RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-045 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... 31 Jan 08:47:25 ntpdate[1871]: adjust time server 10.211.37.1 offset 0.000634 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 /home/buildd/filecache-default/b70461af4419c13dbae7acd6fe74d075a1a9550f Creating target for build PACKAGEBUILD-13870331 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 Starting target for build PACKAGEBUILD-13870331 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 '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-13870331 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 Updating target for build PACKAGEBUILD-13870331 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 [235 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [962 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8166 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4945 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf Packages [177 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [87.6 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf Packages [678 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [329 kB] Fetched 16.5 MB in 8s (1906 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: gnupg-agent libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libustr-1.0-1 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: dirmngr gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm libmpfr6 libnghttp2-14 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential coreutils cpp-7 dash debconf debianutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv hostname 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 libcilkrts5 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi6 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libk5crypto3 libkeyutils1 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 libmount1 libmpc3 libncurses5 libncursesw5 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libprocps6 libpsl5 libreadline7 libroken18-heimdal libseccomp2 libselinux1 libsemanage-common libsemanage1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login lsb-base mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.26 pinentry-curses procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 135 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 57.4 MB of archives. After this operation, 476 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf perl-modules-5.26 all 5.26.1-4 [2761 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libperl5.26 armhf 5.26.1-4 [2874 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf perl armhf 5.26.1-4 [201 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf perl-base armhf 5.26.1-4 [1289 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libc6-dev armhf 2.26-0ubuntu4 [1893 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libc-dev-bin armhf 2.26-0ubuntu4 [60.3 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf linux-libc-dev armhf 4.13.0-32.35 [930 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gcc-7-base armhf 7.3.0-1ubuntu1 [19.4 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgcc1 armhf 1:7.3.0-1ubuntu1 [37.2 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgomp1 armhf 7.3.0-1ubuntu1 [65.7 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libatomic1 armhf 7.3.0-1ubuntu1 [6300 B] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libasan4 armhf 7.3.0-1ubuntu1 [328 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libubsan0 armhf 7.3.0-1ubuntu1 [109 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libcilkrts5 armhf 7.3.0-1ubuntu1 [35.9 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libmpc3 armhf 1.1.0-1 [33.2 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libmpfr6 armhf 4.0.0-7 [194 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf cpp-7 armhf 7.3.0-1ubuntu1 [5287 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libcc1-0 armhf 7.3.0-1ubuntu1 [32.3 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.30-1ubuntu1 [2171 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libbinutils armhf 2.30-1ubuntu1 [309 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf binutils armhf 2.30-1ubuntu1 [3344 B] Get:22 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf binutils-common armhf 2.30-1ubuntu1 [193 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf g++-7 armhf 7.3.0-1ubuntu1 [6041 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gcc-7 armhf 7.3.0-1ubuntu1 [5931 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgcc-7-dev armhf 7.3.0-1ubuntu1 [706 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libstdc++-7-dev armhf 7.3.0-1ubuntu1 [1534 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libstdc++6 armhf 7.3.0-1ubuntu1 [350 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgmp10 armhf 2:6.1.2+dfsg-2 [182 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libc6 armhf 2.26-0ubuntu4 [2199 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf init-system-helpers all 1.51 [37.3 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf base-files armhf 10ubuntu1 [55.9 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf bsdutils armhf 1:2.30.2-0.1ubuntu1 [55.4 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf coreutils armhf 8.28-1ubuntu1 [1128 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf debianutils armhf 4.8.4 [84.5 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf dpkg armhf 1.19.0.5ubuntu1 [1095 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main armhf dash armhf 0.5.8-2.9ubuntu1 [103 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main armhf e2fslibs armhf 1.43.8-2 [144 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main armhf e2fsprogs armhf 1.43.8-2 [479 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main armhf findutils armhf 4.6.0+git+20170828-2 [277 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf hostname armhf 3.19 [10.4 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf login armhf 1:4.5-1ubuntu1 [303 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libncurses5 armhf 6.0+20171125-1ubuntu1 [74.9 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libtinfo5 armhf 6.0+20171125-1ubuntu1 [68.3 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libncursesw5 armhf 6.0+20171125-1ubuntu1 [95.3 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf ncurses-bin armhf 6.0+20171125-1ubuntu1 [154 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main armhf sed armhf 4.4-2 [175 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf libuuid1 armhf 2.30.2-0.1ubuntu1 [14.5 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main armhf libblkid1 armhf 2.30.2-0.1ubuntu1 [106 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libsmartcols1 armhf 2.30.2-0.1ubuntu1 [68.7 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main armhf libfdisk1 armhf 2.30.2-0.1ubuntu1 [144 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre3 armhf 2:8.39-8 [209 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf libselinux1 armhf 2.7-2 [59.1 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf libmount1 armhf 2.30.2-0.1ubuntu1 [116 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf fdisk armhf 2.30.2-0.1ubuntu1 [96.6 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf util-linux armhf 2.30.2-0.1ubuntu1 [823 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf base-passwd armhf 3.5.44 [45.9 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libc-bin armhf 2.26-0ubuntu4 [475 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf ncurses-base all 6.0+20171125-1ubuntu1 [17.3 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main armhf sysvinit-utils armhf 2.88dsf-59.10ubuntu1 [17.2 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main armhf libudev1 armhf 235-3ubuntu3 [49.4 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libapt-pkg5.0 armhf 1.6~alpha7 [724 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage-common all 2.7-2 [6916 B] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage1 armhf 2.7-2 [72.3 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf passwd armhf 1:4.5-1ubuntu1 [769 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf debconf all 1.5.65 [124 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf adduser all 3.116ubuntu1 [163 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf libgpg-error0 armhf 1.27-5 [32.4 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf libgcrypt20 armhf 1.8.1-4 [363 kB] Get:69 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpgv armhf 2.2.4-1ubuntu1 [166 kB] Get:70 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libnettle6 armhf 3.4-1 [123 kB] Get:71 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libhogweed4 armhf 3.4-1 [127 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf libidn2-0 armhf 2.0.4-1 [88.2 kB] Get:73 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libffi6 armhf 3.2.1-8 [16.4 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf libp11-kit0 armhf 0.23.9-2 [162 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf libtasn1-6 armhf 4.13-2 [31.1 kB] Get:76 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgnutls30 armhf 3.5.17-1ubuntu1 [625 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main armhf libseccomp2 armhf 2.3.1-2.1ubuntu3 [29.9 kB] Get:78 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf apt armhf 1.6~alpha7 [1110 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main armhf libapparmor1 armhf 2.11.0-2ubuntu19 [24.8 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf libcap2 armhf 1:2.25-1.2 [11.7 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main armhf libidn11 armhf 1.33-2.1 [42.7 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main armhf libip4tc0 armhf 1.6.1-2ubuntu2 [17.8 kB] Get:83 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkmod2 armhf 24-1ubuntu3 [34.4 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main armhf mount armhf 2.30.2-0.1ubuntu1 [104 kB] Get:85 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libprocps6 armhf 2:3.3.12-3ubuntu1 [28.4 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:87 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf procps armhf 2:3.3.12-3ubuntu1 [214 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf systemd armhf 235-3ubuntu3 [2679 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf libsystemd0 armhf 235-3ubuntu3 [178 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf init armhf 1.51 [5864 B] Get:91 http://ftpmaster.internal/ubuntu bionic/main armhf systemd-sysv armhf 235-3ubuntu3 [13.1 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main armhf libcap-ng0 armhf 0.7.7-3.1 [9816 B] Get:93 http://ftpmaster.internal/ubuntu bionic/main armhf libcomerr2 armhf 1.43.8-2 [10.4 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main armhf libss2 armhf 1.43.8-2 [9380 B] Get:95 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf multiarch-support armhf 2.26-0ubuntu4 [6912 B] Get:96 http://ftpmaster.internal/ubuntu bionic/main armhf sensible-utils all 0.0.11 [14.8 kB] Get:97 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gnupg-l10n all 2.2.4-1ubuntu1 [48.6 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main armhf libassuan0 armhf 2.5.1-1 [28.1 kB] Get:99 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf readline-common all 7.0-3 [52.9 kB] Get:100 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libreadline7 armhf 7.0-3 [103 kB] Get:101 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gnupg armhf 2.2.4-1ubuntu1 [249 kB] Get:102 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gnupg-agent all 2.2.4-1ubuntu1 [4544 B] Get:103 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpgconf armhf 2.2.4-1ubuntu1 [105 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main armhf pinentry-curses armhf 1.0.0-3 [30.4 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main armhf libnpth0 armhf 1.5-3 [6632 B] Get:106 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpg-agent armhf 2.2.4-1ubuntu1 [189 kB] Get:107 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gnupg-utils armhf 2.2.4-1ubuntu1 [106 kB] Get:108 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libsqlite3-0 armhf 3.22.0-1 [421 kB] Get:109 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpg armhf 2.2.4-1ubuntu1 [409 kB] Get:110 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpg-wks-client armhf 2.2.4-1ubuntu1 [76.8 kB] Get:111 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gpg-wks-server armhf 2.2.4-1ubuntu1 [71.8 kB] Get:112 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf gpgsm armhf 2.2.4-1ubuntu1 [183 kB] Get:113 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf dirmngr armhf 2.2.4-1ubuntu1 [275 kB] Get:114 http://ftpmaster.internal/ubuntu bionic/main armhf libdevmapper1.02.1 armhf 2:1.02.145-4.1ubuntu2 [117 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main armhf dmsetup armhf 2:1.02.145-4.1ubuntu2 [73.8 kB] Get:116 http://ftpmaster.internal/ubuntu bionic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-1 [34.1 kB] Get:117 http://ftpmaster.internal/ubuntu bionic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-1 [136 kB] Get:118 http://ftpmaster.internal/ubuntu bionic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-1 [24.1 kB] Get:119 http://ftpmaster.internal/ubuntu bionic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-1 [76.5 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-1 [47.2 kB] Get:121 http://ftpmaster.internal/ubuntu bionic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-1 [87.9 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-1 [168 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-1 [13.1 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-1 [78.8 kB] Get:125 http://ftpmaster.internal/ubuntu bionic/main armhf libslang2 armhf 2.3.1a-1ubuntu1 [381 kB] Get:126 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libssl1.0.0 armhf 1.0.2n-1ubuntu1 [709 kB] Get:127 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf openssl armhf 1.0.2n-1ubuntu1 [480 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/main armhf tzdata all 2018c-1 [188 kB] Get:129 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgssapi-krb5-2 armhf 1.16-2 [101 kB] Get:130 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkrb5-3 armhf 1.16-2 [234 kB] Get:131 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libk5crypto3 armhf 1.16-2 [83.2 kB] Get:132 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libkrb5support0 armhf 1.16-2 [27.5 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu1 [8380 B] Get:134 http://ftpmaster.internal/ubuntu bionic/main armhf libpng16-16 armhf 1.6.34-1 [159 kB] Get:135 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf apt-transport-https all 1.6~alpha7 [1692 B] Get:136 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf dpkg-dev all 1.19.0.5ubuntu1 [607 kB] Get:137 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libdpkg-perl all 1.19.0.5ubuntu1 [211 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main armhf build-essential armhf 12.4ubuntu1 [4752 B] Get:139 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libfakeroot armhf 1.22-2ubuntu1 [21.6 kB] Get:140 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf fakeroot armhf 1.22-2ubuntu1 [60.3 kB] Get:141 http://ftpmaster.internal/ubuntu bionic/main armhf libnghttp2-14 armhf 1.29.0-1 [67.1 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main armhf libpsl5 armhf 0.19.1-4 [39.9 kB] Get:143 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libcurl3-gnutls armhf 7.58.0-2ubuntu1 [181 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile-bin armhf 1.14-1.1 [10.9 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile1 armhf 1.14-1.1 [5784 B] Get:146 http://ftpmaster.internal/ubuntu bionic/main armhf optipng armhf 0.7.6-1.1 [80.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.4 MB in 2s (19.2 MB/s) (Reading database ... 12457 files and directories currently installed.) 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Setting up binutils-common:armhf (2.30-1ubuntu1) ... Setting up sensible-utils (0.0.11) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... Setting up libperl5.26:armhf (5.26.1-4) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libfakeroot:armhf (1.22-2ubuntu1) ... Setting up libsqlite3-0:armhf (3.22.0-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu2) ... Setting up libmpc3:armhf (1.1.0-1) ... Setting up libc-dev-bin (2.26-0ubuntu4) ... Setting up libkeyutils1:armhf (1.5.9-9.2ubuntu1) ... Setting up libc6-dev:armhf (2.26-0ubuntu4) ... Setting up libslang2:armhf (2.3.1a-1ubuntu1) ... Setting up libassuan0:armhf (2.5.1-1) ... Setting up libk5crypto3:armhf (1.16-2) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libbinutils:armhf (2.30-1ubuntu1) ... Setting up init (1.51) ... Setting up libasn1-8-heimdal:armhf (7.5.0+dfsg-1) ... Setting up gpgconf (2.2.4-1ubuntu1) ... Setting up libhcrypto4-heimdal:armhf (7.5.0+dfsg-1) ... Setting up binutils-arm-linux-gnueabihf (2.30-1ubuntu1) ... Setting up fakeroot (1.22-2ubuntu1) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-1) ... Setting up cpp-7 (7.3.0-1ubuntu1) ... Setting up libstdc++-7-dev:armhf (7.3.0-1ubuntu1) ... Setting up perl (5.26.1-4) ... Setting up gpgsm (2.2.4-1ubuntu1) ... Setting up openssl (1.0.2n-1ubuntu1) ... Setting up gnupg-utils (2.2.4-1ubuntu1) ... Setting up pinentry-curses (1.0.0-3) ... Setting up libkrb5-3:armhf (1.16-2) ... Setting up binutils (2.30-1ubuntu1) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-1) ... Setting up dirmngr (2.2.4-1ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up gpg (2.2.4-1ubuntu1) ... Setting up gcc-7 (7.3.0-1ubuntu1) ... Setting up g++-7 (7.3.0-1ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu1) ... Setting up gpg-agent (2.2.4-1ubuntu1) ... Installing new version of config file /etc/X11/Xsession.d/90gpg-agent ... Setting up gpg-wks-server (2.2.4-1ubuntu1) ... Setting up gpg-wks-client (2.2.4-1ubuntu1) ... Setting up libgssapi-krb5-2:armhf (1.16-2) ... Setting up dpkg-dev (1.19.0.5ubuntu1) ... Setting up gnupg-agent (2.2.4-1ubuntu1) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-1) ... Setting up build-essential (12.4ubuntu1) ... Setting up libcurl3-gnutls:armhf (7.58.0-2ubuntu1) ... Setting up gnupg (2.2.4-1ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13870331 armhf bionic-proposed -c chroot:build-PACKAGEBUILD-13870331 --arch=armhf --dist=bionic-proposed --nolog bitseq_0.7.5+dfsg-3.dsc Initiating build PACKAGEBUILD-13870331 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-arm64-045.buildd +==============================================================================+ | bitseq 0.7.5+dfsg-3 (armhf) 31 Jan 2018 08:49 | +==============================================================================+ Package: bitseq Version: 0.7.5+dfsg-3 Source Version: 0.7.5+dfsg-3 Distribution: bionic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/bitseq-5OxKWe/bitseq-0.7.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bitseq-5OxKWe' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13870331/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bitseq_0.7.5+dfsg-3.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-iBkwVC/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-iBkwVC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-iBkwVC/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-iBkwVC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-iBkwVC/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-iBkwVC/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (31.4 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: gnupg-agent libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libustr-1.0-1 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-iBkwVC/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 (54.5 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12645 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), zlib1g-dev, libbam-dev, libboost-dev, help2man, python, python-numpy Filtered Build-Depends: debhelper (>= 10), zlib1g-dev, libbam-dev, libboost-dev, help2man, python, python-numpy dpkg-deb: building package 'sbuild-build-depends-bitseq-dummy' in '/<>/resolver-jeQV4m/apt_archive/sbuild-build-depends-bitseq-dummy.deb'. Ign:1 copy:/<>/resolver-jeQV4m/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jeQV4m/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jeQV4m/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jeQV4m/apt_archive ./ Sources [245 B] Get:5 copy:/<>/resolver-jeQV4m/apt_archive ./ Packages [565 B] Fetched 2929 B in 0s (47.1 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install bitseq 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: gnupg-agent libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libustr-1.0-1 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 help2man intltool-debian libarchive-zip-perl libbam-dev libblas3 libboost-dev libboost1.65-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python-numpy python2.7 python2.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.65-doc libboost-atomic1.65-dev libboost-chrono1.65-dev libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-date-time1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-iostreams1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-regex1.65-dev libboost-serialization1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-system1.65-dev libboost-test1.65-dev libboost-thread1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor libmail-box-perl python-doc python-tk gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python2.7-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs 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 help2man intltool-debian libarchive-zip-perl libbam-dev libblas3 libboost-dev libboost1.65-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python-numpy python2.7 python2.7-minimal sbuild-build-depends-bitseq-dummy zlib1g-dev 0 upgraded, 53 newly installed, 1 to remove and 0 not upgraded. Need to get 31.6 MB of archives. After this operation, 208 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu bionic/main armhf gettext armhf 0.19.8.1-4ubuntu2 [1027 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main armhf debhelper all 11.1.3ubuntu1 [900 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/universe armhf help2man armhf 1.47.5 [155 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/universe armhf libbam-dev armhf 0.1.19-2 [111 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf libblas3 armhf 3.7.1-4ubuntu1 [97.0 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main armhf libboost1.65-dev armhf 1.65.1+dfsg-0ubuntu4 [7217 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libboost-dev armhf 1.65.1.0ubuntu1 [3128 B] Get:50 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libgfortran4 armhf 7.3.0-1ubuntu1 [201 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf liblapack3 armhf 3.7.1-4ubuntu1 [1627 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf python-numpy armhf 1:1.13.3-2ubuntu1 [1742 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.6 MB in 4s (7143 kB/s) (Reading database ... 12645 files and directories currently installed.) 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Setting up liblapack3:armhf (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up python2.7 (2.7.14-4) ... Setting up libharfbuzz0b:armhf (1.7.2-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up libpython-stdlib:armhf (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 help2man (1.47.5) ... Setting up man-db (2.7.6.1-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-dev:armhf (1.65.1.0ubuntu1) ... Setting up python (2.7.14-4) ... Setting up libtool (2.4.6-2) ... Setting up python-numpy (1:1.13.3-2ubuntu1) ... Setting up dh-autoreconf (16) ... Setting up libicu-le-hb0:armhf (1.0.3+git161113-4) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up libicu60:armhf (60.2-3ubuntu1) ... Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up gettext (0.19.8.1-4ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.20) ... Setting up debhelper (11.1.3ubuntu1) ... Setting up sbuild-build-depends-bitseq-dummy (0.invalid.0) ... (Reading database ... 29451 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-101-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-1ubuntu1 dpkg-dev_1.19.0.5ubuntu1 g++-7_7.3.0-1ubuntu1 gcc-7_7.3.0-1ubuntu1 libc6-dev_2.26-0ubuntu4 libstdc++-7-dev_7.3.0-1ubuntu1 libstdc++6_7.3.0-1ubuntu1 linux-libc-dev_4.13.0-32.35 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 apt_1.6~alpha7 apt-transport-https_1.6~alpha7 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_2.30-1ubuntu1 binutils-arm-linux-gnueabihf_2.30-1ubuntu1 binutils-common_2.30-1ubuntu1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.30.2-0.1ubuntu1 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20170717 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passwd_1:4.5-1ubuntu1 patch_2.7.5-1build1 perl_5.26.1-4 perl-base_5.26.1-4 perl-modules-5.26_5.26.1-4 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1 python_2.7.14-4 python-minimal_2.7.14-4 python-numpy_1:1.13.3-2ubuntu1 python2.7_2.7.14-4 python2.7-minimal_2.7.14-4 readline-common_7.0-3 sbuild-build-depends-bitseq-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 systemd_235-3ubuntu3 systemd-sysv_235-3ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2018c-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 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Dec 18 11:34:42 2017 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bitseq_0.7.5+dfsg-3.dsc dpkg-source: info: extracting bitseq in bitseq-0.7.5+dfsg dpkg-source: info: unpacking bitseq_0.7.5+dfsg.orig.tar.xz dpkg-source: info: unpacking bitseq_0.7.5+dfsg-3.debian.tar.xz dpkg-source: info: applying link_against_system_samtools.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_build_options.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-13870331 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13870331 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13870331 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bitseq dpkg-buildpackage: info: source version 0.7.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build bitseq-0.7.5+dfsg dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>/bitseq-0.7.5+dfsg' rm -f *.o convertSamples estimateDE estimateExpression estimateHyperPar estimateVBExpression extractSamples getFoldChange getGeneExpression getPPLR getVariance getWithinGeneExpression parseAlignment transposeLargeFile make[1]: Leaving directory '/<>/bitseq-0.7.5+dfsg' dh_clean 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 '/<>/bitseq-0.7.5+dfsg' g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.cpp In file included from /usr/include/c++/7/vector:69:0, from ArgumentParser.h:6, from misc.h:6, from misc.cpp:5: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from TranscriptInfo.cpp:6:0: TranscriptInfo.cpp: In member function ‘bool TranscriptInfo::updateGeneNames(const std::vector >&)’: common.h:32:78: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘std::vector >::size_type {aka unsigned int}’ [-Wformat=] #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^ TranscriptInfo.cpp:228:7: note: in expansion of macro ‘warning’ warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); ^~~~~~~ TranscriptInfo.cpp: In member function ‘bool TranscriptInfo::updateGeneNames(const std::map, std::__cxx11::basic_string >&)’: common.h:32:78: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘std::map, std::__cxx11::basic_string >::size_type {aka unsigned int}’ [-Wformat=] #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^ TranscriptInfo.cpp:241:7: note: in expansion of macro ‘warning’ warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); ^~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from misc.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/vector:69:0, from ArgumentParser.h:6, from ArgumentParser.cpp:5: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from misc.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from misc.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void ns_misc::computeCI(double, std::vector*, double*, double*)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from misc.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from misc.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ArgumentParser.h:6, from misc.h:6, from misc.cpp:5: /usr/include/c++/7/bits/stl_vector.h: In function ‘bool ns_params::readParams(const string&, std::vector*, std::ofstream*)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from misc.cpp:1: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp In file included from /usr/include/c++/7/vector:69:0, from TranscriptInfo.h:4, from TranscriptInfo.cpp:4: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const transcriptT&}; _Tp = transcriptT; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from TranscriptInfo.h:4, from TranscriptInfo.cpp:4: /usr/include/c++/7/bits/stl_vector.h: In member function ‘bool TranscriptInfo::setInfo(std::vector >, std::vector >, std::vector)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h: In member function ‘bool TranscriptInfo::readInfo(std::__cxx11::string)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp In file included from /usr/include/c++/7/vector:69:0, from Sampler.h:4, from Sampler.cpp:5: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from Sampler.h:4, from Sampler.cpp:5: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void Sampler::appendFile()’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp In file included from /usr/include/c++/7/vector:69:0, from TagAlignments.h:5, from TagAlignments.cpp:3: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from TagAlignments.h:5, from TagAlignments.cpp:3: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void TagAlignments::pushAlignmentL(long int, double)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from lowess.cpp:17: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from lowess.cpp:17: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from lowess.cpp:17: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void lowess(const std::vector&, const std::vector&, double, long int, double, std::vector&, std::vector&, std::vector&)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from TranscriptExpression.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from TranscriptExpression.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = trExpInfoT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from TranscriptExpression.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples /usr/include/c++/7/bits/stl_algo.h: In member function ‘void TranscriptExpression::doSort(bool)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression In file included from /usr/include/c++/7/vector:69:0, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from VariationalBayes.h:4, from VariationalBayes.cpp:12: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::random::gamma_distribution::param_type}; _Tp = boost::random::gamma_distribution::param_type; _Alloc = std::allocator::param_type>]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::param_type>::iterator {aka __gnu_cxx::__normal_iterator::param_type*, std::vector::param_type> >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void VariationalBayes::generateSamples(long int, const string&, const std::vector*, std::ofstream*)’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator::param_type*, std::vector::param_type> >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile ReadDistribution.cpp: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’: ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ ReadDistribution.cpp: In member function ‘bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)’: ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE In file included from /usr/include/c++/7/vector:69:0, from TranscriptSequence.h:6, from TranscriptSequence.cpp:6: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from TranscriptSequence.h:6, from TranscriptSequence.cpp:6: /usr/include/c++/7/bits/stl_vector.h: In member function ‘bool TranscriptSequence::readSequence(std::__cxx11::string, refFormatT)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression In file included from /usr/include/c++/7/vector:69:0, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void ReadDistribution::updateMismatchFreq(bam1_t*)’: /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar In file included from /usr/include/c++/7/map:60:0, from ReadDistribution.h:5, from ReadDistribution.cpp:7: /usr/include/c++/7/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/map:61:0, from ReadDistribution.h:5, from ReadDistribution.cpp:7: /usr/include/c++/7/bits/stl_map.h: In member function ‘double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)’: /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’: /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ /usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator {aka std::_Rb_tree_const_iterator >}’ changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, ^~~ In file included from /usr/include/c++/7/vector:64:0, from ReadDistribution.h:4, from ReadDistribution.cpp:7: /usr/include/c++/7/bits/stl_vector.h: In constructor ‘ReadDistribution::ReadDistribution()’: /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from estimateExpression.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from estimateExpression.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from estimateExpression.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression In file included from /usr/include/c++/7/vector:69:0, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:153:5: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from estimateHyperPar.cpp:6: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from estimateHyperPar.cpp:6: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from estimateHyperPar.cpp:6: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/7/bits/stl_vector.h: In function ‘int estimateHyperPar(int*, char**)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from estimateHyperPar.cpp:6: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, from estimateHyperPar.cpp:10: /usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ g++ -g -O2 -fdebug-prefix-map=/<>/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lz -lbam -o parseAlignment In file included from /usr/include/c++/7/vector:69:0, from ArgumentParser.h:6, from parseAlignment.cpp:7: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ns_parseAlignment::TagAlignment}; _Tp = ns_parseAlignment::TagAlignment; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In function ‘int parseAlignment(int*, char**)’: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bam_import.o): In function `ks_getuntil2.constprop.3': (.text+0x70): undefined reference to `gzread' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bam_import.o): In function `__bam_get_lines': (.text+0x2b4): undefined reference to `gzdopen' (.text+0x34e): undefined reference to `gzclose' (.text+0x378): undefined reference to `gzopen64' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bam_import.o): In function `sam_header_read2': (.text+0x3dc): undefined reference to `gzdopen' (.text+0x56c): undefined reference to `gzread' (.text+0x8d8): undefined reference to `gzclose' (.text+0xb88): undefined reference to `gzopen64' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bam_import.o): In function `sam_open': (.text+0x1c8a): undefined reference to `gzdopen' (.text+0x1cc8): undefined reference to `gzopen64' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bam_import.o): In function `sam_close': (.text+0x1cfc): undefined reference to `gzclose' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_compress.constprop.3': (.text+0x184): undefined reference to `deflateInit2_' (.text+0x190): undefined reference to `deflate' (.text+0x19a): undefined reference to `deflateEnd' (.text+0x1d6): undefined reference to `crc32' (.text+0x1de): undefined reference to `crc32' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_open': (.text+0x4a2): undefined reference to `compressBound' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_dopen': (.text+0x542): undefined reference to `compressBound' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(bgzf.o): In function `bgzf_read_block': (.text+0x7ca): undefined reference to `inflateInit2_' (.text+0x7d8): undefined reference to `inflate' (.text+0x7e4): undefined reference to `inflateEnd' (.text+0x9f2): undefined reference to `inflateEnd' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `_razf_write': (.text+0x2e): undefined reference to `deflate' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_open_w': (.text+0x160): undefined reference to `deflateInit2_' (.text+0x1b0): undefined reference to `deflateSetHeader' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_open_r': (.text+0x32e): undefined reference to `inflateInit2_' (.text+0x3bc): undefined reference to `inflateEnd' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `_razf_read.constprop.6': (.text+0x634): undefined reference to `inflate' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_write': (.text+0x7cc): undefined reference to `deflate' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_jump': (.text+0xdc6): undefined reference to `inflateReset' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_seek': (.text+0xf3c): undefined reference to `inflateReset' /usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib/libbam.a(razf.o): In function `razf_close': (.text+0x10c8): undefined reference to `inflateEnd' (.text+0x110c): undefined reference to `deflate' (.text+0x112a): undefined reference to `deflateEnd' collect2: error: ld returned 1 exit status Makefile:71: recipe for target 'parseAlignment' failed make[1]: *** [parseAlignment] Error 1 make[1]: Leaving directory '/<>/bitseq-0.7.5+dfsg' dh_auto_build: make -j4 returned exit code 2 debian/rules:16: 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 20180131-0852 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 33064 Build-Time: 105 Distribution: bionic-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 60 Job: bitseq_0.7.5+dfsg-3.dsc Machine Architecture: arm64 Package: bitseq Package-Time: 170 Source-Version: 0.7.5+dfsg-3 Space: 33064 Status: attempted Version: 0.7.5+dfsg-3 -------------------------------------------------------------------------------- Finished at 20180131-0852 Build needed 00:02:50, 33064k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 Scanning for processes to kill in build PACKAGEBUILD-13870331 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 Stopping target for build PACKAGEBUILD-13870331 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-13870331 Removing build PACKAGEBUILD-13870331