: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:158: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:216: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:229: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:279: Warning: Undefined label: 'sec:seq_features' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:288: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:296: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:528: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:632: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_seq_annot.tex:640: Warning: Undefined label: 'sec:locations' ./Tutorial/chapter_seq_annot.tex:676: Warning: Undefined label: 'chapter:Bio.SeqIO' 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argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:22: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_cookbook.tex:58: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:146: Warning: Undefined label: 'sec:Bio.SeqIO-and-StringIO' ./Tutorial/chapter_cookbook.tex:192: Warning: Undefined label: 'sec:translation' ./Tutorial/chapter_cookbook.tex:197: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_cookbook.tex:317: Warning: Undefined label: 'sec:seqio-index-getraw' ./Tutorial/chapter_cookbook.tex:415: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:429: Warning: Undefined label: 'sec:low-level-fasta-fastq' ./Tutorial/chapter_cookbook.tex:449: Warning: Undefined label: 'sec:SeqRecord-slicing' ./Tutorial/chapter_cookbook.tex:597: Warning: Undefined label: 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may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:880: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1004: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1007: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:329: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:751: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:956: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1346: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:41: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial/chapter_seq_annot.tex:282: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_align.tex:880: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1004: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1007: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_entrez.tex:1094: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:329: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:751: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:956: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:254: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:301: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:327: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:384: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:464: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:557: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:671: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1346: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:41: Warning: '_' occurring outside math mode Fixpoint reached in 3 step(s) hevea -fix -text Tutorial.tex Exclude comment 'comment' ./Tutorial.tex:68: Warning: tt_mode is an empty style ./Tutorial.tex:95: Warning: Application of '\'' on 'n' failed ./Tutorial.htoc:353: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:123: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:394: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_annot.tex:121: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:140: Warning: line too long ./Tutorial/chapter_seq_annot.tex:203: Warning: '_' occurring outside math mode ./Tutorial/chapter_seq_annot.tex:222: Warning: line too long 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occurring outside math mode ./Tutorial/chapter_seqio.tex:241: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:280: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:362: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:374: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:404: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:454: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:507: Warning: '_' occurring outside math mode ./Tutorial/chapter_seqio.tex:771: Warning: line too long ./Tutorial/chapter_seqio.tex:1009: Warning: line too long ./Tutorial/chapter_seqio.tex:1016: Warning: line too long ./Tutorial/chapter_seqio.tex:1021: Warning: line 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./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:1: Warning: line too long ./Tutorial/chapter_uniprot.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:27: Warning: line too long ./Tutorial/chapter_uniprot.tex:66: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:66: Warning: '_' occurring outside math mode ./Tutorial/chapter_uniprot.tex:329: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:1: Warning: line too long ./Tutorial/chapter_pdb.tex:202: Warning: Image in text ./Tutorial/chapter_pdb.tex:751: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:956: Warning: '_' occurring outside math mode ./Tutorial/chapter_pdb.tex:961: Warning: line too long ./Tutorial/chapter_phylo.tex:104: Warning: Image in text ./Tutorial/chapter_phylo.tex:199: Warning: 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./Tutorial/chapter_cluster.tex:595: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:600: Warning: Cannot output that numerical entity: U+00B7 ./Tutorial/chapter_cluster.tex:732: Warning: overfull line in array : array too wide ./Tutorial/chapter_cluster.tex:732: Warning: line too long ./Tutorial/chapter_cluster.tex:732: Warning: line too long ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:38: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:69: Warning: overfull line in array : array too wide ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:69: Warning: line too long ./Tutorial/chapter_learning.tex:406: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode 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math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:1: Warning: line too long ./Tutorial/chapter_cookbook.tex:103: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:424: Warning: line too long ./Tutorial/chapter_cookbook.tex:519: Warning: line too long ./Tutorial/chapter_cookbook.tex:753: Warning: line too long ./Tutorial/chapter_cookbook.tex:854: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:996: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1034: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1034: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1067: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1098: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1098: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1146: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1194: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1194: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1268: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1268: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1268: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1290: Warning: line too long ./Tutorial/chapter_cookbook.tex:1291: Warning: line too long ./Tutorial/chapter_cookbook.tex:1337: Warning: Image in text ./Tutorial/chapter_cookbook.tex:1346: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1470: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:2: Warning: '_' occurring outside math mode ./Tutorial/chapter_testing.tex:349: Warning: line too long ./Tutorial/chapter_testing.tex:402: Warning: line too long ./Tutorial/chapter_testing.tex:494: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_testing.tex:502: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_testing.tex:508: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_testing.tex:514: Warning: Undefined block in text mode: 'DIV' [] ./Tutorial/chapter_advanced.tex:190: Warning: line too long ./Tutorial/chapter_advanced.tex:223: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:8: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:41: Warning: '_' occurring outside math mode ./Tutorial.tex:187: Warning: line too long ./Tutorial.tex:197: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:197: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:201: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:252: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:252: Warning: Application of '\"' on 'u' failed HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial.tex:68: Warning: tt_mode is an empty style ./Tutorial.haux:507: Giving up command: \@hevea@cbrace ./Tutorial.tex:68: Giving up command: \input ./Tutorial.tex:68: Warning: Failure while reading .haux ./Tutorial.tex:95: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' 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outside math mode ./Tutorial/chapter_blast.tex:188: Warning: '_' occurring outside math mode ./Tutorial/chapter_blast.tex:192: Warning: Undefined label: 'sec:alignment-tools' ./Tutorial/chapter_blast.tex:236: Warning: Undefined label: 'sec:parsing-blast' ./Tutorial/chapter_blast.tex:268: Warning: Undefined label: 'sec:parsing-blast-deprecated' ./Tutorial/chapter_blast.tex:282: Warning: Undefined label: 'sec:running-www-blast' ./Tutorial/chapter_blast.tex:284: Warning: Undefined label: 'sec:running-local-blast' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_blast.tex:335: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_blast.tex:433: Warning: line too long ./Tutorial/chapter_blast.tex:435: Warning: line too long ./Tutorial/chapter_blast.tex:445: Warning: Undefined label: 'fig:blastrecord' ./Tutorial/chapter_blast.tex:449: Warning: Image in text ./Tutorial/chapter_blast.tex:461: Warning: Undefined label: 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outside math mode ./Tutorial/chapter_cluster.tex:5: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_cluster.tex:29: Warning: Undefined citation: 'lecuyer1988' ./Tutorial/chapter_cluster.tex:29: Warning: Undefined citation: 'kachitvichyanukul1988' ./Tutorial/chapter_cluster.tex:83: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:83: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:85: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:85: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'x' failed ./Tutorial/chapter_cluster.tex:116: Warning: Application of '\=' on 'y' failed ./Tutorial/chapter_cluster.tex:153: Warning: Undefined citation: 'snedecor1989' ./Tutorial/chapter_cluster.tex:185: Warning: Undefined label: 'sec:distancefunctions' ./Tutorial/chapter_cluster.tex:266: Warning: Undefined label: 'sec:distancefunctions' 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'table:training' ./Tutorial/chapter_learning.tex:296: Warning: Undefined label: 'subsec:LogisticRegressionTraining' ./Tutorial/chapter_learning.tex:406: Warning: Application of '\"' on 'i' failed ./Tutorial/chapter_graphics.tex:18: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_graphics.tex:28: Warning: Undefined citation: 'toth2006' ./Tutorial/chapter_graphics.tex:31: Warning: Undefined citation: 'vanderauwera2009' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_graphics.tex:36: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:61: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:64: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_graphics.tex:68: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:125: Warning: Image in text 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occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:762: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: Image in text ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:801: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:828: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:834: Warning: Image in text ./Tutorial/chapter_graphics.tex:834: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:834: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:919: Warning: Undefined citation: 'jupe2012' ./Tutorial/chapter_graphics.tex:1011: Warning: Image in text ./Tutorial/chapter_graphics.tex:1011: Warning: '_' occurring outside math mode ./Tutorial/chapter_graphics.tex:1088: Warning: Image in text ./Tutorial/chapter_graphics.tex:1088: Warning: '_' occurring outside math mode ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_kegg.tex:1: Warning: line too long ./Tutorial/chapter_phenotype.tex:10: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:16: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:32: Warning: '_' occurring outside math mode ./Tutorial/chapter_phenotype.tex:229: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:231: Warning: Optional argument to \item in itemize environment ./Tutorial/chapter_phenotype.tex:233: Warning: 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mode ./Tutorial/chapter_cookbook.tex:1497: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1516: Warning: Undefined label: 'sec:freq_table' ./Tutorial/chapter_cookbook.tex:1570: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1579: Warning: '_' occurring outside math mode ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_cookbook.tex:1603: Warning: Undefined label: 'sec:summary_info' ./Tutorial/chapter_cookbook.tex:1701: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long ./Tutorial/chapter_testing.tex:1: Warning: line too long 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./Tutorial/chapter_contributing.tex:8: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:35: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_contributing.tex:41: Warning: '_' occurring outside math mode ./Tutorial/chapter_contributing.tex:85: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_contributing.tex:101: Warning: Undefined label: 'sec:regr_test' ./Tutorial/chapter_appendix.tex:88: Warning: Undefined label: 'sec:SeqIO_compressed' ./Tutorial.tex:187: Warning: line too long ./Tutorial.tex:197: Warning: Application of '\'' on 'e' failed ./Tutorial.tex:197: Warning: Application of '\'' on 'o' failed ./Tutorial.tex:201: Warning: Application of '\"' on 'u' failed ./Tutorial.tex:252: Warning: Application of '\"' on 'o' failed ./Tutorial.tex:252: Warning: Application of '\"' on 'u' failed HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Tutorial.tex:68: Warning: tt_mode is an empty style ./Tutorial.haux:507: Giving up command: \@hevea@cbrace ./Tutorial.tex:68: Giving up command: \input ./Tutorial.tex:68: Warning: Failure while reading .haux ./Tutorial.tex:95: Warning: Application of '\'' on 'n' failed ./Tutorial/chapter_introduction.tex:110: Warning: Undefined citation: 'cock2009' ./Tutorial/chapter_introduction.tex:114: Warning: Undefined citation: 'chapman2000' ./Tutorial/chapter_introduction.tex:115: Warning: Undefined citation: 'hamelryck2003a' ./Tutorial/chapter_introduction.tex:116: Warning: Undefined citation: 'dehoon2004' ./Tutorial/chapter_introduction.tex:117: Warning: Undefined citation: 'pritchard2006' ./Tutorial/chapter_introduction.tex:118: Warning: Undefined citation: 'talevich2012' ./Tutorial/chapter_introduction.tex:119: Warning: Undefined citation: 'cock2010' ./Tutorial/chapter_introduction.tex:237: Warning: Undefined label: 'sec:seq-comparison' ./Tutorial/chapter_introduction.tex:250: Warning: Undefined label: 'sec:appendix-handles' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:SeqIO-conversion' ./Tutorial/chapter_introduction.tex:292: Warning: Undefined label: 'sec:converting-alignments' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:14: Warning: Undefined label: 'chapter:advanced' ./Tutorial/chapter_quick_start.tex:19: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:35: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_quick_start.tex:49: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:sequence-parsing' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:69: Warning: Undefined label: 'sec:align_clustal' ./Tutorial/chapter_quick_start.tex:76: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:78: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:83: Warning: Undefined label: 'sec:connecting-with-biological-databases' ./Tutorial/chapter_quick_start.tex:88: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:123: Warning: '_' occurring outside math mode ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_quick_start.tex:149: Warning: Undefined label: 'chapter:Bio.AlignIO' ./Tutorial/chapter_quick_start.tex:154: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_quick_start.tex:162: Warning: Undefined label: 'chapter:entrez' ./Tutorial/chapter_quick_start.tex:163: Warning: Undefined label: 'chapter:swiss_prot' ./Tutorial/chapter_quick_start.tex:173: Warning: Undefined label: 'chapter:cookbook' ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:1: Warning: line too long ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:SeqRecord' ./Tutorial/chapter_seq_objects.tex:5: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:137: Warning: Undefined label: 'sec:mutable-seq' ./Tutorial/chapter_seq_objects.tex:207: Warning: Undefined label: 'sec:SeqRecord-format' ./Tutorial/chapter_seq_objects.tex:209: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_objects.tex:376: Warning: Undefined label: 'sec:SeqIO-reverse-complement' ./Tutorial/chapter_seq_objects.tex:394: Warning: Command not found: \downarrow ./Tutorial/chapter_seq_objects.tex:449: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:564: Warning: Undefined label: 'sec:SeqIO-translate' ./Tutorial/chapter_seq_objects.tex:570: Warning: Undefined label: 'sec:seq-module-functions' ./Tutorial/chapter_seq_objects.tex:719: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:810: Warning: Undefined label: 'sec:seq-to-string' ./Tutorial/chapter_seq_objects.tex:871: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:4: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.Seq' ./Tutorial/chapter_seq_annot.tex:21: Warning: Undefined label: 'chapter:Bio.SeqIO' ./Tutorial/chapter_seq_annot.tex:34: Warning: Undefined label: 'sec:FASTQ-filtering-example' ./Tutorial/chapter_seq_annot.tex:38: Warning: Undefined label: 'sec:seq_features' 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[1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map} <./images/biopython_logo.pdf>]pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already us ed, duplicate ignored \relax l.99 \include{Tutorial/chapter_introduction} [1] (./Tutorial/chapter_introduction.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] LaTeX Warning: Citation `cock2009' on page 3 undefined on input line 110. [3] LaTeX Warning: Citation `chapman2000' on page 4 undefined on input line 114. LaTeX Warning: Citation `hamelryck2003a' on page 4 undefined on input line 115. LaTeX Warning: Citation `dehoon2004' on page 4 undefined on input line 116. LaTeX Warning: Citation `pritchard2006' on page 4 undefined on input line 117. LaTeX Warning: Citation `talevich2012' on page 4 undefined on input line 118. LaTeX Warning: Citation `cock2010' on page 4 undefined on input line 119. Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 141--147 Underfull \hbox (badness 10000) in paragraph at lines 153--155 [4 <./images/biopython_logo_old.jpg>] LaTeX Warning: Reference `sec:seq-comparison' on page 5 undefined on input line 237. [5] Overfull \hbox (2.99303pt too wide) in paragraph at lines 246--248 \OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or see [][]$\OT1/cmtt/m/n/10 http : / / biopython . LaTeX Warning: Reference `sec:appendix-handles' on page 6 undefined on input li ne 250. [6] LaTeX Warning: Reference `sec:SeqIO-conversion' on page 7 undefined on input li ne 292. LaTeX Warning: Reference `sec:converting-alignments' on page 7 undefined on inp ut line 292. ) [7] (./Tutorial/chapter_quick_start.tex Chapter 2. LaTeX Warning: Reference `chapter:cookbook' on page 8 undefined on input line 1 4. 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Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [10] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 11 undefined on input line 149. LaTeX Warning: Reference `chapter:Bio.AlignIO' on page 11 undefined on input li ne 149. LaTeX Warning: Reference `chapter:cookbook' on page 11 undefined on input line 154. LaTeX Warning: Reference `chapter:entrez' on page 11 undefined on input line 16 2. LaTeX Warning: Reference `chapter:swiss_prot' on page 11 undefined on input lin e 163. [11] LaTeX Warning: Reference `chapter:cookbook' on page 12 undefined on input line 173. ) [12] (./Tutorial/chapter_seq_objects.tex Chapter 3. LaTeX Warning: Reference `chapter:SeqRecord' on page 13 undefined on input line 5. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 13 undefined on input line 5. [13] [14] LaTeX Warning: Reference `sec:mutable-seq' on page 15 undefined on input line 1 37. [15] LaTeX Warning: Reference `sec:SeqRecord-format' on page 16 undefined on input l ine 207. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 16 undefined on input line 209. [16] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [17] [18] LaTeX Warning: Reference `sec:SeqIO-reverse-complement' on page 19 undefined on input line 376. 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Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 30 undefined on input line 158. Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [30] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 31 undefined on input line 216. Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 31 undefined on input line 229. [31] LaTeX Warning: Reference `sec:seq_features' on page 32 undefined on input line 279. LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 288 . LaTeX Warning: Reference `sec:locations' on page 32 undefined on input line 296 . [32] [33] [34] [35] LaTeX Warning: Reference `sec:locations' on page 36 undefined on input line 528 . Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [36] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] LaTeX Warning: Reference `sec:seq-comparison' on page 37 undefined on input lin e 632. LaTeX Warning: Reference `sec:locations' on page 37 undefined on input line 640 . [37] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 38 undefined on input line 676. LaTeX Warning: Reference `sec:Bio.SeqIO-and-StringIO' on page 38 undefined on i nput line 679. Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [38] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [39] LaTeX Warning: Reference `sec:SeqRecord-format' on page 40 undefined on input l ine 833. Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] LaTeX Warning: Reference `sec:FASTQ-slicing-off-primer' on page 40 undefined on input line 841. LaTeX Warning: Reference `sec:FASTQ-slicing-off-adaptor' on page 40 undefined o n input line 842. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 40 undefined on input line 855. [40] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [41] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [42] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [43] (./Tutorial/chapter_seqio.tex Chapter 5. LaTeX Warning: Reference `chapter:quick-start' on page 44 undefined on input li ne 4. LaTeX Warning: Reference `chapter:SeqRecord' on page 44 undefined on input line 4. LaTeX Warning: Reference `chapter:SeqRecord' on page 44 undefined on input line 13. LaTeX Warning: Reference `chapter:Bio.Seq' on page 44 undefined on input line 1 3. LaTeX Warning: Reference `sec:low-level-fasta-fastq' on page 44 undefined on in put line 15. LaTeX Warning: Reference `sec:SeqIO_Online' on page 44 undefined on input line 23. LaTeX Warning: Reference `sec:appendix-handles' on page 44 undefined on input l ine 23. [44] LaTeX Warning: Reference `sec:sequence-parsing' on page 45 undefined on input l ine 45. Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] LaTeX Warning: Reference `seq:sequence-parsing-plus-pylab' on page 45 undefined on input line 69. [45] [46] LaTeX Warning: Reference `chapter:SeqRecord' on page 47 undefined on input line 148. [47] [48] LaTeX Warning: Reference `sec:appendix-handles' on page 49 undefined on input l ine 283. [49] LaTeX Warning: Reference `sec:SeqIO-index-bgzf' on page 50 undefined on input l ine 359. LaTeX Warning: Reference `sec:efetch' on page 50 undefined on input line 375. Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [50] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] LaTeX Warning: Reference `chapter:entrez' on page 51 undefined on input line 45 1. LaTeX Warning: Reference `sec:entrez-guidelines' on page 51 undefined on input line 451. LaTeX Warning: Reference `chapter:swiss_prot' on page 51 undefined on input lin e 456. Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [51] LaTeX Warning: Reference `SeqIO:to_dict' on page 52 undefined on input line 491 . LaTeX Warning: Reference `sec:SeqIO-index' on page 52 undefined on input line 4 97. LaTeX Warning: Reference `sec:SeqIO-index-db' on page 52 undefined on input lin e 501. LaTeX Warning: Reference `sec:SeqIO-indexing-discussion' on page 52 undefined o n input line 504. LaTeX Warning: Reference `sec:SeqIO-index' on page 52 undefined on input line 5 14. [52] LaTeX Warning: Reference `sec:fasta-parsing' on page 53 undefined on input line 588. Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [53] [54] LaTeX Warning: Reference `sec:fastq-indexing' on page 55 undefined on input lin e 704. LaTeX Warning: Reference `seq:seqio-todict-functionkey' on page 55 undefined on input line 725. Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [55] LaTeX Warning: Reference `sec:SeqIO-sort' on page 56 undefined on input line 78 7. Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , [56] LaTeX Warning: Reference `sec:seqio-index-getraw' on page 57 undefined on input line 869. [57] [58] [59] LaTeX Warning: Reference `sec:seqio-index-getraw' on page 60 undefined on input line 1097. [60] LaTeX Warning: Reference `sec:SeqIO-fastq-conversion' on page 61 undefined on i nput line 1139. LaTeX Warning: Reference `sec:SeqIO-fasta-qual-conversion' on page 61 undefined on input line 1139. LaTeX Warning: Reference `sec:seq-reverse-complement' on page 61 undefined on i nput line 1154. LaTeX Warning: Reference `sec:SeqRecord-reverse-complement' on page 61 undefine d on input line 1164. Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [61] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] LaTeX Warning: Reference `sec:SeqIO-translate' on page 62 undefined on input li ne 1205. LaTeX Warning: Reference `sec:SeqRecord-format' on page 62 undefined on input l ine 1224. Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [62] Overfull \hbox (21.32593pt too wide) in paragraph at lines 1284--1288 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator LaTeX Warning: Reference `chapter:cookbook' on page 63 undefined on input line 1303. ) [63] (./Tutorial/chapter_align.tex Chapter 6. LaTeX Warning: Reference `sec:appendix-handles' on page 64 undefined on input l ine 31. LaTeX Warning: Reference `sec:AlignIO-count-argument' on page 64 undefined on i nput line 35. [64] [65] LaTeX Warning: Reference `sec:alignment-format-method' on page 66 undefined on input line 114. [66] [67] [68] [69] [70] [71] Overfull \hbox (5.54102pt too wide) in paragraph at lines 432--433 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/it-er-a-tor. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() LaTeX Warning: Reference `sec:SeqIO-conversion' on page 72 undefined on input l ine 442. Overfull \hbox (39.68698pt too wide) in paragraph at lines 440--445 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() [72] [73] [74] LaTeX Warning: Reference `sec:SeqRecord-format' on page 75 undefined on input l ine 614. Overfull \hbox (16.49278pt too wide) in paragraph at lines 616--619 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [75] [76] LaTeX Warning: Reference `sec:SeqRecord-addition' on page 77 undefined on input line 788. [77] LaTeX Warning: Reference `sec:pairwise2' on page 78 undefined on input line 840 . LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 78 undefined on input line 845. LaTeX Warning: Reference `seq:emboss-needle-water' on page 78 undefined on inpu t line 872. [78] [79] LaTeX Warning: Reference `sec:Phylo' on page 80 undefined on input line 1019. [80] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1053--1057 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO [81] [82] LaTeX Warning: Reference `sec:appendix-handles' on page 83 undefined on input l ine 1241. [83] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [84] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1360--1360 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [85] [86]) [87] (./Tutorial/chapter_blast.tex Chapter 7. LaTeX Warning: Reference `chapter:searchio' on page 88 undefined on input line 18. [88] LaTeX Warning: Reference `sec:parsing-blast' on page 89 undefined on input line 58. LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 89 undefined on input line 119. LaTeX Warning: Reference `sec:parsing-blast' on page 89 undefined on input line 124. [89] LaTeX Warning: Reference `sec:parsing-blast' on page 90 undefined on input line 146. LaTeX Warning: Reference `sec:parsing-blast' on page 90 undefined on input line 155. LaTeX Warning: Reference `sec:running-www-blast' on page 90 undefined on input line 164. LaTeX Warning: Reference `sec:alignment-tools' on page 90 undefined on input li ne 192. [90] LaTeX Warning: Reference `sec:parsing-blast' on page 91 undefined on input line 236. LaTeX Warning: Reference `sec:parsing-blast-deprecated' on page 91 undefined on input line 268. LaTeX Warning: Reference `sec:running-www-blast' on page 91 undefined on input line 282. LaTeX Warning: Reference `sec:running-local-blast' on page 91 undefined on inpu t line 284. [91] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 92 undefined on input line 335. LaTeX Warning: Reference `chapter:Bio.AlignIO' on page 92 undefined on input li ne 335. [92] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [93] LaTeX Warning: Reference `fig:blastrecord' on page 94 undefined on input line 4 45. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:psiblastrecord' on page 94 undefined on input lin e 461. Excluding 'htmlonly' comment. LaTeX Warning: Reference `sec:parsing-blast' on page 94 undefined on input line 485. [94] [95 <./images/BlastRecord.png>] [96 <./images/PSIBlastRecord.png>] LaTeX Warning: Reference `sec:parsing-blast' on page 97 undefined on input line 524. [97] [98]) [99] (./Tutorial/chapter_searchio.tex Chapter 8. LaTeX Warning: Reference `chapter:blast' on page 100 undefined on input line 11 . [100] Overfull \hbox (2.9019pt too wide) in paragraph at lines 94--102 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 114--116 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult [101] [102] [103] [104] [105] Overfull \hbox (44.7405pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split('|')[3] # renames 'gi|301171 322|ref|NR_035857.1|' to 'NR_035857.1'[] [106] [107] [108] [109] Overfull \hbox (469.98679pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] LaTeX Warning: Reference `chapter:SeqRecord' on page 110 undefined on input lin e 743. Overfull \hbox (27.24287pt too wide) in paragraph at lines 747--749 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment [110] [111] Overfull \hbox (65.74031pt too wide) in paragraph at lines 879--879 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [112] Overfull \hbox (769.23418pt too wide) in paragraph at lines 971--971 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [113] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1059--1063 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , [114] LaTeX Warning: Reference `sec:SeqIO-index' on page 115 undefined on input line 1091. Overfull \hbox (20.13245pt too wide) in paragraph at lines 1089--1094 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . Overfull \hbox (13.24077pt too wide) in paragraph at lines 1132--1132 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index('tab_2226_tblastn_001.txt', 'blast- tab', key_function=key_function)[] [115] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1169--1172 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse ) [116] (./Tutorial/chapter_entrez.tex Chapter 9. LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 117 undefined on input line 22. [117] LaTeX Warning: Reference `sec:entrez-webenv' on page 118 undefined on input lin e 50. LaTeX Warning: Reference `sec:BioSQL' on page 118 undefined on input line 53. [118] [119] [120] LaTeX Warning: Reference `sec:efetch' on page 121 undefined on input line 200. LaTeX Warning: Reference `sec:entrez-einfo' on page 121 undefined on input line 204. Overfull \hbox (70.99026pt too wide) in paragraph at lines 215--215 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] LaTeX Warning: Reference `sec:efetch' on page 121 undefined on input line 218. [121] LaTeX Warning: Reference `sec:entrez-webenv' on page 122 undefined on input lin e 280. [122] LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 123 undefined on in put line 305. LaTeX Warning: Reference `sec:efetch' on page 123 undefined on input line 305. [123] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 124 undefined on input lin e 399. [124] Overfull \hbox (13.24077pt too wide) in paragraph at lines 440--440 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] LaTeX Warning: Reference `sec:entrez-specialized-parsers' on page 125 undefined on input line 456. LaTeX Warning: Reference `sec:entrez-webenv' on page 125 undefined on input lin e 458. [125] [126] LaTeX Warning: Reference `sec:elink-citations' on page 127 undefined on input l ine 539. LaTeX Warning: Reference `subsec:entrez_example_genbank' on page 127 undefined on input line 545. [127] [128] Overfull \hbox (312.48816pt too wide) in paragraph at lines 646--646 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 667--667 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 674--674 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 [] [129] Overfull \hbox (585.48578pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 130 undefined on in put line 736. LaTeX Warning: Reference `sec:efetch' on page 130 undefined on input line 736. [130] [131] LaTeX Warning: Reference `sec:entrez-webenv' on page 132 undefined on input lin e 853. [132] Overfull \hbox (133.98972pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] [133] Overfull \hbox (102.48999pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] Overfull \hbox (160.23949pt too wide) in paragraph at lines 961--961 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [134] LaTeX Warning: Reference `sec:orchids' on page 135 undefined on input line 1011 . LaTeX Warning: Reference `sec:entrez-webenv' on page 135 undefined on input lin e 1051. [135] LaTeX Warning: Reference `sec:orchids' on page 136 undefined on input line 1096 . [136] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1119--1119 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] LaTeX Warning: Reference `sec:entrez-webenv' on page 137 undefined on input lin e 1147. [137] LaTeX Warning: Reference `sec:entrez-webenv' on page 138 undefined on input lin e 1182. LaTeX Warning: Reference `sec:SeqIO_GenBank_Online' on page 138 undefined on in put line 1189. LaTeX Warning: Reference `sec:entrez-webenv' on page 138 undefined on input lin e 1190. [138] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 139 undefined on input lin e 1242. LaTeX Warning: Reference `sec:entrez-guidelines' on page 139 undefined on input line 1266. LaTeX Warning: Reference `sec:entrez-webenv' on page 139 undefined on input lin e 1267. [139] LaTeX Warning: Reference `sec:entrez-search-fetch-genbank' on page 140 undefine d on input line 1325. [140] LaTeX Warning: Reference `subsec:entrez_example_genbank' on page 141 undefined on input line 1356. [141] [142] LaTeX Warning: Reference `subsec:entrez-and-medline' on page 143 undefined on i nput line 1454. LaTeX Warning: Reference `sec:elink' on page 143 undefined on input line 1459. LaTeX Warning: Reference `sec:entrez-webenv' on page 143 undefined on input lin e 1483. ) [143] (./Tutorial/chapter_uniprot.tex Chapter 10. LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 144 undefined on input line 10. Overfull \hbox (1.49112pt too wide) in paragraph at lines 28--28 []\OT1/cmtt/m/n/10 >>> handle = urllib.urlopen("http://www.somelocation.org/da ta/someswissprotfile.dat")[] LaTeX Warning: Reference `subsec:expasy_swissprot' on page 144 undefined on inp ut line 30. LaTeX Warning: Reference `sec:SeqIO_ExPASy_and_SwissProt' on page 144 undefined on input line 38. [144] Overfull \hbox (28.99063pt too wide) in paragraph at lines 61--61 []\OT1/cmtt/m/n/10 'RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Fu ll=Naringenin-chalcone synthase 3;'[] [145] [146] [147] [148] [149] LaTeX Warning: Reference `sec:orchids' on page 150 undefined on input line 331. Overfull \hbox (24.29903pt too wide) in paragraph at lines 350--351 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) [150] Overfull \hbox (65.93893pt too wide) in paragraph at lines 415--416 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord [151] Overfull \hbox (133.98972pt too wide) in paragraph at lines 499--499 []\OT1/cmtt/m/n/10 {'signature_ac': u'PS50948', 'level': u'0', 'stop': 98, 'seq uence_ac': u'USERSEQ1', 'start': 16, 'score': u'8.873'}[] [152]) [153] (./Tutorial/chapter_pdb.tex Chapter 11. LaTeX Warning: Reference `problem structures' on page 154 undefined on input li ne 18. [154] [155] Overfull \hbox (13.022pt too wide) in paragraph at lines 176--178 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/-Mod-el/Chain/Residue/A tom) LaTeX Warning: Reference `fig:smcra' on page 156 undefined on input line 189. LaTeX Warning: Reference `problem structures' on page 156 undefined on input li ne 198. [156] Excluding 'htmlonly' comment. [157 <./images/smcra.png (PNG copy)>] [158] LaTeX Warning: Reference `hetero problems' on page 159 undefined on input line 335. [159] LaTeX Warning: Reference `point mutations' on page 160 undefined on input line 380. LaTeX Warning: Reference `disordered atoms' on page 160 undefined on input line 397. [160] [161] LaTeX Warning: Reference `fig:smcra' on page 162 undefined on input line 522. LaTeX Warning: Reference `fig:smcra' on page 162 undefined on input line 568. [162] [163] [164] [165] [166] LaTeX Warning: Citation `golub1989' on page 167 undefined on input line 852. LaTeX Warning: Citation `hamelryck2005' on page 167 undefined on input line 880 . LaTeX Warning: Command \r invalid in math mode on input line 883. [167] LaTeX Warning: Reference `cap:DSSP-codes' on page 168 undefined on input line 9 15. LaTeX Warning: Reference `subsec:residue_depth' on page 168 undefined on input line 954. [168] LaTeX Warning: Citation `hamelryck2003a' on page 169 undefined on input line 10 04. [169] [170] [171] LaTeX Warning: Citation `hamelryck2003b' on page 172 undefined on input line 12 16. LaTeX Warning: Citation `majumdar2005' on page 172 undefined on input line 1217 . ) [172] (./Tutorial/chapter_popgen.tex Chapter 12. [173]) [174] (./Tutorial/chapter_phylo.tex Chapter 13. LaTeX Warning: Citation `talevich2012' on page 175 undefined on input line 9. [175] LaTeX Warning: Reference `fig:phylo-simple-draw' on page 176 undefined on input line 96. Excluding 'htmlonly' comment. [176] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor LaTeX Warning: Reference `fig:phylo-color-draw' on page 177 undefined on input line 192. [177 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [178 <./im ages/phylo-color-draw.png>] [179] Overfull \hbox (406.98734pt too wide) in paragraph at lines 326--326 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-dot' on page 180 undefined on input line 37 4. Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:phylo-rooted' on page 180 undefined on input line 410. Excluding 'htmlonly' comment. 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That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [185] [186] LaTeX Warning: Reference `sec:alignment-tools' on page 187 undefined on input l ine 830. [187] LaTeX Warning: Reference `sec:PhyloXML' on page 188 undefined on input line 901 . [188]) [189] (./Tutorial/chapter_motifs.tex Chapter 14. LaTeX Warning: Reference `sec:links' on page 190 undefined on input line 7. [190] [191] LaTeX Warning: Citation `cornish1985' on page 192 undefined on input line 152. LaTeX Warning: Citation `cavener1987' on page 192 undefined on input line 153. [192] [193] Overfull \hbox (128.73976pt too wide) in paragraph at lines 270--270 []\OT1/cmtt/m/n/10 [Seq('CACGTG', IUPACUnambiguousDNA()), Seq('CACGTG', IUPACUn ambiguousDNA()), Seq('CACGTG', IUPACUnambiguousDNA())][] [194] [195] [196] [197] [198] LaTeX Warning: Citation `bailey1994' on page 199 undefined on input line 522. [199] Overfull \hbox (13.10551pt too wide) in paragraph at lines 582--586 \OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man d reads the com-plete file di-rectly, so you can close the file af-ter call-ing [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 . [200] [201] LaTeX Warning: Citation `matys2003' on page 202 undefined on input line 658. [202] LaTeX Warning: Reference `table:transfaccodes' on page 203 undefined on input l ine 733. LaTeX Warning: `h' float specifier changed to `ht'. [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]) [215] (./Tutorial/chapter_cluster.tex Chapter 15. LaTeX Warning: Citation `dehoon2004' on page 216 undefined on input line 5. LaTeX Warning: Citation `lecuyer1988' on page 216 undefined on input line 29. LaTeX Warning: Citation `kachitvichyanukul1988' on page 216 undefined on input line 29. [216] [217] [218] LaTeX Warning: Citation `snedecor1989' on page 219 undefined on input line 153. [219] LaTeX Warning: Reference `sec:distancefunctions' on page 220 undefined on input line 185. [220] Overfull \hbox (78.60634pt too wide) in paragraph at lines 233--234 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ [221] LaTeX Warning: Reference `sec:distancefunctions' on page 222 undefined on input line 266. [222] [223] LaTeX Warning: Reference `sec:distancefunctions' on page 224 undefined on input line 333. [224] [225] Overfull \hbox (16.73593pt too wide) in paragraph at lines 415--416 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, [226] [227] LaTeX Warning: Reference `sec:distancefunctions' on page 228 undefined on input line 536. [228] LaTeX Warning: Citation `kohonen1997' on page 229 undefined on input line 584. 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LaTeX Warning: Reference `sec:gd_multiple_tracks' on page 262 undefined on inpu t line 658. LaTeX Warning: Citation `proux2002' on page 262 undefined on input line 678. [262 <./images/three_track_simple.png>] [263] Overfull \hbox (28.99063pt too wide) in paragraph at lines 782--782 [] \OT1/cmtt/m/n/10 color = colors.linearlyInterpolatedColor(colors.whit e, colors.firebrick, 0, 100, score)[] Overfull \hbox (2.65141pt too wide) in paragraph at lines 784--790 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. LaTeX Warning: Reference `fig:three_track_cl' on page 264 undefined on input li ne 805. LaTeX Warning: Reference `sec:gd_cross_links' on page 264 undefined on input li ne 812. LaTeX Warning: Reference `sec:gd_cross_links' on page 264 undefined on input li ne 812. Excluding 'htmlonly' comment. 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[300 <./images/SRR001666.png>] [301] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . [302] LaTeX Warning: Reference `sec:summary_info' on page 303 undefined on input line 1497. LaTeX Warning: Reference `sec:freq_table' on page 303 undefined on input line 1 516. [303] LaTeX Warning: Reference `sec:align_clustal' on page 304 undefined on input lin e 1603. LaTeX Warning: Reference `sec:summary_info' on page 304 undefined on input line 1603. [304] LaTeX Warning: Reference `chapter:Bio.SeqIO' on page 305 undefined on input lin e 1701. [305]) [306] (./Tutorial/chapter_testing.tex Chapter 21. LaTeX Warning: Reference `section:doctest' on page 307 undefined on input line 49. [307] [308] [309] [310] [311] [312] LaTeX Warning: Reference `section:doctest' on page 313 undefined on input line 409. [313] (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)) [314] (./Tutorial/chapter_advanced.tex Chapter 22. [315] [316] LaTeX Warning: Reference `sec:freq_table' on page 317 undefined on input line 1 63. Overfull \hbox (30.74179pt too wide) in paragraph at lines 198--199 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor [317] [318]) [319] (./Tutorial/chapter_contributing.tex Chapter 23. LaTeX Warning: Reference `chapter:cookbook' on page 320 undefined on input line 35. [320] LaTeX Warning: Reference `sec:regr_test' on page 321 undefined on input line 85 . [321] LaTeX Warning: Reference `sec:regr_test' on page 322 undefined on input line 10 1. ) [322] (./Tutorial/chapter_appendix.tex Chapter 24. [323] LaTeX Warning: Reference `sec:SeqIO_compressed' on page 324 undefined on input line 88. ) [324] Underfull \hbox (badness 2005) in paragraph at lines 194--196 []\OT1/cmr/m/n/10 Ian K. Toth, Leighton Pritchard, Paul R. J. Birch: ``Com-par- a-tive ge-nomics re-veals what Underfull \hbox (badness 3758) in paragraph at lines 216--217 []\OT1/cmr/m/n/10 Douglas R. Cavener: ``Com-par-i-son of the con-sen-sus se-que nce flank-ing trans-la-tional start Underfull \hbox (badness 3838) in paragraph at lines 216--217 \OT1/cmr/m/n/10 sites in Drosophila and ver-te-brates.'' \OT1/cmr/m/it/10 Nu-cl eic Acids Re-search \OT1/cmr/bx/n/10 15 \OT1/cmr/m/n/10 (4): 1353--1361 (1987). 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LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (328 pages, 2418189 bytes). Transcript written on Tutorial.log. pdflatex Tutorial.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Tutorial.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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Excluding 'rawhtml' comment. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.m ap} <./images/biopython_logo.pdf>] (./Tutorial.tocpdfTeX warning (ext4): destin ation with the same identifier (name{page.1}) has been already used, duplicate ignored \relax l.39 ...tions and locations}{33}{subsection.4.3.2} [1] [2] [3] [4] [5] [6] [7]) [8] (./Tutorial/chapter_introduction.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [9] [10] Excluding 'rawhtml' comment. Underfull \hbox (badness 10000) in paragraph at lines 141--147 Underfull \hbox (badness 10000) in paragraph at lines 153--155 [11 <./images/biopython_logo_old.jpg>] [12] Overfull \hbox (2.99303pt too wide) in paragraph at lines 246--248 \OT1/cmr/m/n/10 Check the built in doc-strings (\OT1/cmtt/m/n/10 from Bio impor t SeqIO\OT1/cmr/m/n/10 , then \OT1/cmtt/m/n/10 help(SeqIO)\OT1/cmr/m/n/10 ), or see [][]$\OT1/cmtt/m/n/10 http : / / biopython . [13]) [14] (./Tutorial/chapter_quick_start.tex Chapter 2. [15] [16] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [17] [18]) [19] (./Tutorial/chapter_seq_objects.tex Chapter 3. [20] [21] [22] [23] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33]) [34] (./Tutorial/chapter_seq_annot.tex Chapter 4. [35] [36] Overfull \hbox (2.74086pt too wide) in paragraph at lines 129--129 []\OT1/cmtt/m/n/10 >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence[] Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [37] Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [38] [39] [40] [41] [42] Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [43] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] [44] Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [45] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [46] Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] [47] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [48] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [49] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [50] (./Tutorial/chapter_seqio.tex Chapter 5. [51] Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] [52] [53] [54] [55] [56] Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [57] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [58] [59] Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [60] [61] Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [62] Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , [63] [64] [65] [66] [67] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [68] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) 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There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 440--445 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() [79] [80] [81] Overfull \hbox (16.49278pt too wide) in paragraph at lines 616--619 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [82] [83] [84] [85] [86] [87] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1053--1057 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO [88] [89] [90] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [91] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1360--1360 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [92] [93]) [94] (./Tutorial/chapter_blast.tex Chapter 7. [95] [96] [97] [98] [99] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [100] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [101] [102 <./images/BlastRecord.png>] [103 <./images/PSIBlastRecord.png>] [104] [105]) [106] (./Tutorial/chapter_searchio.tex Chapter 8. [107] Overfull \hbox (2.9019pt too wide) in paragraph at lines 94--102 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 114--116 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult [108] [109] [110] [111] [112] Overfull \hbox (44.7405pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split('|')[3] # renames 'gi|301171 322|ref|NR_035857.1|' to 'NR_035857.1'[] [113] [114] [115] [116] Overfull \hbox (469.98679pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] Overfull \hbox (27.24287pt too wide) in paragraph at lines 747--749 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment [117] [118] Overfull \hbox (65.74031pt too wide) in paragraph at lines 879--879 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [119] Overfull \hbox (769.23418pt too wide) in paragraph at lines 971--971 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [120] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1059--1063 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , [121] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1089--1094 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . Overfull \hbox (13.24077pt too wide) in paragraph at lines 1132--1132 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index('tab_2226_tblastn_001.txt', 'blast- tab', key_function=key_function)[] [122] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1169--1172 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse ) [123] (./Tutorial/chapter_entrez.tex Chapter 9. [124] [125] [126] [127] Overfull \hbox (70.99026pt too wide) in paragraph at lines 215--215 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] [128] [129] [130] [131] Overfull \hbox (13.24077pt too wide) in paragraph at lines 440--440 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] [132] [133] [134] [135] Overfull \hbox (312.48816pt too wide) in paragraph at lines 646--646 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 667--667 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 674--674 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 [] [136] Overfull \hbox (585.48578pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] [137] [138] [139] Overfull \hbox (133.98972pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] [140] Overfull \hbox (102.48999pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] Overfull \hbox (160.23949pt too wide) in paragraph at lines 961--961 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [141] [142] [143] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1119--1119 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] [144] [145] [146] [147] [148] [149]) [150] (./Tutorial/chapter_uniprot.tex Chapter 10. 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[161] [162] Overfull \hbox (13.022pt too wide) in paragraph at lines 176--178 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/-Mod-el/Chain/Residue/A tom) [163] Excluding 'htmlonly' comment. [164 <./images/smcra.png (PNG copy)>] [165] [166] [167] [168] [169] [170] [171] [172] [173] LaTeX Warning: Command \r invalid in math mode on input line 883. [174] [175] [176] [177] [178]) [179] (./Tutorial/chapter_popgen.tex Chapter 12. [180]) [181] (./Tutorial/chapter_phylo.tex Chapter 13. [182] Excluding 'htmlonly' comment. [183] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor [184 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [185 <./im ages/phylo-color-draw.png>] [186] Overfull \hbox (406.98734pt too wide) in paragraph at lines 326--326 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [187] [188 <./images/phylo-draw-example.png> <./i mages/phylo-dot.png>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [189 <./images/phylo-rooted.png> <./images/phylo- color.png>] [190 <./images/phylo-apaf.png> <./images/phylo-apaf-zoom.png>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 557--564 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [191] Overfull \hbox (13.48741pt too wide) in paragraph at lines 612--615 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. 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[223] [224] [225] [226] [227] Overfull \hbox (78.60634pt too wide) in paragraph at lines 233--234 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ [228] [229] [230] [231] [232] Overfull \hbox (16.73593pt too wide) in paragraph at lines 415--416 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, [233] [234] [235] [236] [237] Overfull \hbox (106.77225pt too wide) in paragraph at lines 638--640 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [238] Overfull \hbox (25.39864pt too wide) in paragraph at lines 722--733 [] [239] [240] [241] [242] Overfull \hbox (106.77225pt too wide) in paragraph at lines 911--913 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [243] Overfull \hbox (26.21434pt too wide) in paragraph at lines 965--966 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [244]) [245] (./Tutorial/chapter_learning.tex Chapter 16. [246] [247] [248] [249] [250] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. [251] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. [252] [253]) [254] (./Tutorial/chapter_graphics.tex Chapter 17. [255] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [256] [257 <./images/plasmid_linear.png (PNG copy)> <./images/plasmid_circular.png (P NG copy)>] [258] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [259] [260 <./images/GD_sigil_labels.png (PNG copy)>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [261] [262 <./images/GD_sigils.png>] [263 <./imag es/GD_sigil_arrow_shafts.png>] Excluding 'htmlonly' comment. [264 <./images/GD_ sigil_arrow_heads.png>] [265] Excluding 'htmlonly' comment. [266 <./images/plas mid_linear_nice.png (PNG copy)>] [267 <./images/plasmid_circular_nice.png>] Overfull \hbox (2.74086pt too wide) in paragraph at lines 605--605 []\OT1/cmtt/m/n/10 A_colors = [red]*5 + [grey]*7 + [orange]*2 + [grey]*2 + [ora nge] + [grey]*11 + [green]*4 \[] [268] Excluding 'htmlonly' comment. [269 <./images/three_track_simple.png>] [270] Overfull \hbox (28.99063pt too wide) in paragraph at lines 782--782 [] \OT1/cmtt/m/n/10 color = colors.linearlyInterpolatedColor(colors.whit e, colors.firebrick, 0, 100, score)[] Overfull \hbox (2.65141pt too wide) in paragraph at lines 784--790 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [271] [272 <./image s/three_track_cl.png>] [273 <./images/three_track_cl2a.png>] [274] [275 <./imag es/simple_chrom.pdf> <./images/tRNA_chrom.pdf>] [276] Excluding 'htmlonly' comment. [277] Excluding 'htmlonly' comment.) [278] (./Tutorial/chapter_kegg.tex Chapter 18. [279] [280]) [281] (./Tutorial/chapter_phenotype.tex Chapter 19. [282] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['A12']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['B01'], WellReco rd['C01'], ..., WellRecord['H01']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['C03']')[] [283] [284] [285]) [286] (./Tutorial/chapter_cookbook.tex Chapter 20. [287] [288] [289] [290] [291] [292] Overfull \hbox (5.83499pt too wide) in paragraph at lines 426--430 \OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator Overfull \hbox (4.57849pt too wide) in paragraph at lines 444--446 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . [293] [294] [295] [296] Overfull \hbox (7.99081pt too wide) in paragraph at lines 765--765 []\OT1/cmtt/m/n/10 Seq('GTCCCAGTATTCGGATTTGTCTGCCAAAACAATGAAATTGACACAGTTTACAAC. ..CCG', SingleLetterAlphabet())[] [297] [298] [299] [300] Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1057--1060 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) [301] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [302 <./image s/hist_plot.png>] [303 <./images/gc_plot.png>] Excluding 'htmlonly' comment. [304 <./images/dot_plot.png>] Excluding 'htmlonly' comment. [305] Excluding 'htmlonly' comment. [306 <./images/dot_plot_scatter.png>] [307 <./ima ges/SRR001666.png>] [308] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . [309] [310] [311] [312]) [313] (./Tutorial/chapter_testing.tex Chapter 21. [314] [315] [316] [317] [318] [319] [320] (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)) [321] (./Tutorial/chapter_advanced.tex Chapter 22. [322] [323] Overfull \hbox (30.74179pt too wide) in paragraph at lines 198--199 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor [324] [325]) [326] (./Tutorial/chapter_contributing.tex Chapter 23. [327] [328]) [329] (./Tutorial/chapter_appendix.tex Chapter 24. [330]) [331] Underfull \hbox (badness 2005) in paragraph at lines 194--196 []\OT1/cmr/m/n/10 Ian K. Toth, Leighton Pritchard, Paul R. J. Birch: ``Com-par- a-tive ge-nomics re-veals what Underfull \hbox (badness 3758) in paragraph at lines 216--217 []\OT1/cmr/m/n/10 Douglas R. Cavener: ``Com-par-i-son of the con-sen-sus se-que nce flank-ing trans-la-tional start Underfull \hbox (badness 3838) in paragraph at lines 216--217 \OT1/cmr/m/n/10 sites in Drosophila and ver-te-brates.'' \OT1/cmr/m/it/10 Nu-cl eic Acids Re-search \OT1/cmr/bx/n/10 15 \OT1/cmr/m/n/10 (4): 1353--1361 (1987). [332] [333] [334] (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_advanced.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (335 pages, 2475386 bytes). Transcript written on Tutorial.log. pdflatex Tutorial.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Tutorial.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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[15] [16] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG. ..CGC', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 117--117 []\OT1/cmtt/m/n/10 Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT. ..GCC', SingleLetterAlphabet())[] [17] [18]) [19] (./Tutorial/chapter_seq_objects.tex Chapter 3. [20] [21] [22] [23] Overfull \hbox (39.49054pt too wide) in paragraph at lines 274--274 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] Overfull \hbox (39.49054pt too wide) in paragraph at lines 285--285 []\OT1/cmtt/m/n/10 >>> list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", ge neric_dna), Seq("GGTT", generic_dna)][] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33]) [34] (./Tutorial/chapter_seq_annot.tex Chapter 4. [35] [36] Overfull \hbox (2.74086pt too wide) in paragraph at lines 129--129 []\OT1/cmtt/m/n/10 >gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence[] Overfull \hbox (34.24059pt too wide) in paragraph at lines 144--144 []\OT1/cmtt/m/n/10 SingleLetterAlphabet()), id='gi|45478711|ref|NC_005816.1|', name='gi|45478711|ref|NC_005816.1|',[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 153--153 []\OT1/cmtt/m/n/10 Seq('TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGG. ..CTG', SingleLetterAlphabet())[] Overfull \hbox (7.99081pt too wide) in paragraph at lines 169--169 []\OT1/cmtt/m/n/10 'gi|45478711|ref|NC_005816.1| Yersinia pestis biovar Microtu s ... pPCP1, complete sequence'[] [37] Overfull \hbox (7.99081pt too wide) in paragraph at lines 226--226 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [38] [39] [40] [41] [42] Overfull \hbox (44.7405pt too wide) in paragraph at lines 536--536 []\OT1/cmtt/m/n/10 >>> example_parent = Seq("ACCGAGACGGCAAAGGCTAGCATAGGTATGAGAC TTCCTTCCTGCCAGTGCTGAGGAACTGGGAGCCTAC")[] Overfull \hbox (128.73976pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 >>> feature_seq = example_parent[example_feature.location.st art:example_feature.location.end].reverse_complement()[] [43] Overfull \hbox (165.48944pt too wide) in paragraph at lines 618--618 []\OT1/cmtt/m/n/10 NotImplementedError: SeqRecord comparison is deliberately no t implemented. Explicitly compare the attributes of interest.[] [44] Overfull \hbox (2.74086pt too wide) in paragraph at lines 703--703 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence',[] [45] Overfull \hbox (7.99081pt too wide) in paragraph at lines 762--762 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [46] Overfull \hbox (39.49054pt too wide) in paragraph at lines 839--839 []\OT1/cmtt/m/n/10 >>> sub_record.description = "Yersinia pestis biovar Microtu s str. 91001 plasmid pPCP1, partial."[] [47] Overfull \hbox (7.99081pt too wide) in paragraph at lines 930--930 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [48] Overfull \hbox (7.99081pt too wide) in paragraph at lines 960--960 []\OT1/cmtt/m/n/10 description='Yersinia pestis biovar Microtus str. 91001 plas mid pPCP1, complete sequence.',[] [49] Overfull \hbox (170.7394pt too wide) in paragraph at lines 1032--1032 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (record.id, len(record), len(re cord.features), len(record.dbxrefs), len(record.annotations)))[] Overfull \hbox (65.74031pt too wide) in paragraph at lines 1042--1042 []\OT1/cmtt/m/n/10 >>> print("%s %i %i %i %i" % (rc.id, len(rc), len(rc.feature s), len(rc.dbxrefs), len(rc.annotations)))[] ) [50] (./Tutorial/chapter_seqio.tex Chapter 5. [51] Overfull \hbox (7.99081pt too wide) in paragraph at lines 66--66 []\OT1/cmtt/m/n/10 >>> identifiers = [seq_record.id for seq_record in SeqIO.par se("ls_orchid.gbk", "genbank")][] [52] [53] [54] [55] [56] Overfull \hbox (18.49072pt too wide) in paragraph at lines 391--391 []\OT1/cmtt/m/n/10 with Entrez.efetch(db="nucleotide", rettype="fasta", retmode ="text", id="6273291") as handle:[] [57] Overfull \hbox (23.74068pt too wide) in paragraph at lines 438--438 [] \OT1/cmtt/m/n/10 % (len(seq_record), len(seq_record.features), seq_record.annotations["source"]))[] Overfull \hbox (18.49072pt too wide) in paragraph at lines 482--482 []\OT1/cmtt/m/n/10 RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Ful l=Naringenin-chalcone synthase 3;[] [58] [59] Overfull \hbox (34.24059pt too wide) in paragraph at lines 609--609 []\OT1/cmtt/m/n/10 orchid_dict = SeqIO.to_dict(SeqIO.parse("ls_orchid.fasta", " fasta"), key_function=get_accession)[] [60] [61] Overfull \hbox (9.93459pt too wide) in paragraph at lines 769--774 \OT1/cmr/m/n/10 FTP site ([][]$\OT1/cmtt/m/n/10 ftp : / / ftp . uniprot . org / pub / databases / uniprot / current _ release / knowledgebase / complete / [62] Overfull \hbox (4.48064pt too wide) in paragraph at lines 812--815 []\OT1/cmr/m/n/10 As of Gen-Bank re-lease $210$, there are $38$ files mak-ing u p the vi-ral se-quences, \OT1/cmtt/m/n/10 gbvrl1.seq\OT1/cmr/m/n/10 , ..., \OT1 /cmtt/m/n/10 gbvrl38.seq\OT1/cmr/m/n/10 , [63] [64] [65] [66] [67] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1174--1174 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1184--1184 []\OT1/cmtt/m/n/10 >>> records = [rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1192--1192 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] [68] Overfull \hbox (13.24077pt too wide) in paragraph at lines 1203--1203 []\OT1/cmtt/m/n/10 >>> records = (rec.reverse_complement(id="rc_"+rec.id, descr iption = "reverse complement") \[] Overfull \hbox (19.46596pt too wide) in paragraph at lines 1240--1242 \OT1/cmr/m/n/10 Making a sin-gle call to [][]\OT1/cmtt/m/n/10 SeqIO.write(...) []\OT1/cmr/m/n/10 is also much quicker than mul-ti-ple calls to the [][]\OT1/cm tt/m/n/10 SeqRecord.format(...) [69] Overfull \hbox (21.32593pt too wide) in paragraph at lines 1284--1288 []\OT1/cmr/m/n/10 Likewise, when pars-ing FASTQ files, in-ter-nally [][]\OT1/cm tt/m/n/10 Bio.SeqIO.parse() []\OT1/cmr/m/n/10 calls the low-level [][]\OT1/cmtt /m/n/10 FastqGeneralIterator ) [70] (./Tutorial/chapter_align.tex Chapter 6. [71] [72] [73] [74] [75] [76] [77] [78] Overfull \hbox (5.54102pt too wide) in paragraph at lines 432--433 \OT1/cmr/m/n/10 ever you can't do that when your records come from a gen-er-a-t or/it-er-a-tor. There-fore the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() Overfull \hbox (39.68698pt too wide) in paragraph at lines 440--445 [][]\OT1/cmtt/m/n/10 Bio.AlignIO.parse() []\OT1/cmr/m/n/10 and then save them u s-ing the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write() []\OT1/cmr/m/n/10 -- or just use the [][]\OT1/cmtt/m/n/10 Bio.AlignIO.convert() [79] [80] [81] Overfull \hbox (16.49278pt too wide) in paragraph at lines 616--619 []\OT1/cmr/m/n/10 Internally the [][]\OT1/cmtt/m/n/10 format() []\OT1/cmr/m/n/1 0 method is us-ing the [][]\OT1/cmtt/m/n/10 StringIO []\OT1/cmr/m/n/10 string b ased han-dle and call-ing [][]\OT1/cmtt/m/n/10 Bio.AlignIO.write()[]\OT1/cmr/m/ n/10 . [82] [83] [84] [85] [86] [87] Overfull \hbox (8.40039pt too wide) in paragraph at lines 1053--1057 []\OT1/cmr/m/n/10 By de-fault MUS-CLE will out-put the align-ment as a FASTA fi le (us-ing gapped se-quences). The [][]\OT1/cmtt/m/n/10 Bio.AlignIO [88] [89] [90] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [91] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1360--1360 []\OT1/cmtt/m/n/10 needle -outfile=needle.txt -asequence=alpha.faa -bsequence=b eta.faa -gapopen=10 -gapextend=0.5[] [92] [93]) [94] (./Tutorial/chapter_blast.tex Chapter 7. [95] [96] [97] [98] [99] Overfull \hbox (55.2404pt too wide) in paragraph at lines 436--436 []\OT1/cmtt/m/n/10 sequence: >gb|AF283004.1|AF283004 Arabidopsis thaliana cold acclimation protein WCOR413-like protein[] [100] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [101] [102 <./images/BlastRecord.png>] [103 <./images/PSIBlastRecord.png>] [104] [105]) [106] (./Tutorial/chapter_searchio.tex Chapter 8. [107] Overfull \hbox (2.9019pt too wide) in paragraph at lines 94--102 [][][]\OT1/cmtt/m/n/10 HSPFragment[]\OT1/cmr/m/n/10 , to rep-re-sent a sin-gle con-tigu-ous align-ment be-tween query and hit se-quences. [][]\OT1/cmtt/m/n/10 HSPFragment Overfull \hbox (8.43927pt too wide) in paragraph at lines 114--116 [][][]\OT1/cmtt/m/n/10 parse []\OT1/cmr/m/n/10 is used for search out-put files with mul-ti-ple queries and re-turns a gen-er-a-tor that yields [][]\OT1/cmtt/ m/n/10 QueryResult [108] [109] [110] [111] [112] Overfull \hbox (44.7405pt too wide) in paragraph at lines 471--471 []\OT1/cmtt/m/n/10 ... hit.id = hit.id.split('|')[3] # renames 'gi|301171 322|ref|NR_035857.1|' to 'NR_035857.1'[] [113] [114] [115] [116] Overfull \hbox (469.98679pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='42291', name='aligned query sequence' , description='mystery_seq', dbxrefs=[])[] Overfull \hbox (769.23418pt too wide) in paragraph at lines 740--740 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] Overfull \hbox (27.24287pt too wide) in paragraph at lines 747--749 []\OT1/cmr/m/n/10 It should not sur-prise you now that the [][]\OT1/cmtt/m/n/10 HSP []\OT1/cmr/m/n/10 ob-ject has an [][]\OT1/cmtt/m/n/10 alignment []\OT1/cmr /m/n/10 prop-erty which is a [][]\OT1/cmtt/m/n/10 MultipleSeqAlignment [117] [118] Overfull \hbox (65.74031pt too wide) in paragraph at lines 879--879 []\OT1/cmtt/m/n/10 >>> blat_hsp2.hit_inter_ranges # start and end coordinates of intervening regions in the hit sequence[] [119] Overfull \hbox (769.23418pt too wide) in paragraph at lines 971--971 []\OT1/cmtt/m/n/10 SeqRecord(seq=Seq('CCCTCTACAGGGAAGCGCTTTCTGTTGTCTGAAAGAAAAGA AAGTGCTTCCTTT...GGG', DNAAlphabet()), id='gi|262205317|ref|NR_030195.1|', name= 'aligned hit sequence', description='Homo sapiens microRNA 520b (MIR520B), micr oRNA', dbxrefs=[])[] [120] Overfull \hbox (14.20721pt too wide) in paragraph at lines 1059--1063 \OT1/cmr/m/n/10 func-tion re-turns a gen-er-a-tor ob-ject that yields a [][]\OT 1/cmtt/m/n/10 QueryResult []\OT1/cmr/m/n/10 ob-ject in each it-er-a-tion. Like [][]\OT1/cmtt/m/n/10 Bio.SearchIO.read[]\OT1/cmr/m/n/10 , [121] Overfull \hbox (20.13245pt too wide) in paragraph at lines 1089--1094 []\OT1/cmr/m/n/10 In this case, the ideal choice would be to in-dex the file us -ing [][]\OT1/cmtt/m/n/10 Bio.SearchIO.index []\OT1/cmr/m/n/10 or [][]\OT1/cmtt /m/n/10 Bio.SearchIO.index_db[]\OT1/cmr/m/n/10 . Overfull \hbox (13.24077pt too wide) in paragraph at lines 1132--1132 []\OT1/cmtt/m/n/10 >>> idx = SearchIO.index('tab_2226_tblastn_001.txt', 'blast- tab', key_function=key_function)[] [122] Overfull \hbox (11.82602pt too wide) in paragraph at lines 1169--1172 []\OT1/cmr/m/n/10 Finally, [][]\OT1/cmtt/m/n/10 Bio.SearchIO []\OT1/cmr/m/n/10 also pro-vides a [][]\OT1/cmtt/m/n/10 convert []\OT1/cmr/m/n/10 func-tion, whic h is sim-ply a short-cut for [][]\OT1/cmtt/m/n/10 Bio.SearchIO.parse ) [123] (./Tutorial/chapter_entrez.tex Chapter 9. [124] [125] [126] [127] Overfull \hbox (70.99026pt too wide) in paragraph at lines 215--215 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae[Orgn] AND matK[Gene]", idtype="acc")[] [128] [129] [130] [131] Overfull \hbox (13.24077pt too wide) in paragraph at lines 440--440 [] \OT1/cmtt/m/n/10 net_handle = Entrez.efetch(db="nucleotide", id="EU490707 ", rettype="gb", retmode="text")[] [132] [133] [134] [135] Overfull \hbox (312.48816pt too wide) in paragraph at lines 646--646 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in X ML format.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 667--667 []\OT1/cmtt/m/n/10 [] Overfull \hbox (370.23766pt too wide) in paragraph at lines 674--674 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input da ta are not corrupted.[] Overfull \hbox (244.23875pt too wide) in paragraph at lines 705--705 []\OT1/cmtt/m/n/10 [] [136] Overfull \hbox (585.48578pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10 Bio.Entrez.Parser.ValidationError: Failed to find tag 'Docsu mList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.[] [137] [138] [139] Overfull \hbox (133.98972pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 EXPRESS bone| connective tissue| intestine| liver| live r tumor| normal| soft tissue/muscle tissue tumor| adult[] [140] Overfull \hbox (102.48999pt too wide) in paragraph at lines 939--939 []\OT1/cmtt/m/n/10 SEQUENCE ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:47225 96; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214[] Overfull \hbox (160.23949pt too wide) in paragraph at lines 961--961 []\OT1/cmtt/m/n/10 ['bone', 'connective tissue', 'intestine', 'liver', 'liver t umor', 'normal', 'soft tissue/muscle tissue tumor', 'adult'][] [141] [142] [143] Overfull \hbox (23.74068pt too wide) in paragraph at lines 1119--1119 []\OT1/cmtt/m/n/10 >>> handle = Entrez.esearch(db="nucleotide", term="Cypripedi oideae", retmax=814, idtype="acc")[] [144] [145] [146] [147] [148] [149]) [150] (./Tutorial/chapter_uniprot.tex Chapter 10. Overfull \hbox (1.49112pt too wide) in paragraph at lines 28--28 []\OT1/cmtt/m/n/10 >>> handle = urllib.urlopen("http://www.somelocation.org/da ta/someswissprotfile.dat")[] [151] Overfull \hbox (28.99063pt too wide) in paragraph at lines 61--61 []\OT1/cmtt/m/n/10 'RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Fu ll=Naringenin-chalcone synthase 3;'[] [152] [153] [154] [155] [156] Overfull \hbox (24.29903pt too wide) in paragraph at lines 350--351 []\OT1/cmr/m/n/10 If the ac-ces-sion num-ber you pro-vided to [][]\OT1/cmtt/m/n /10 ExPASy.get_sprot_raw []\OT1/cmr/m/n/10 does not ex-ist, then [][]\OT1/cmtt/ m/n/10 SwissProt.read(handle) [157] Overfull \hbox (65.93893pt too wide) in paragraph at lines 415--416 []\OT1/cmr/m/n/10 The same func-tion can be used to re-trieve a Prosite doc-u-m en-ta-tion record and parse it into a [][]\OT1/cmtt/m/n/10 Bio.ExPASy.Prodoc.Re cord [158] Overfull \hbox (133.98972pt too wide) in paragraph at lines 499--499 []\OT1/cmtt/m/n/10 {'signature_ac': u'PS50948', 'level': u'0', 'stop': 98, 'seq uence_ac': u'USERSEQ1', 'start': 16, 'score': u'8.873'}[] [159]) [160] (./Tutorial/chapter_pdb.tex Chapter 11. [161] [162] Overfull \hbox (13.022pt too wide) in paragraph at lines 176--178 \OT1/cmr/m/n/10 The over-all lay-out of a \OT1/cmtt/m/n/10 Structure \OT1/cmr/m /n/10 ob-ject fol-lows the so-called SM-CRA (Struc-ture/-Mod-el/Chain/Residue/A tom) [163] Excluding 'htmlonly' comment. [164 <./images/smcra.png (PNG copy)>] [165] [166] [167] [168] [169] [170] [171] [172] [173] LaTeX Warning: Command \r invalid in math mode on input line 883. [174] [175] [176] [177] [178]) [179] (./Tutorial/chapter_popgen.tex Chapter 12. [180]) [181] (./Tutorial/chapter_phylo.tex Chapter 13. [182] Excluding 'htmlonly' comment. [183] Overfull \hbox (25.13162pt too wide) in paragraph at lines 175--178 []\OT1/cmr/m/n/10 Let's tar-get the most re-cent com-mon an-ces-tor (MRCA) of t he nodes named ``E'' and ``F''. The [][]\OT1/cmtt/m/n/10 common_ancestor [184 <./images/phylo-simple-draw.png>] Excluding 'htmlonly' comment. [185 <./im ages/phylo-color-draw.png>] [186] Overfull \hbox (406.98734pt too wide) in paragraph at lines 326--326 []\OT1/cmtt/m/n/10 Phylogeny(description='phyloXML allows to use either a "bran ch_length" attribute...', name='example from Prof. Joe Felsenstein's book "Infe rring Phyl...', rooted=True)[] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [187] [188 <./images/phylo-draw-example.png> <./i mages/phylo-dot.png>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [189 <./images/phylo-rooted.png> <./images/phylo- color.png>] [190 <./images/phylo-apaf.png> <./images/phylo-apaf-zoom.png>] Overfull \hbox (19.85507pt too wide) in paragraph at lines 557--564 \OT1/cmr/m/n/10 For ex-am-ple, in a tree with clade names Foo1, Foo2 and Foo3, [][]\OT1/cmtt/m/n/10 tree.find_clades({"name": "Foo1"}) [191] Overfull \hbox (13.48741pt too wide) in paragraph at lines 612--615 []\OT1/cmr/m/n/10 Find each clade con-tain-ing a match-ing el-e-ment. That is, find each el-e-ment as with [][]\OT1/cmtt/m/n/10 find_elements[]\OT1/cmr/m/n/10 , [192] [193] [194] [195]) [196] (./Tutorial/chapter_motifs.tex Chapter 14. [197] [198] [199] [200] Overfull \hbox (128.73976pt too wide) in paragraph at lines 270--270 []\OT1/cmtt/m/n/10 [Seq('CACGTG', IUPACUnambiguousDNA()), Seq('CACGTG', IUPACUn ambiguousDNA()), Seq('CACGTG', IUPACUnambiguousDNA())][] [201] [202] [203] [204] [205] [206] Overfull \hbox (13.10551pt too wide) in paragraph at lines 582--586 \OT1/cmr/m/n/10 The [][]\OT1/cmtt/m/n/10 motifs.parse []\OT1/cmr/m/n/10 com-man d reads the com-plete file di-rectly, so you can close the file af-ter call-ing [][]\OT1/cmtt/m/n/10 motifs.parse[]\OT1/cmr/m/n/10 . [207] [208] [209] LaTeX Warning: `h' float specifier changed to `ht'. [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221]) [222] (./Tutorial/chapter_cluster.tex Chapter 15. [223] [224] [225] [226] [227] Overfull \hbox (78.60634pt too wide) in paragraph at lines 233--234 \OT1/cmr/m/n/10 men-sions of these ar-rays are $[]$ if [][]\OT1/cmtt/m/n/10 tra nspose []\OT1/cmr/m/n/10 is [][]\OT1/cmtt/m/n/10 0[]\OT1/cmr/m/n/10 , or $[]$ [228] [229] [230] [231] [232] Overfull \hbox (16.73593pt too wide) in paragraph at lines 415--416 [][]\OT1/cmtt/m/n/10 distance []\OT1/cmr/m/n/10 is the dis-tance be-tween them. The items be-ing clus-tered are num-bered from 0 to $[]$, [233] [234] [235] [236] [237] Overfull \hbox (106.77225pt too wide) in paragraph at lines 638--640 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [238] Overfull \hbox (25.39864pt too wide) in paragraph at lines 722--733 [] [239] [240] [241] [242] Overfull \hbox (106.77225pt too wide) in paragraph at lines 911--913 \OT1/cmr/m/n/10 An ar-ray with di-men-sions $[]$ if rows are be-ing clus-tered, or $[]$ [243] Overfull \hbox (26.21434pt too wide) in paragraph at lines 965--966 []\OT1/cmr/m/n/10 This will cre-ate the files [][]\OT1/cmtt/m/n/10 cyano_result _K_G2_A2.cdt[]\OT1/cmr/m/n/10 , [][]\OT1/cmtt/m/n/10 cyano_result_K_G2.kgg[]\OT 1/cmr/m/n/10 , and [][]\OT1/cmtt/m/n/10 cyano_result_K_A2.kag[]\OT1/cmr/m/n/10 . [244]) [245] (./Tutorial/chapter_learning.tex Chapter 16. [246] [247] [248] [249] [250] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 278. [251] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 286. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 298. [252] [253]) [254] (./Tutorial/chapter_graphics.tex Chapter 17. [255] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [256] [257 <./images/plasmid_linear.png (PNG copy)> <./images/plasmid_circular.png (P NG copy)>] [258] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [259] [260 <./images/GD_sigil_labels.png (PNG copy)>] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [261] [262 <./images/GD_sigils.png>] [263 <./imag es/GD_sigil_arrow_shafts.png>] Excluding 'htmlonly' comment. [264 <./images/GD_ sigil_arrow_heads.png>] [265] Excluding 'htmlonly' comment. [266 <./images/plas mid_linear_nice.png (PNG copy)>] [267 <./images/plasmid_circular_nice.png>] Overfull \hbox (2.74086pt too wide) in paragraph at lines 605--605 []\OT1/cmtt/m/n/10 A_colors = [red]*5 + [grey]*7 + [orange]*2 + [grey]*2 + [ora nge] + [grey]*11 + [green]*4 \[] [268] Excluding 'htmlonly' comment. [269 <./images/three_track_simple.png>] [270] Overfull \hbox (28.99063pt too wide) in paragraph at lines 782--782 [] \OT1/cmtt/m/n/10 color = colors.linearlyInterpolatedColor(colors.whit e, colors.firebrick, 0, 100, score)[] Overfull \hbox (2.65141pt too wide) in paragraph at lines 784--790 []\OT1/cmr/m/n/10 There are sev-eral im-por-tant pieces to this code. First the [][]\OT1/cmtt/m/n/10 GenomeDiagram []\OT1/cmr/m/n/10 ob-ject has a [][]\OT1/cm tt/m/n/10 cross_track_links Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [271] [272 <./image s/three_track_cl.png>] [273 <./images/three_track_cl2a.png>] [274] [275 <./imag es/simple_chrom.pdf> <./images/tRNA_chrom.pdf>] [276] Excluding 'htmlonly' comment. [277] Excluding 'htmlonly' comment.) [278] (./Tutorial/chapter_kegg.tex Chapter 18. [279] [280]) [281] (./Tutorial/chapter_phenotype.tex Chapter 19. [282] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['A12']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['B01'], WellReco rd['C01'], ..., WellRecord['H01']')[] Overfull \hbox (48.7407pt too wide) in paragraph at lines 102--102 []\OT1/cmtt/m/n/10 PlateRecord('WellRecord['A01'], WellRecord['A02'], WellReco rd['A03'], ..., WellRecord['C03']')[] [283] [284] [285]) [286] (./Tutorial/chapter_cookbook.tex Chapter 20. [287] [288] [289] [290] [291] [292] Overfull \hbox (5.83499pt too wide) in paragraph at lines 426--430 \OT1/cmr/m/n/10 mat (e.g. FASTA files). How-ever, for large FASTQ files it woul d be faster the low-level [][]\OT1/cmtt/m/n/10 FastqGeneralIterator Overfull \hbox (4.57849pt too wide) in paragraph at lines 444--446 \OT1/cmr/m/n/10 That should find $13819$ reads from \OT1/cmtt/m/n/10 SRR014849. fastq \OT1/cmr/m/n/10 and save them to a new FASTQ file, \OT1/cmtt/m/n/10 with[ ]primer.fastq\OT1/cmr/m/n/10 . [293] [294] [295] [296] Overfull \hbox (7.99081pt too wide) in paragraph at lines 765--765 []\OT1/cmtt/m/n/10 Seq('GTCCCAGTATTCGGATTTGTCTGCCAAAACAATGAAATTGACACAGTTTACAAC. ..CCG', SingleLetterAlphabet())[] [297] [298] [299] [300] Excluding 'htmlonly' comment. Overfull \hbox (4.00363pt too wide) in paragraph at lines 1057--1060 []\OT1/cmr/m/it/10 Tip: \OT1/cmr/m/n/10 Rather than us-ing [][]\OT1/cmtt/m/n/10 pylab.show() []\OT1/cmr/m/n/10 to show the plot in a win-dow, you can also use [][]\OT1/cmtt/m/n/10 pylab.savefig(...) [301] Excluding 'htmlonly' comment. Excluding 'htmlonly' comment. [302 <./image s/hist_plot.png>] [303 <./images/gc_plot.png>] Excluding 'htmlonly' comment. [304 <./images/dot_plot.png>] Excluding 'htmlonly' comment. [305] Excluding 'htmlonly' comment. [306 <./images/dot_plot_scatter.png>] [307 <./ima ges/SRR001666.png>] [308] Overfull \hbox (49.0755pt too wide) in paragraph at lines 1460--1461 []\OT1/cmr/m/n/10 You can ac-cess any el-e-ment of the PSSM by sub-script-ing l ike [][]\OT1/cmtt/m/n/10 your_pssm[sequence_number][residue_count_name][]\OT1/c mr/m/n/10 . [309] [310] [311] [312]) [313] (./Tutorial/chapter_testing.tex Chapter 21. [314] [315] [316] [317] [318] [319] [320] (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmr.fd)) [321] (./Tutorial/chapter_advanced.tex Chapter 22. [322] [323] Overfull \hbox (30.74179pt too wide) in paragraph at lines 198--199 [][][]\OT1/cmtt/m/n/10 factor[]\OT1/cmr/m/n/10 : fac-tor used to mul-ti-ply the log-odds val-ues. Each en-try is gen-er-ated by log(LOM[key])*factor [324] [325]) [326] (./Tutorial/chapter_contributing.tex Chapter 23. [327] [328]) [329] (./Tutorial/chapter_appendix.tex Chapter 24. [330]) [331] Underfull \hbox (badness 2005) in paragraph at lines 194--196 []\OT1/cmr/m/n/10 Ian K. Toth, Leighton Pritchard, Paul R. J. Birch: ``Com-par- a-tive ge-nomics re-veals what Underfull \hbox (badness 3758) in paragraph at lines 216--217 []\OT1/cmr/m/n/10 Douglas R. Cavener: ``Com-par-i-son of the con-sen-sus se-que nce flank-ing trans-la-tional start Underfull \hbox (badness 3838) in paragraph at lines 216--217 \OT1/cmr/m/n/10 sites in Drosophila and ver-te-brates.'' \OT1/cmr/m/it/10 Nu-cl eic Acids Re-search \OT1/cmr/bx/n/10 15 \OT1/cmr/m/n/10 (4): 1353--1361 (1987). [332] [333] [334] (./Tutorial.aux (./Tutorial/chapter_introduction.aux) (./Tutorial/chapter_quick_start.aux) (./Tutorial/chapter_seq_objects.aux) (./Tutorial/chapter_seq_annot.aux) (./Tutorial/chapter_seqio.aux) (./Tutorial/chapter_align.aux) (./Tutorial/chapter_blast.aux) (./Tutorial/chapter_searchio.aux) (./Tutorial/chapter_entrez.aux) (./Tutorial/chapter_uniprot.aux) (./Tutorial/chapter_pdb.aux) (./Tutorial/chapter_popgen.aux) (./Tutorial/chapter_phylo.aux) (./Tutorial/chapter_motifs.aux) (./Tutorial/chapter_cluster.aux) (./Tutorial/chapter_learning.aux) (./Tutorial/chapter_graphics.aux) (./Tutorial/chapter_kegg.aux) (./Tutorial/chapter_phenotype.aux) (./Tutorial/chapter_cookbook.aux) (./Tutorial/chapter_testing.aux) (./Tutorial/chapter_advanced.aux) (./Tutorial/chapter_contributing.aux) (./Tutorial/chapter_appendix.aux)) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb> Output written on Tutorial.pdf (335 pages, 2475391 bytes). Transcript written on Tutorial.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pbk.fd) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: a4paper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(89.62709pt, 418.25368pt, 89.6271pt) * v-part:(T,H,B)=(56.9055pt, 731.23584pt, 56.9055pt) * \paperwidth=597.50787pt * \paperheight=845.04684pt * \textwidth=418.25368pt * \textheight=731.23584pt * \oddsidemargin=17.3571pt * \evensidemargin=17.3571pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=10.0pt * \footskip=30.0pt * \marginparwidth=65.0pt * \marginparsep=11.0pt * \columnsep=10.0pt * \skip\footins=9.0pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (40.90678pt too wide) in paragraph at lines 112--119 []\T1/pbk/l/n/10 However, the [][]\T1/pcr/m/n/10 Bio.PDB.mmCIF.MMCIFlex []\T1/p bk/l/n/10 mod-ule (used in-ter-nally by [][]\T1/pcr/m/n/10 Bio.PDB.MMCIFParser [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omspbk.fd) [2] Overfull \hbox (21.75009pt too wide) in paragraph at lines 257--262 \T1/pbk/l/n/10 file to their val-ues. If there are mul-ti-ple val-ues (like in the case of tag \T1/pcr/m/n/10 _atom_site.Cartn_y\T1/pbk/l/n/10 , [3] Overfull \hbox (13.9754pt too wide) in paragraph at lines 298--303 \T1/pbk/l/n/10 The avail-able keys are \T1/pcr/m/n/10 name, head, deposition_-d ate, release_-date, structure_- Overfull \hbox (11.71707pt too wide) in paragraph at lines 298--303 \T1/pcr/m/n/10 method, resolution, structure_-reference \T1/pbk/l/n/10 (maps to a list of ref-er-ences), \T1/pcr/m/n/10 journal_- LaTeX Warning: Reference `sub:The-Structure-object' on page 4 undefined on inpu t line 320. [4] [5] LaTeX Warning: Reference `cap:SMCRA' on page 6 undefined on input line 527. [6] [7 <./images/smcra.png (PNG copy)>] [8] LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 729. LaTeX Warning: Reference `cap:SMCRA' on page 9 undefined on input line 758. LaTeX Warning: Reference `sub:Analysis' on page 9 undefined on input line 800. [9] LaTeX Warning: Reference `sub:Analysis' on page 10 undefined on input line 805. [10] Overfull \hbox (45.08351pt too wide) in paragraph at lines 960--964 \T1/pbk/l/n/10 Note that in the above case only model 0 of the struc-ture is co n-sid-ered by \T1/pcr/m/n/10 PolypeptideBuilder\T1/pbk/l/n/10 . Overfull \hbox (10.80998pt too wide) in paragraph at lines 968--973 \T1/pbk/l/n/10 try). The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide LaTeX Warning: Reference `cap:DSSP-codes' on page 11 undefined on input line 99 0. [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1097--1098 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1118--1123 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1280--1288 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) Package rerunfilecheck Warning: File `biopdb_faq.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 162757 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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The se-quence of each polypep-tide can then eas-ily be ob- tained from the \T1/pcr/m/n/10 Polypeptide [11] Overfull \hbox (87.74638pt too wide) in paragraph at lines 1097--1098 []\T1/pcr/m/n/10 # Calculate classical coordination number exp_fs=hse.calc_fs_e xposure(model) [12] Overfull \hbox (20.6135pt too wide) in paragraph at lines 1118--1123 \T1/pcr/m/n/10 Atom \T1/pbk/l/n/10 ob-jects re-turn a \T1/pcr/m/n/10 Vector \T1 /pbk/l/n/10 ob-ject rep-re-sen-ta-tion of the co-or-di-nates with the \T1/pcr/m /n/10 get_vector [13] [14] Overfull \hbox (1.21811pt too wide) in paragraph at lines 1280--1288 []\T1/pbk/l/n/10 THE CON-TRIB-U-TORS AND COPY-RIGHT HOLD-ERS OF THIS SOFT-WARE DIS-CLAIM [15] (./biopdb_faq.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on biopdb_faq.pdf (15 pages, 164421 bytes). Transcript written on biopdb_faq.log. pdflatex biopdb_faq.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./biopdb_faq.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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Transcript written on biopdb_faq.log. make -C install make[3]: Entering directory '/<>/python-biopython-1.70+dfsg/Doc/install' pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] LaTeX Warning: Reference `sec:is_working' on page 7 undefined on input line 460 . [7] LaTeX Warning: Reference `sec:unix_install' on page 8 undefined on input line 5 37. Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . LaTeX Warning: Reference `sec:is_working' on page 8 undefined on input line 558 . Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' [8] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) Package rerunfilecheck Warning: File `Installation.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 144363 bytes). Transcript written on Installation.log. pdflatex Installation.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Installation.tex LaTeX2e <2017-04-15> Babel <3.15> and hyphenation patterns for 3 language(s) loaded. 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[8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150116 bytes). 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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/preprint/fullpage.sty) (/usr/share/texmf/tex/latex/misc/hevea.sty (/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty Excluding comment 'comment') Excluding comment 'rawhtml' Excluding comment 'htmlonly') (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. 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(./Installation.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Installation.out) (./Installation.out) (./Installation.toc) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] [7] Overfull \hbox (9.0224pt too wide) in paragraph at lines 540--541 []\OT1/cmr/m/n/10 For Python 2.6 we cur-rently use Mi-crosoft's free VC++ 2008 Ex-press Edi-tion from [][]$\OT1/cmtt/m/n/10 http : / / www . microsoft . [8] Overfull \hbox (27.57379pt too wide) in paragraph at lines 563--565 [][]\OT1/cmtt/m/n/10 PYTHONPATH []\OT1/cmr/m/n/10 with some-thing like [][]\OT1 /cmtt/m/n/10 export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopytho n' (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (9.6602pt too wide) in paragraph at lines 600--601 []\OT1/cmr/m/n/10 NCBI Stan-dalone BLAST, which can used with the [][]\OT1/cmtt /m/n/10 Bio.Blast []\OT1/cmr/m/n/10 mod-ule and parsed with the [][]\OT1/cmtt/m /n/10 Bio.SearchIO [9] [10] (./Installation.aux) ) (see the transcript file for additional information) Output written on Installation.pdf (10 pages, 150261 bytes). Transcript written on Installation.log. hevea -fix Installation.tex Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:108: Warning: Undefined label: 'sec:windows_install' ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:460: Warning: Undefined label: 'sec:is_working' ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:537: Warning: Undefined label: 'sec:unix_install' ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:558: Warning: Undefined label: 'sec:is_working' ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:67: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:114: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:140: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:218: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:230: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:255: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:314: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:317: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:387: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:400: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:406: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:413: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:419: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:421: Warning: Suppressing nested a element ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:456: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:467: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:497: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:516: Warning: Suppressing nested a element ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:540: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:548: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:556: Warning: Suppressing nested a element ./Installation.tex:561: Warning: '_' occurring outside math mode ./Installation.tex:609: Warning: Suppressing nested a element ./Installation.tex:609: Warning: Suppressing nested a element Fixpoint reached in 2 step(s) hevea -fix -text Installation.tex Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode HeVeA Warning: Label(s) may have changed. Rerun me to get cross-references right. Run, run, again... Exclude comment 'comment' ./Installation.tex:55: Warning: tt_mode is an empty style ./Installation.tex:61: Warning: No date given ./Installation.tex:430: Warning: '_' occurring outside math mode ./Installation.tex:535: Warning: '_' occurring outside math mode ./Installation.tex:561: Warning: '_' occurring outside math mode Fixpoint reached in 2 step(s) make[3]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc/install' make[2]: Leaving directory '/<>/python-biopython-1.70+dfsg/Doc' make[1]: Leaving directory '/<>/python-biopython-1.70+dfsg' rm -f debian/python-biopython.debhelper.log debian/python3-biopython.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>/python-biopython-1.70+dfsg' mkdir -p Tests_avoid for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool BWA_tool raxml_tool BioSQL_MySQLdb BioSQL_psycopg2 phyml_tool samtools_tool \ ; do \ mv Tests/test_${avoid}.py Tests_avoid ; \ done mv: cannot stat 'Tests/test_PopGen_DFDist.py': No such file or directory mv: cannot stat 'Tests/test_PopGen_FDist.py': No such file or directory mv: cannot stat 'Tests/test_PopGen_SimCoal.py': No such file or directory # For the doc package we need a clean testsuite without all the remaining files. So keep a clean copy here mkdir -p debian/tmp_tests cp -a Tests debian/tmp_tests # remove duplicated file rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz # We also keep the tests we need to avoid for later inspection cp -a Tests_avoid debian/tmp_tests # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir # to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \ --test-args='set -e; \ mkdir -p {build_dir}/home; \ mkdir -p {build_dir}/Doc/examples; \ cp -a Doc/Tutorial.tex {build_dir}/Doc; \ cp -a Doc/Tutorial {build_dir}/Doc; \ cp -a Doc/examples {build_dir}/Doc; \ cp -a Tests {build_dir}; \ cd {build_dir}/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline' pybuild --test -i python{version} -p 2.7 --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" I: pybuild base:184: set -e; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/home; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \ cp -a Tests /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build; \ cd /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline test_Ace ... ok test_Affy ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Application ... ok test_BioSQL_MySQLdb_online ... skipping. internet not available test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) test_BioSQL_mysql_connector_online ... skipping. internet not available test_BioSQL_psycopg2_online ... skipping. internet not available test_BioSQL_sqlite3 ... ok test_BioSQL_sqlite3_online ... skipping. internet not available test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_CodonUsage ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_DocSQL ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GACrossover ... ok test_GAMutation ... ok test_GAOrganism ... ok test_GAQueens ... ok test_GARepair ... ok test_GASelection ... ok test_GenBank ... ok test_GenBank_unittest ... ok test_GenomeDiagram ... x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! ok test_GraphicsBitmaps ... ok test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_Location ... ok test_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... ok test_NCBI_qblast ... skipping. internet not available test_NNExclusiveOr ... ok test_NNGene ... ok test_NNGeneral ... ok test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDBList ... skipping. internet not available test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFParser ... ok test_PDB_Polypetide ... ok test_PDB_StructureAlignment ... /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. PDBConstructionWarning) /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. PDBConstructionWarning) ok test_PDB_Superimposer ... ok test_ParserSupport ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_matplotlib ... ok test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo test_PopGen_GenePop_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... ok test_RCSBFormats ... ok test_Restriction ... skipping. Under Python 2 this test needs the unittest2 library test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqFeature ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Insdc ... ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... ok test_UniGene ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... ok test_geo ... ok test_kNN ... ok test_lowess ... ok test_mmtf ... skipping. Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_mmtf_online ... skipping. Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_phenotype ... ok test_phenotype_fit ... ok test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_seq ... skipping. Under Python 2 this test needs the unittest2 library test_translate ... ok test_trie ... ok Bio.Align docstring test ... ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Dialign docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Application docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonalphabet docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.GenBank docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.Seq docstring test ... /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Seq.py:349: BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead of my_seq.tostring(). BiopythonDeprecationWarning) ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.SwissProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.psw docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SVDSuperimposer docstring test ... ok ---------------------------------------------------------------------- Ran 261 tests in 847.916 seconds Skipping any tests requiring internet access Python version: 2.7.14+ (default, Dec 5 2017, 15:17:02) [GCC 7.2.1 20171205] Operating system: posix linux2 pybuild --test -i python{version} -p 3.6 --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" I: pybuild base:184: set -e; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/home; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Tests /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build; \ cd /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/home python3.6 run_tests.py --offline x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! x_order_2: colinear and horizontally aligned! test_Ace ... ok test_Affy ... ok test_AlignIO ... ok test_AlignIO_ClustalIO ... ok test_AlignIO_EmbossIO ... ok test_AlignIO_FastaIO ... ok test_AlignIO_MauveIO ... ok test_AlignIO_PhylipIO ... ok test_AlignIO_convert ... ok test_AlignInfo ... ok test_Application ... ok test_BioSQL_MySQLdb_online ... skipping. internet not available test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) test_BioSQL_mysql_connector_online ... skipping. internet not available test_BioSQL_psycopg2_online ... skipping. internet not available test_BioSQL_sqlite3 ... ok test_BioSQL_sqlite3_online ... skipping. internet not available test_CAPS ... ok test_CelFile ... ok test_Chi2 ... ok test_ClustalOmega_tool ... ok test_Clustalw_tool ... ok test_Cluster ... ok test_CodonTable ... ok test_CodonUsage ... ok test_ColorSpiral ... ok test_Compass ... ok test_Consensus ... ok test_Crystal ... ok test_DSSP_tool ... ok test_Dialign_tool ... ok test_DocSQL ... ok test_EMBL_unittest ... ok test_Emboss ... ok test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... skipping. internet not available test_Entrez_parser ... ok test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_FSSP ... ok test_Fasttree_tool ... ok test_File ... ok test_GACrossover ... ok test_GAMutation ... ok test_GAOrganism ... ok test_GAQueens ... ok test_GARepair ... ok test_GASelection ... ok test_GenBank ... ok test_GenBank_unittest ... ok test_GenomeDiagram ... ok test_GraphicsBitmaps ... ok test_GraphicsChromosome ... ok test_GraphicsDistribution ... ok test_GraphicsGeneral ... ok test_HMMCasino ... ok test_HMMGeneral ... ok test_KDTree ... ok test_KEGG ... ok test_KEGG_online ... skipping. internet not available test_KGML_graphics ... ok test_KGML_graphics_online ... skipping. internet not available test_KGML_nographics ... ok test_KeyWList ... ok test_Location ... ok test_LogisticRegression ... ok test_MafIO_index ... ok test_Mafft_tool ... ok test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... ok test_NCBITextParser ... ok test_NCBIXML ... ok test_NCBI_BLAST_tools ... ok test_NCBI_qblast ... skipping. internet not available test_NNExclusiveOr ... ok test_NNGene ... ok test_NNGeneral ... ok test_NaiveBayes ... ok test_Nexus ... ok test_PAML_baseml ... ok test_PAML_codeml ... ok test_PAML_yn00 ... ok test_PDB ... ok test_PDBList ... skipping. internet not available test_PDB_FragmentMapper ... ok test_PDB_KDTree ... ok test_PDB_MMCIF2Dict ... ok test_PDB_MMCIFParser ... ok test_PDB_Polypetide ... ok test_PDB_StructureAlignment ... /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298. PDBConstructionWarning) /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344. PDBConstructionWarning) ok test_PDB_Superimposer ... ok test_ParserSupport ... ok test_Pathway ... ok test_Phd ... ok test_Phylo ... ok test_PhyloXML ... ok test_Phylo_CDAO ... ok test_Phylo_NeXML ... ok test_Phylo_matplotlib ... ok test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo test_PopGen_GenePop_nodepend ... ok test_Prank_tool ... ok test_Probcons_tool ... ok test_ProtParam ... ok test_QCPSuperimposer ... ok test_RCSBFormats ... ok test_Restriction ... ok test_SCOP_Astral ... ok test_SCOP_Cla ... ok test_SCOP_Des ... ok test_SCOP_Dom ... ok test_SCOP_Hie ... ok test_SCOP_Raf ... ok test_SCOP_Residues ... ok test_SCOP_Scop ... ok test_SCOP_online ... skipping. internet not available test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... ok test_SearchIO_blast_tab_index ... ok test_SearchIO_blast_text ... ok test_SearchIO_blast_xml ... ok test_SearchIO_blast_xml_index ... ok test_SearchIO_blat_psl ... ok test_SearchIO_blat_psl_index ... ok test_SearchIO_exonerate ... ok test_SearchIO_exonerate_text_index ... ok test_SearchIO_exonerate_vulgar_index ... ok test_SearchIO_fasta_m10 ... ok test_SearchIO_fasta_m10_index ... ok test_SearchIO_hmmer2_text ... ok test_SearchIO_hmmer2_text_index ... ok test_SearchIO_hmmer3_domtab ... ok test_SearchIO_hmmer3_domtab_index ... ok test_SearchIO_hmmer3_tab ... ok test_SearchIO_hmmer3_tab_index ... ok test_SearchIO_hmmer3_text ... ok test_SearchIO_hmmer3_text_index ... ok test_SearchIO_model ... ok test_SearchIO_write ... ok test_SeqFeature ... ok test_SeqIO ... ok test_SeqIO_AbiIO ... ok test_SeqIO_FastaIO ... ok test_SeqIO_Insdc ... /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Bio/GenBank/Scanner.py:287: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? BiopythonParserWarning) ok test_SeqIO_PdbIO ... ok test_SeqIO_QualityIO ... ok test_SeqIO_SeqXML ... ok test_SeqIO_convert ... ok test_SeqIO_features ... ok test_SeqIO_index ... ok test_SeqIO_online ... skipping. internet not available test_SeqIO_write ... ok test_SeqRecord ... ok test_SeqUtils ... ok test_Seq_objs ... ok test_SffIO ... ok test_SubsMat ... ok test_SwissProt ... ok test_TCoffee_tool ... ok test_TogoWS ... skipping. internet not available test_TreeConstruction ... ok test_Tutorial ... loading tests failed: Failed to import test module: test_Tutorial Traceback (most recent call last): File "/usr/lib/python3.6/unittest/loader.py", line 153, in loadTestsFromName module = __import__(module_name) File "/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Tests/test_Tutorial.py", line 76, in from lib2to3 import refactor ModuleNotFoundError: No module named 'lib2to3' test_UniGene ... ok test_Uniprot ... ok test_Wise ... ok test_align ... ok test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... ok test_geo ... ok test_kNN ... ok test_lowess ... ok test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) test_motifs ... ok test_motifs_online ... skipping. internet not available test_pairwise2 ... ok test_phenotype ... ok test_phenotype_fit ... ok test_prodoc ... ok test_prosite1 ... ok test_prosite2 ... ok test_psw ... ok test_seq ... ok test_translate ... ok test_trie ... ok Bio.Align docstring test ... ok Bio.Align.Applications._Clustalw docstring test ... ok Bio.Align.Applications._ClustalOmega docstring test ... ok Bio.Align.Applications._Dialign docstring test ... ok Bio.Align.Applications._MSAProbs docstring test ... ok Bio.Align.Applications._Mafft docstring test ... ok Bio.Align.Applications._Muscle docstring test ... ok Bio.Align.Applications._Probcons docstring test ... ok Bio.Align.Applications._Prank docstring test ... ok Bio.Align.Applications._TCoffee docstring test ... ok Bio.AlignIO docstring test ... ok Bio.AlignIO.StockholmIO docstring test ... ok Bio.Alphabet docstring test ... ok Bio.Application docstring test ... ok Bio.bgzf docstring test ... ok Bio.codonalign docstring test ... ok Bio.codonalign.codonalignment docstring test ... ok Bio.codonalign.codonalphabet docstring test ... ok Bio.codonalign.codonseq docstring test ... ok Bio.Blast.Applications docstring test ... ok Bio.Emboss.Applications docstring test ... ok Bio.GenBank docstring test ... ok Bio.Graphics.GenomeDiagram._Colors docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.motifs docstring test ... ok Bio.motifs.applications._xxmotif docstring test ... ok Bio.pairwise2 docstring test ... ok Bio.Phylo.Applications._Raxml docstring test ... ok Bio.Phylo.Consensus docstring test ... ok Bio.Phylo.BaseTree docstring test ... ok Bio.SearchIO docstring test ... ok Bio.SearchIO._model docstring test ... ok Bio.SearchIO._model.query docstring test ... ok Bio.SearchIO._model.hit docstring test ... ok Bio.SearchIO._model.hsp docstring test ... ok Bio.SearchIO.BlastIO docstring test ... ok Bio.SearchIO.HmmerIO docstring test ... ok Bio.SearchIO.FastaIO docstring test ... ok Bio.SearchIO.BlatIO docstring test ... ok Bio.SearchIO.ExonerateIO docstring test ... ok Bio.SeqIO docstring test ... ok Bio.SeqIO.AceIO docstring test ... ok Bio.SeqIO.FastaIO docstring test ... ok Bio.SeqIO.IgIO docstring test ... ok Bio.SeqIO.InsdcIO docstring test ... ok Bio.SeqIO.PhdIO docstring test ... ok Bio.SeqIO.PirIO docstring test ... ok Bio.SeqIO.QualityIO docstring test ... ok Bio.SeqIO.SffIO docstring test ... ok Bio.SeqIO.TabIO docstring test ... ok Bio.SeqFeature docstring test ... ok Bio.SeqRecord docstring test ... ok Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.Sequencing.Applications._Novoalign docstring test ... ok Bio.Sequencing.Applications._bwa docstring test ... ok Bio.Sequencing.Applications._samtools docstring test ... ok Bio.SwissProt docstring test ... ok Bio.UniProt.GOA docstring test ... ok Bio.Wise docstring test ... ok Bio.Wise.psw docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.MaxEntropy docstring test ... ok Bio.PDB.Polypeptide docstring test ... ok Bio.PDB.Selection docstring test ... ok Bio.SeqIO.PdbIO docstring test ... ok Bio.Statistics.lowess docstring test ... ok Bio.SVDSuperimposer docstring test ... ok ---------------------------------------------------------------------- Ran 260 tests in 927.901 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 3.6.4 (default, Dec 27 2017, 13:02:49) [GCC 7.2.0] Operating system: posix linux E: pybuild pybuild:283: test: plugin custom failed with: exit code=1: set -e; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/home; \ mkdir -p /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc/examples; \ cp -a Doc/Tutorial.tex /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Doc/Tutorial /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Doc/examples /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Doc; \ cp -a Tests /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build; \ cd /<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/Tests; \ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<>/python-biopython-1.70+dfsg/.pybuild/pythonX.Y_3.6/build/home python3.6 run_tests.py --offline dh_auto_test: pybuild --test -i python{version} -p 3.6 --test --system=custom "--test-args=set -e; \\\ mkdir -p {build_dir}/home; \\\ mkdir -p {build_dir}/Doc/examples; \\\ cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ cp -a Doc/Tutorial {build_dir}/Doc; \\\ cp -a Doc/examples {build_dir}/Doc; \\\ cp -a Tests {build_dir}; \\\ cd {build_dir}/Tests; \\\ env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline" returned exit code 13 debian/rules:96: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/python-biopython-1.70+dfsg' debian/rules:56: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20180110-2206 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 234468 Build-Time: 1982 Distribution: bionic Fail-Stage: build Host Architecture: arm64 Install-Time: 192 Job: python-biopython_1.70+dfsg-4.dsc Machine Architecture: arm64 Package: python-biopython Package-Time: 2178 Source-Version: 1.70+dfsg-4 Space: 234468 Status: attempted Version: 1.70+dfsg-4 -------------------------------------------------------------------------------- Finished at 20180110-2206 Build needed 00:36:18, 234468k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Scanning for processes to kill in build PACKAGEBUILD-14051892 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Stopping target for build PACKAGEBUILD-14051892 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-14051892 Removing build PACKAGEBUILD-14051892