RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-034 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:30:44 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_156 python-lpbuildd_156 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_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 22 Nov 22:44:43 ntpdate[1848]: adjust time server 10.211.37.1 offset 0.003185 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 /home/buildd/filecache-default/b70461af4419c13dbae7acd6fe74d075a1a9550f Creating target for build PACKAGEBUILD-13763564 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 Starting target for build PACKAGEBUILD-13763564 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-13763564 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 Updating target for build PACKAGEBUILD-13763564 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [1018 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [535 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [7996 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4859 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf Packages [40.7 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [23.2 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf Packages [125 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [84.0 kB] Fetched 15.1 MB in 8s (1844 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 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils binutils-arm-linux-gnueabihf 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 libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed4 libip4tc0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmount1 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libubsan0 libudev1 libuuid1 linux-libc-dev mount multiarch-support openssl perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 92 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 51.6 MB of archives. After this operation, 2878 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu bionic/main armhf base-files armhf 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf bsdutils armhf 1:2.30.2-0.1ubuntu1 [55.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf coreutils armhf 8.26-3ubuntu4 [1111 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf debianutils armhf 4.8.3 [84.7 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg armhf 1.19.0.4ubuntu1 [1100 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf libc6-dev armhf 2.26-0ubuntu2 [1900 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf libc-dev-bin armhf 2.26-0ubuntu2 [60.1 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf linux-libc-dev armhf 4.13.0-17.20 [943 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf libgomp1 armhf 7.2.0-16ubuntu1 [65.6 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7-base armhf 7.2.0-16ubuntu1 [18.6 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc1 armhf 1:7.2.0-16ubuntu1 [37.3 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libatomic1 armhf 7.2.0-16ubuntu1 [6308 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf libasan4 armhf 7.2.0-16ubuntu1 [327 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main armhf libubsan0 armhf 7.2.0-16ubuntu1 [108 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libcilkrts5 armhf 7.2.0-16ubuntu1 [36.0 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf cpp-7 armhf 7.2.0-16ubuntu1 [5287 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf libcc1-0 armhf 7.2.0-16ubuntu1 [32.3 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf g++-7 armhf 7.2.0-16ubuntu1 [6033 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7 armhf 7.2.0-16ubuntu1 [5921 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc-7-dev armhf 7.2.0-16ubuntu1 [707 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++-7-dev armhf 7.2.0-16ubuntu1 [1528 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++6 armhf 7.2.0-16ubuntu1 [350 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgmp10 armhf 2:6.1.2+dfsg-1.1 [182 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf libbinutils armhf 2.29.1-8ubuntu1 [307 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf binutils armhf 2.29.1-8ubuntu1 [3376 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-common armhf 2.29.1-8ubuntu1 [190 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-arm-linux-gnueabihf armhf 2.29.1-8ubuntu1 [2188 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf libc6 armhf 2.26-0ubuntu2 [2212 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf e2fslibs armhf 1.43.7-1 [145 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf e2fsprogs armhf 1.43.7-1 [477 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf findutils armhf 4.6.0+git+20170828-2 [277 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf perl-modules-5.26 all 5.26.1-2ubuntu1 [2760 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main armhf libperl5.26 armhf 5.26.1-2ubuntu1 [2878 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf perl armhf 5.26.1-2ubuntu1 [201 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main armhf perl-base armhf 5.26.1-2ubuntu1 [1289 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libuuid1 armhf 2.30.2-0.1ubuntu1 [14.5 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libblkid1 armhf 2.30.2-0.1ubuntu1 [106 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libsmartcols1 armhf 2.30.2-0.1ubuntu1 [68.7 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libfdisk1 armhf 2.30.2-0.1ubuntu1 [144 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre3 armhf 2:8.39-5ubuntu3 [209 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf libselinux1 armhf 2.7-2 [59.1 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libmount1 armhf 2.30.2-0.1ubuntu1 [116 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf fdisk armhf 2.30.2-0.1ubuntu1 [96.6 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf util-linux armhf 2.30.2-0.1ubuntu1 [823 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main armhf base-passwd armhf 3.5.44 [45.9 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main armhf libc-bin armhf 2.26-0ubuntu2 [477 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf sysvinit-utils armhf 2.88dsf-59.10ubuntu1 [17.2 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libudev1 armhf 235-3ubuntu2 [49.4 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libapt-pkg5.0 armhf 1.6~alpha5 [709 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main armhf libgpg-error0 armhf 1.27-5 [32.4 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libgcrypt20 armhf 1.8.1-4 [363 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf gpgv armhf 2.1.15-1ubuntu8 [157 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf libseccomp2 armhf 2.3.1-2.1ubuntu3 [29.9 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf apt armhf 1.6~alpha5 [1104 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf debconf all 1.5.65 [124 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libapparmor1 armhf 2.11.0-2ubuntu18 [24.6 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf libcap2 armhf 1:2.25-1.1 [11.9 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libip4tc0 armhf 1.6.1-2ubuntu2 [17.8 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf mount armhf 2.30.2-0.1ubuntu1 [104 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf systemd armhf 235-3ubuntu2 [2680 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libsystemd0 armhf 235-3ubuntu2 [179 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf systemd-sysv armhf 235-3ubuntu2 [13.1 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libcap-ng0 armhf 0.7.7-3.1 [9816 B] Get:64 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libcomerr2 armhf 1.43.7-1 [10.6 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage-common all 2.7-2 [6916 B] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage1 armhf 2.7-2 [72.3 kB] Get:67 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libss2 armhf 1.43.7-1 [9376 B] Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf libnettle6 armhf 3.3-2 [106 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf libhogweed4 armhf 3.3-2 [126 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf libp11-kit0 armhf 0.23.9-2 [162 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main armhf sensible-utils all 0.0.11 [14.8 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf pinentry-curses armhf 1.0.0-3 [30.4 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf libnpth0 armhf 1.5-3 [6632 B] Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg armhf 2.1.15-1ubuntu8 [711 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg-agent armhf 2.1.15-1ubuntu8 [211 kB] Get:76 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libsqlite3-0 armhf 3.21.0-1 [417 kB] Get:77 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libssl1.0.0 armhf 1.0.2g-1ubuntu14 [706 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf multiarch-support armhf 2.26-0ubuntu2 [6832 B] Get:79 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf openssl armhf 1.0.2g-1ubuntu14 [477 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf tzdata all 2017c-1 [188 kB] Get:81 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgssapi-krb5-2 armhf 1.15.2-2 [99.2 kB] Get:82 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkrb5-3 armhf 1.15.2-2 [231 kB] Get:83 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkrb5support0 armhf 1.15.2-2 [27.4 kB] Get:84 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libk5crypto3 armhf 1.15.2-2 [83.5 kB] Get:85 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu1 [8380 B] Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf libpng16-16 armhf 1.6.34-1 [159 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main armhf apt-transport-https all 1.6~alpha5 [1692 B] Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf build-essential armhf 12.4ubuntu1 [4752 B] Get:91 http://ftpmaster.internal/ubuntu bionic/main armhf libpsl5 armhf 0.19.1-3 [39.9 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl3-gnutls armhf 7.55.1-1ubuntu2.1 [167 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.6 MB in 5s (8696 kB/s) (Reading database ... 12457 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_armhf.deb ... Unpacking base-files (10ubuntu1) over (9.6ubuntu101) ... Setting up base-files (10ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12457 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.2-0.1ubuntu1_armhf.deb ... Unpacking bsdutils (1:2.30.2-0.1ubuntu1) over (1:2.30.1-0ubuntu4) ... Setting up bsdutils (1:2.30.2-0.1ubuntu1) ... (Reading database ... 12457 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_armhf.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12457 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13763564 armhf bionic-proposed -c chroot:build-PACKAGEBUILD-13763564 --arch=armhf --dist=bionic-proposed --nolog readseq_1-12.dsc Initiating build PACKAGEBUILD-13763564 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 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-034.buildd +==============================================================================+ | readseq 1-12 (armhf) 22 Nov 2017 22:46 | +==============================================================================+ Package: readseq Version: 1-12 Source Version: 1-12 Distribution: bionic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/readseq-Fr36D4/readseq-1' with '<>' I: NOTICE: Log filtering will replace 'build/readseq-Fr36D4' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13763564/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- readseq_1-12.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-KjIXYk/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-KjIXYk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KjIXYk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-KjIXYk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KjIXYk/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-KjIXYk/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (36.1 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 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libustr-1.0-1 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KjIXYk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (36.6 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12457 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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), ncbi-tools-dev Filtered Build-Depends: debhelper (>= 10), ncbi-tools-dev dpkg-deb: building package 'sbuild-build-depends-readseq-dummy' in '/<>/resolver-ed9cQ2/apt_archive/sbuild-build-depends-readseq-dummy.deb'. Ign:1 copy:/<>/resolver-ed9cQ2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-ed9cQ2/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-ed9cQ2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-ed9cQ2/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-ed9cQ2/apt_archive ./ Packages [533 B] Fetched 2866 B in 0s (37.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install readseq 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 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libustr-1.0-1 libwind0-heimdal Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libncbi6 libncbi6-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db ncbi-data po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs ncbi-tools-bin libltdl-dev libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libncbi6 libncbi6-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db ncbi-data po-debconf sbuild-build-depends-readseq-dummy 0 upgraded, 33 newly installed, 1 to remove and 0 not upgraded. Need to get 27.6 MB of archives. After this operation, 110 MB of additional disk space will be used. Get:1 copy:/<>/resolver-ed9cQ2/apt_archive ./ sbuild-build-depends-readseq-dummy 0.invalid.0 [864 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf groff-base armhf 1.22.3-9 [1013 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf libbsd0 armhf 0.8.6-3 [40.6 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf bsdmainutils armhf 9.0.14ubuntu1 [173 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf man-db armhf 2.7.6.1-3 [872 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf libmagic-mgc armhf 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main armhf libmagic1 armhf 1:5.32-1 [62.6 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf file armhf 1:5.32-1 [21.4 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-0 armhf 2.54.1-1ubuntu1 [1013 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf libicu60 armhf 60.1-1ubuntu2 [7798 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libxml2 armhf 2.9.4+dfsg1-5ubuntu2 [574 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf gettext-base armhf 0.19.8.1-4ubuntu1 [45.4 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main armhf libsigsegv2 armhf 2.11-1 [12.6 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf automake all 1:1.15.1-3ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf dh-autoreconf all 15 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf dh-strip-nondeterminism all 0.040-1 [5196 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf libcroco3 armhf 0.6.12-1 [69.7 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf gettext armhf 0.19.8.1-4ubuntu1 [1014 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf debhelper all 10.10.9ubuntu1 [871 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/universe armhf ncbi-data all 6.1.20170106-2 [3645 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/universe armhf libncbi6 armhf 6.1.20170106-2 [3259 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/universe armhf libncbi6-dev armhf 6.1.20170106-2 [4811 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.6 MB in 2s (13.1 MB/s) (Reading database ... 12457 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12448 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_armhf.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../01-libbsd0_0.8.6-3_armhf.deb ... Unpacking libbsd0:armhf (0.8.6-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.14ubuntu1_armhf.deb ... Unpacking bsdmainutils (9.0.14ubuntu1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-3_armhf.deb ... Unpacking man-db (2.7.6.1-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_armhf.deb ... 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Setting up libbsd0:armhf (0.8.6-3) ... Setting up libxml2:armhf (2.9.4+dfsg1-5ubuntu2) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:armhf (1:5.32-1) ... Setting up libcroco3:armhf (0.6.12-1) ... Setting up ncbi-data (6.1.20170106-2) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20161112.1+nmu1) ... 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 autopoint (0.19.8.1-4ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libncbi6:armhf (6.1.20170106-2) ... Setting up libncbi6-dev:armhf (6.1.20170106-2) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... 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 man-db (2.7.6.1-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (15) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up debhelper (10.10.9ubuntu1) ... Setting up sbuild-build-depends-readseq-dummy (0.invalid.0) ... (Reading database ... 14976 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-101-generic arm64 (armv7l) Toolchain package versions: binutils_2.29.1-8ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-16ubuntu1 gcc-7_7.2.0-16ubuntu1 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-16ubuntu1 libstdc++6_7.2.0-16ubuntu1 linux-libc-dev_4.13.0-17.20 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.6~alpha5 apt-transport-https_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1+nmu1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.1-8ubuntu1 binutils-arm-linux-gnueabihf_2.29.1-8ubuntu1 binutils-common_2.29.1-8ubuntu1 bsdmainutils_9.0.14ubuntu1 bsdutils_1:2.30.2-0.1ubuntu1 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3ubuntu4 cpp_4:7.2.0-1ubuntu1 cpp-7_7.2.0-16ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.65 debhelper_10.10.9ubuntu1 debianutils_4.8.3 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.19.0.4ubuntu1 dpkg-dev_1.19.0.4ubuntu1 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.2-0.1ubuntu1 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1ubuntu1 g++-7_7.2.0-16ubuntu1 gcc_4:7.2.0-1ubuntu1 gcc-7_7.2.0-16ubuntu1 gcc-7-base_7.2.0-16ubuntu1 gettext_0.19.8.1-4ubuntu1 gettext-base_0.19.8.1-4ubuntu1 gnupg_2.1.15-1ubuntu8 gnupg-agent_2.1.15-1ubuntu8 gpgv_2.1.15-1ubuntu8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49ubuntu1 init-system-helpers_1.49ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu18 libapt-pkg5.0_1.6~alpha5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-16ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-16ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libbinutils_2.29.1-8ubuntu1 libblkid1_2.30.2-0.1ubuntu1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-0ubuntu2 libc-dev-bin_2.26-0ubuntu2 libc6_2.26-0ubuntu2 libc6-dev_2.26-0ubuntu2 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-16ubuntu1 libcilkrts5_7.2.0-16ubuntu1 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3-gnutls_7.55.1-1ubuntu2.1 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu3 libdpkg-perl_1.19.0.4ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.2-0.1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-16ubuntu1 libgcc1_1:7.2.0-16ubuntu1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1ubuntu1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-16ubuntu1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.15.2-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-2 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu60_60.1-1ubuntu2 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2ubuntu2 libisl15_0.18-1 libk5crypto3_1.15.2-2 libkeyutils1_1.5.9-9.2ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.2-2 libkrb5support0_1.15.2-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 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 libmpfr4_3.1.6-1 libncbi6_6.1.20170106-2 libncbi6-dev_6.1.20170106-2 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-2 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-5ubuntu3 libperl5.26_5.26.1-2ubuntu1 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.19.1-3 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu3 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.2-0.1ubuntu1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.0.0_1.0.2g-1ubuntu14 libstdc++-7-dev_7.2.0-16ubuntu1 libstdc++6_7.2.0-16ubuntu1 libsystemd0_235-3ubuntu2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.2.0-16ubuntu1 libudev1_235-3ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1ubuntu1 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-5ubuntu2 linux-libc-dev_4.13.0-17.20 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-3 mawk_1.3.3-17ubuntu2 mount_2.30.2-0.1ubuntu1 multiarch-support_2.26-0ubuntu2 ncbi-data_6.1.20170106-2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu14 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.1-2ubuntu1 perl-base_5.26.1-2ubuntu1 perl-modules-5.26_5.26.1-2ubuntu1 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-readseq-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-3ubuntu2 systemd-sysv_235-3ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.2-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Nov 17 15:19:49 2017 UTC gpgv: using RSA key gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./readseq_1-12.dsc dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-12.debian.tar.xz dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-13763564 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13763564 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13763564 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-12 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build readseq-1 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' rm -f *.o core test.* readseq make[1]: Leaving directory '/<>' debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f readseq make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 make[1]: Entering directory '/<>' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now readseq.c: In function ‘formatstr’: readseq.c:267:41: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] case kASNseqset : return formats[kASN1-1]; ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] case kPhylipSequential: return formats[kPhylip-1]; ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] else return formats[format-1]; ~~~~~~~^~~~~~~~~~ readseq.c: In function ‘Nlm_Main’: readseq.c:801:5: warning: implicit declaration of function ‘gets’; did you mean ‘fgets’? [-Wimplicit-function-declaration] gets(oname= onamestore); ^~~~ fgets readseq.c:936:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] sprintf( stemp,"%s_%d", oname, whichSeq); ~^ %ld readseq.c:938:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); ~^ %ld readseq.c:980:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %ld readseq.c:980:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %ld readseq.c:980:65: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", ~^ %lX readseq.c:998:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ~^ %ld readseq.c:998:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ~^ %ld readseq.c:999:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] else fprintf(foo," %d %d YF\n", i, seqlen); ~^ %ld readseq.c:999:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] else fprintf(foo," %d %d YF\n", i, seqlen); ~^ %ld readseq.c:1117:31: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ ~^ %ld readseq.c:1117:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long unsigned int’ [-Wformat=] fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ ~^ %ld readseq.c:1133:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); ~^ %ld readseq.c:1134:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] else fprintf(foo," %d %d YF\n", seqout, seqlen); ~^ %ld readseq.c:1158:49: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); ~^ %ld readseq.c: In function ‘chooseFormat’: readseq.c:429:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(sform, 127, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~ readseq.c: In function ‘Nlm_Main’: readseq.c:783:5: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(tempname); ^~~~~~~~~~~~~~~~ readseq.c:937:13: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result [-Wunused-result] freopen( stemp, "w", fout); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c: In function ‘seqFileFormatFp’: ureadseq.c:1535:19: warning: format ‘%d’ expects argument of type ‘int *’, but argument 3 has type ‘long int *’ [-Wformat=] sscanf( sp, "%d%d", &nspp, &nlen); ~^ ~~~~~ %ld ureadseq.c:1535:21: warning: format ‘%d’ expects argument of type ‘int *’, but argument 4 has type ‘long int *’ [-Wformat=] sscanf( sp, "%d%d", &nspp, &nlen); ~^ ~~~~~ %ld ureadseq.c: In function ‘writeSeq’: ureadseq.c:1784:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] sprintf(numform, "%d", seqlen); ~^ %ld ureadseq.c:1813:43: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); ~^ %ld ureadseq.c:1814:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1814:48: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1828:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1828:52: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1838:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); ~~~^ %10ld ureadseq.c:1848:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1848:36: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1857:31: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1857:41: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1858:37: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(outf,"SQ %d BP\n", seqlen); ~^ %ld ureadseq.c:1869:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); ~^ %ld ureadseq.c:1869:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); ~^ %ld ureadseq.c:1878:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1878:52: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1884:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1884:36: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1915:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); ~^ %ld ureadseq.c:1937:41: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); ~~^ %6ld ureadseq.c:1937:53: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); ~~^ %8lX ureadseq.c:1954:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); ~~^ %6ld ureadseq.c:1954:54: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); ~~^ %8lX ureadseq.c:1960:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", ~~^ %6ld ureadseq.c:1960:52: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", ~~^ %5ld ureadseq.c:1972:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:1972:37: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:1979:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(outf,"%4d %-60s\n",seqlen,seqname); ~~^ %4ld ureadseq.c:2002:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %ld ureadseq.c:2002:37: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ~^ %lX ureadseq.c:2043:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] if (numline==1) fprintf(outf,"%-9d ",i+1); ~~~^ ~~~ %-9ld ureadseq.c:2007:45: warning: ‘%d’ directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); ^~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from ureadseq.c:20: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: ‘__builtin___sprintf_chk’ output between 7 and 17 bytes into a destination of size 10 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function ‘listASNSeqs’: ureadasn.c:189:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; ^~~~~~~~ In file included from /usr/include/ncbi/objsset.h:48:0, from /usr/include/ncbi/sequtil.h:43, from /usr/include/ncbi/seqport.h:47, from ureadasn.c:14: /usr/include/ncbi/asn.h:384:29: note: expected ‘Nlm_CharPtr {aka char *}’ but argument is of type ‘const char *’ NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); ^~~~~~~~~ ureadasn.c: In function ‘readASNSeq’: ureadasn.c:261:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; ^~~~~~~~ In file included from /usr/include/ncbi/objsset.h:48:0, from /usr/include/ncbi/sequtil.h:43, from /usr/include/ncbi/seqport.h:47, from ureadasn.c:14: /usr/include/ncbi/asn.h:384:29: note: expected ‘Nlm_CharPtr {aka char *}’ but argument is of type ‘const char *’ NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); ^~~~~~~~~ ureadasn.c: In function ‘listASNSeqs’: ureadasn.c:190:31: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i=0; ifp); /* this may mess up asn routines... */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function ‘readASNSeq’: ureadasn.c:262:31: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i=0; ifp); /* this may mess up asn routines... */ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from ureadasn.c:8: In function ‘fgets’, inlined from ‘readASNSeq’ at ureadasn.c:262:31: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:260:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/ccNGXmnF.o: In function `Nlm_Main': ./readseq.c:783: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ./readseq.c:801: warning: the `gets' function is dangerous and should not be used. make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 test make[1]: Entering directory '/<>' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std 1c1 < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum. --- > >alphabet['!'..'~'], 83 bases, 9429 checksum. Makefile:54: recipe for target 'test' failed make[1]: [test] Error 1 (ignored) Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, Makefile:54: recipe for target 'test' failed make[1]: [test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss Makefile:54: recipe for target 'test' failed make[1]: [test] Error 1 (ignored) Test of NCBI ASN.1 conversions: ./readseq -p -f=asn test.m-ig -otest.m-asn ./readseq -p -f=ig test.m-asn -otest.m-ig-c ========================[ Nov 17, 2017 3:18 PM ]======================== ========================[ Nov 17, 2017 3:18 PM ]======================== ========================[ Nov 17, 2017 3:18 PM ]======================== ========================[ Nov 17, 2017 3:18 PM ]======================== ========================[ Nov 17, 2017 3:18 PM ]======================== ========================[ Nov 17, 2017 3:18 PM ]======================== diff test.m-ig test.m-ig-c 1,30c1,30 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst < a-------actcctaacaacGgAtatCTtGgtT-CtcgcgagGatGAaGa < acGcAGcg--AaatGcGatacgtagtgtgaatcgc-agggatcagtgaat < catcgaatctttgaacgcaagttgcgctctcgtg--gtttaaccccccgg < gagc-acgttcgcttgagtgcc--gctt-----1 < ;amgrrbst , 183 bases, C886D2FB checksum. < amgrrbst < ----cgt--ccccgaacggcGgAtcaCTtGgcT-CgtggatcGatGAaGa < ccGcAGc--tAtctGcGcgtcgtcgtgtaatccgc-aggttatac--gaa < catcgaccagtcgaacgcacattgcggcctcggt--gacccgcgggcccc < gggccacgcctgtctgagggtc--gt------a1 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. < bmorrbst < aaatgattaccctggacggtGgAtcaCTtGgcT-CgcgggtcGatGAaGa < acGcAGt--tAactGcGcgtcatagtgtgaactgc-aggacacatttgaa < catcgacatttcgaacgcacattgcggtc-cgtg--gagacaca--tcca < ggaccactcctgtctgagggcc--ggct-----1 < ;crerrbst , 183 bases, AC88A337 checksum. < crerrbst < a-------actctcaacaacGgAtatCTtGgcT-CtcggatcGatGAaGg < acGcAGcg--AaatGcGatacgtagtgtgaactgc-agaaatacgtgaac < tatcgaatccctgaacgtatactgcgccc--gag--gcc---ccggt--a < gagc-atgtctgccttagtgct--gggt----t1 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst < t-----taagcataaacggtGaAtacCTcGacTcC-caaattGatGAaGa < ccGtAGca--AactGcGataattcacttgaattgc-agcctactg-ggat < agttgaaatgttgaacgcacatgatgacatcggt---cctttcggattag < gtgttatacttgggtgagagt--------ggtc1 --- > ;lcl|1 acarr58sst, 183 bases, D7F81A0A checksum. > lcl|1 > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿGÿAÿÿÿCTÿGÿÿTÿCÿÿÿÿÿÿÿGÿÿGAÿGÿ > ÿÿGÿAGÿÿÿÿAÿÿÿGÿGÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ1 > ;lcl|2 amgrrbst, 183 bases, D7F81A0A checksum. > lcl|2 > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿGÿAÿÿÿCTÿGÿÿTÿCÿÿÿÿÿÿÿGÿÿGAÿGÿ > ÿÿGÿAGÿÿÿÿAÿÿÿGÿGÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ1 > ;lcl|3 bmorrbst, 183 bases, D7F81A0A checksum. > lcl|3 > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿGÿAÿÿÿCTÿGÿÿTÿCÿÿÿÿÿÿÿGÿÿGAÿGÿ > ÿÿGÿAGÿÿÿÿAÿÿÿGÿGÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ1 > ;lcl|4 crerrbst, 183 bases, D7F81A0A checksum. > lcl|4 > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿGÿAÿÿÿCTÿGÿÿTÿCÿÿÿÿÿÿÿGÿÿGAÿGÿ > ÿÿGÿAGÿÿÿÿAÿÿÿGÿGÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ1 > ;lcl|5 ddirr58sst, 183 bases, D7F81A0A checksum. > lcl|5 > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿGÿAÿÿÿCTÿGÿÿTÿCÿÿÿÿÿÿÿGÿÿGAÿGÿ > ÿÿGÿAGÿÿÿÿAÿÿÿGÿGÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ1 Makefile:54: recipe for target 'test' failed make[1]: [test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make -j4 install DESTDIR=/<>/debian/readseq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' install readseq /<>/debian/readseq/usr/bin install *.std /<>/debian/readseq/usr/share/doc/readseq/tests install Makefile /<>/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing readseq (in debian/readseq); do_strip: , oemstrip: pkgstriptranslations: processing readseq-dbgsym (in debian/.debhelper/readseq/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/readseq/DEBIAN/control, package readseq, directory debian/readseq pkgstripfiles: Truncating usr/share/doc/readseq/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package readseq ... pkgstripfiles: processing control file: debian/.debhelper/readseq/dbgsym-root/DEBIAN/control, package readseq-dbgsym, directory debian/.debhelper/readseq/dbgsym-root pkgstripfiles: No PNG files. pkgstripfiles: Running PNG optimization (using 4 cpus) for package readseq-dbgsym ... dpkg-deb: building package 'readseq' in '../readseq_1-12_armhf.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'readseq-dbgsym' in 'debian/.debhelper/scratch-space/build-readseq/readseq-dbgsym_1-12_armhf.deb'. Renaming readseq-dbgsym_1-12_armhf.deb to readseq-dbgsym_1-12_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../readseq_1-12_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build readseq-1 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171122-2247 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ readseq_1-12_armhf.changes: --------------------------- Format: 1.8 Date: Fri, 17 Nov 2017 16:18:41 +0100 Source: readseq Binary: readseq Architecture: armhf Version: 1-12 Distribution: bionic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: readseq - Conversion between sequence formats Changes: readseq (1-12) unstable; urgency=medium . * Moved packaging from SVN to Git * Moved debian/upstream to debian/upstream/metadata * debhelper 10 * Standards-Version: 4.1.1 * Add fake watch file * hardening=+all Checksums-Sha1: d62d5ea9d30bc457564450938de0d166674ba797 54108 readseq-dbgsym_1-12_armhf.ddeb ba0b1b14ed7e5f5739a13c34a915c70f1c8e786c 5054 readseq_1-12_armhf.buildinfo 3ea7ad8aaeda94acd8d0577eaf50d2a8e82ca6da 52744 readseq_1-12_armhf.deb Checksums-Sha256: fd896a3f8d2eaeda4d1f506d907cb2d8645c079f099a5b79a00223f3bf5b4c41 54108 readseq-dbgsym_1-12_armhf.ddeb c0b6f070f4c85adb34734c167f256b643ce97bda0a1e5e48d5ef4f80a12ad2b3 5054 readseq_1-12_armhf.buildinfo 093156add53a54fe06f29d5e83d1435dd63b30d35b9734a645d56994b69abf1a 52744 readseq_1-12_armhf.deb Files: fa6a1a6d71bb7236df853375e7e5df6a 54108 debug optional readseq-dbgsym_1-12_armhf.ddeb 475b770ff4e4e928a0b39086bc69be7f 5054 science optional readseq_1-12_armhf.buildinfo e08b560f38d825c3590810495531b6f0 52744 science optional readseq_1-12_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ readseq_1-12_armhf.deb ---------------------- new debian package, version 2.0. size 52744 bytes: control archive=1112 bytes. 647 bytes, 15 lines control 1030 bytes, 15 lines md5sums Package: readseq Version: 1-12 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 96 Depends: libc6 (>= 2.7), libncbi6 (>= 6.1.20030421) Section: science Priority: optional Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/ Description: Conversion between sequence formats Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences. Readseq is particularly useful as it automatically detects many sequence formats, and converts between them. drwxr-xr-x root/root 0 2017-11-17 15:18 ./ drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/ drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/bin/ -rwxr-xr-x root/root 42576 2017-11-17 15:18 ./usr/bin/readseq drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/ drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/doc/readseq/ -rw-r--r-- root/root 13869 2017-11-17 15:18 ./usr/share/doc/readseq/Formats.gz -rw-r--r-- root/root 2018 2017-11-17 15:18 ./usr/share/doc/readseq/README.Debian -rw-r--r-- root/root 323 2017-11-17 15:18 ./usr/share/doc/readseq/README.test -rw-r--r-- root/root 2923 1993-02-01 00:00 ./usr/share/doc/readseq/Readme.gz -rw-r--r-- root/root 4138 1992-12-30 00:00 ./usr/share/doc/readseq/Readseq.help.gz -rw-r--r-- root/root 3731 1992-12-30 00:00 ./usr/share/doc/readseq/Stdfiles -rw-r--r-- root/root 1506 2017-11-17 15:18 ./usr/share/doc/readseq/changelog.Debian.gz -rw-r--r-- root/root 994 2017-11-17 15:18 ./usr/share/doc/readseq/copyright drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/doc/readseq/tests/ -rw-r--r-- root/root 2008 2017-11-17 15:18 ./usr/share/doc/readseq/tests/Makefile -rw-r--r-- root/root 131 1992-12-30 00:00 ./usr/share/doc/readseq/tests/alphabet.std -rw-r--r-- root/root 1180 1992-12-30 00:00 ./usr/share/doc/readseq/tests/multi.std -rw-r--r-- root/root 253 1992-12-30 00:00 ./usr/share/doc/readseq/tests/nucleic.std -rw-r--r-- root/root 131 1992-12-30 00:00 ./usr/share/doc/readseq/tests/upper.std drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/man/ drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/man/man1/ -rw-r--r-- root/root 2003 2017-11-17 15:18 ./usr/share/man/man1/readseq.1.gz drwxr-xr-x root/root 0 2017-11-17 15:18 ./usr/share/readseq/ lrwxrwxrwx root/root 0 2017-11-17 15:18 ./usr/share/readseq/readseq_help.gz -> ../doc/readseq/Readseq.help.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 1456 Build-Time: 32 Distribution: bionic-proposed Host Architecture: armhf Install-Time: 33 Job: readseq_1-12.dsc Machine Architecture: arm64 Package: readseq Package-Time: 69 Source-Version: 1-12 Space: 1456 Status: successful Version: 1-12 -------------------------------------------------------------------------------- Finished at 20171122-2247 Build needed 00:01:09, 1456k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 Scanning for processes to kill in build PACKAGEBUILD-13763564 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 Stopping target for build PACKAGEBUILD-13763564 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13763564 Removing build PACKAGEBUILD-13763564