RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-004 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 06:33:29 ntpdate[1921]: adjust time server 10.211.37.1 offset -0.028007 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 /home/buildd/filecache-default/78cf3583c71e53d2c7312b9d7596a64d82c6adad Creating target for build PACKAGEBUILD-13629024 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 Starting target for build PACKAGEBUILD-13629024 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 'deb http://ftpmaster.internal/ubuntu bionic main universe' Overriding sources.list in build-PACKAGEBUILD-13629024 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 Updating target for build PACKAGEBUILD-13629024 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main arm64 Packages [1021 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main Translation-en [537 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/universe arm64 Packages [8050 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4864 kB] Fetched 14.7 MB in 8s (1746 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 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: liblsan0 libtsan0 The following packages will be upgraded: apt apt-transport-https base-files base-passwd binutils binutils-aarch64-linux-gnu binutils-common build-essential coreutils cpp-7 debianutils dpkg dpkg-dev findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcurl3-gnutls libdpkg-perl libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libkeyutils1 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-7-dev libstdc++6 libsystemd0 libubsan0 libudev1 linux-libc-dev multiarch-support perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata 71 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 48.4 MB of archives. After this operation, 5457 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main arm64 base-files arm64 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main arm64 coreutils arm64 8.26-3ubuntu4 [1059 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main arm64 debianutils arm64 4.8.3 [84.9 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main arm64 dpkg arm64 1.19.0.4ubuntu1 [1100 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main arm64 findutils arm64 4.6.0+git+20170828-2 [278 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main arm64 perl-modules-5.26 all 5.26.1-2ubuntu1 [2760 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main arm64 libperl5.26 arm64 5.26.1-2ubuntu1 [3329 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main arm64 perl arm64 5.26.1-2ubuntu1 [201 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main arm64 perl-base arm64 5.26.1-2ubuntu1 [1235 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main arm64 libc6-dev arm64 2.26-0ubuntu2 [2013 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main arm64 libc-dev-bin arm64 2.26-0ubuntu2 [59.1 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main arm64 linux-libc-dev arm64 4.13.0-16.19 [930 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main arm64 libgomp1 arm64 7.2.0-16ubuntu1 [62.0 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main arm64 libitm1 arm64 7.2.0-16ubuntu1 [25.5 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main arm64 gcc-7-base arm64 7.2.0-16ubuntu1 [18.6 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcc1 arm64 1:7.2.0-16ubuntu1 [33.4 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main arm64 libatomic1 arm64 7.2.0-16ubuntu1 [6640 B] Get:18 http://ftpmaster.internal/ubuntu bionic/main arm64 libasan4 arm64 7.2.0-16ubuntu1 [335 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main arm64 liblsan0 arm64 7.2.0-16ubuntu1 [122 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main arm64 libtsan0 arm64 7.2.0-16ubuntu1 [265 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main arm64 libubsan0 arm64 7.2.0-16ubuntu1 [117 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main arm64 cpp-7 arm64 7.2.0-16ubuntu1 [5319 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main arm64 libcc1-0 arm64 7.2.0-16ubuntu1 [35.4 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main arm64 g++-7 arm64 7.2.0-16ubuntu1 [6127 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main arm64 gcc-7 arm64 7.2.0-16ubuntu1 [5963 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcc-7-dev arm64 7.2.0-16ubuntu1 [835 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main arm64 libstdc++-7-dev arm64 7.2.0-16ubuntu1 [1455 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main arm64 libstdc++6 arm64 7.2.0-16ubuntu1 [377 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main arm64 libbinutils arm64 2.29.1-8ubuntu1 [426 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main arm64 binutils arm64 2.29.1-8ubuntu1 [3384 B] Get:31 http://ftpmaster.internal/ubuntu bionic/main arm64 binutils-common arm64 2.29.1-8ubuntu1 [190 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main arm64 binutils-aarch64-linux-gnu arm64 2.29.1-8ubuntu1 [2151 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main arm64 libc6 arm64 2.26-0ubuntu2 [2246 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main arm64 base-passwd arm64 3.5.44 [45.6 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main arm64 libc-bin arm64 2.26-0ubuntu2 [475 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main arm64 sysvinit-utils arm64 2.88dsf-59.10ubuntu1 [17.7 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main arm64 libudev1 arm64 235-2ubuntu3 [45.7 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main arm64 libapt-pkg5.0 arm64 1.6~alpha5 [740 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main arm64 libgpg-error0 arm64 1.27-5 [32.8 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main arm64 libgcrypt20 arm64 1.8.1-4 [325 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main arm64 gpgv arm64 2.1.15-1ubuntu8 [156 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main arm64 libseccomp2 arm64 2.3.1-2.1ubuntu3 [33.9 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main arm64 apt arm64 1.6~alpha5 [1112 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main arm64 libapparmor1 arm64 2.11.0-2ubuntu18 [25.8 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main arm64 libcap2 arm64 1:2.25-1.1 [12.4 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main arm64 libip4tc0 arm64 1.6.1-2ubuntu2 [18.3 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main arm64 libpcre3 arm64 2:8.39-5ubuntu3 [203 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main arm64 libselinux1 arm64 2.7-2 [57.4 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main arm64 systemd arm64 235-2ubuntu3 [2488 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main arm64 libsystemd0 arm64 235-2ubuntu3 [164 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main arm64 systemd-sysv arm64 235-2ubuntu3 [12.4 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main arm64 libcap-ng0 arm64 0.7.7-3.1 [10.0 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main arm64 libsemanage-common all 2.7-2 [6916 B] Get:54 http://ftpmaster.internal/ubuntu bionic/main arm64 libsemanage1 arm64 2.7-2 [70.1 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main arm64 libnettle6 arm64 3.3-2 [96.3 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main arm64 libhogweed4 arm64 3.3-2 [128 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main arm64 libp11-kit0 arm64 0.23.9-2 [138 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main arm64 sensible-utils all 0.0.11 [14.8 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main arm64 pinentry-curses arm64 1.0.0-3 [31.3 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main arm64 libnpth0 arm64 1.5-3 [6844 B] Get:61 http://ftpmaster.internal/ubuntu bionic/main arm64 gnupg arm64 2.1.15-1ubuntu8 [706 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main arm64 gnupg-agent arm64 2.1.15-1ubuntu8 [213 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main arm64 libsqlite3-0 arm64 3.20.1-2 [422 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main arm64 multiarch-support arm64 2.26-0ubuntu2 [6832 B] Get:65 http://ftpmaster.internal/ubuntu bionic/main arm64 tzdata all 2017c-1 [188 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main arm64 libkeyutils1 arm64 1.5.9-9.1ubuntu1 [8884 B] Get:67 http://ftpmaster.internal/ubuntu bionic/main arm64 libpng16-16 arm64 1.6.34-1 [161 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main arm64 apt-transport-https all 1.6~alpha5 [1692 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main arm64 dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main arm64 libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main arm64 build-essential arm64 12.4ubuntu1 [4754 B] Get:72 http://ftpmaster.internal/ubuntu bionic/main arm64 libpsl5 arm64 0.19.1-3 [40.3 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main arm64 libcurl3-gnutls arm64 7.55.1-1ubuntu2.1 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.4 MB in 2s (21.8 MB/s) (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_arm64.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 ... 12563 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_arm64.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.3_arm64.deb ... Unpacking debianutils (4.8.3) over (4.8.2) ... Setting up debianutils (4.8.3) ... (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.4ubuntu1_arm64.deb ... Unpacking dpkg (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Setting up dpkg (1.19.0.4ubuntu1) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (Reading database ... 12565 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20170828-2_arm64.deb ... Unpacking findutils (4.6.0+git+20170828-2) over (4.6.0+git+20170729-2) ... Setting up findutils (4.6.0+git+20170828-2) ... (Reading database ... 12565 files and directories currently installed.) Preparing to unpack .../perl_5.26.1-2ubuntu1_arm64.deb ... Unpacking perl (5.26.1-2ubuntu1) over (5.26.0-8ubuntu1) ... Preparing to unpack .../perl-modules-5.26_5.26.1-2ubuntu1_all.deb ... Unpacking perl-modules-5.26 (5.26.1-2ubuntu1) over (5.26.0-8ubuntu1) ... Preparing to unpack .../libperl5.26_5.26.1-2ubuntu1_arm64.deb ... Unpacking libperl5.26:arm64 (5.26.1-2ubuntu1) over (5.26.0-8ubuntu1) ... Preparing to unpack .../perl-base_5.26.1-2ubuntu1_arm64.deb ... Unpacking perl-base (5.26.1-2ubuntu1) over (5.26.0-8ubuntu1) ... Setting up perl-base (5.26.1-2ubuntu1) ... (Reading database ... 12565 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.26-0ubuntu2_arm64.deb ... Unpacking libc6-dev:arm64 (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../1-libc-dev-bin_2.26-0ubuntu2_arm64.deb ... Unpacking libc-dev-bin (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../2-linux-libc-dev_4.13.0-16.19_arm64.deb ... Unpacking linux-libc-dev:arm64 (4.13.0-16.19) over (4.13.0-11.12) ... Preparing to unpack .../3-libgomp1_7.2.0-16ubuntu1_arm64.deb ... Unpacking libgomp1:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../4-libitm1_7.2.0-16ubuntu1_arm64.deb ... Unpacking libitm1:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../5-gcc-7-base_7.2.0-16ubuntu1_arm64.deb ... Unpacking gcc-7-base:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Setting up gcc-7-base:arm64 (7.2.0-16ubuntu1) ... (Reading database ... 12565 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a7.2.0-16ubuntu1_arm64.deb ... Unpacking libgcc1:arm64 (1:7.2.0-16ubuntu1) over (1:7.2.0-6ubuntu1) ... Setting up libgcc1:arm64 (1:7.2.0-16ubuntu1) ... (Reading database ... 12565 files and directories currently installed.) Preparing to unpack .../00-libatomic1_7.2.0-16ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../01-libasan4_7.2.0-16ubuntu1_arm64.deb ... Unpacking libasan4:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Selecting previously unselected package liblsan0:arm64. Preparing to unpack .../02-liblsan0_7.2.0-16ubuntu1_arm64.deb ... Unpacking liblsan0:arm64 (7.2.0-16ubuntu1) ... Selecting previously unselected package libtsan0:arm64. Preparing to unpack .../03-libtsan0_7.2.0-16ubuntu1_arm64.deb ... Unpacking libtsan0:arm64 (7.2.0-16ubuntu1) ... Preparing to unpack .../04-libubsan0_7.2.0-16ubuntu1_arm64.deb ... Unpacking libubsan0:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../05-cpp-7_7.2.0-16ubuntu1_arm64.deb ... Unpacking cpp-7 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../06-libcc1-0_7.2.0-16ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../07-g++-7_7.2.0-16ubuntu1_arm64.deb ... Unpacking g++-7 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../08-gcc-7_7.2.0-16ubuntu1_arm64.deb ... Unpacking gcc-7 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../09-libgcc-7-dev_7.2.0-16ubuntu1_arm64.deb ... Unpacking libgcc-7-dev:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../10-libstdc++-7-dev_7.2.0-16ubuntu1_arm64.deb ... Unpacking libstdc++-7-dev:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Preparing to unpack .../11-libstdc++6_7.2.0-16ubuntu1_arm64.deb ... Unpacking libstdc++6:arm64 (7.2.0-16ubuntu1) over (7.2.0-6ubuntu1) ... Setting up libstdc++6:arm64 (7.2.0-16ubuntu1) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libbinutils_2.29.1-8ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.29.1-8ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils_2.29.1-8ubuntu1_arm64.deb ... Unpacking binutils (2.29.1-8ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils-common_2.29.1-8ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.29.1-8ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../binutils-aarch64-linux-gnu_2.29.1-8ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.29.1-8ubuntu1) over (2.29.1-1ubuntu1) ... Preparing to unpack .../libc6_2.26-0ubuntu2_arm64.deb ... Unpacking libc6:arm64 (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Setting up libc6:arm64 (2.26-0ubuntu2) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.44_arm64.deb ... Unpacking base-passwd (3.5.44) over (3.5.43) ... Setting up base-passwd (3.5.44) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libc-bin_2.26-0ubuntu2_arm64.deb ... Unpacking libc-bin (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Setting up libc-bin (2.26-0ubuntu2) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.88dsf-59.10ubuntu1_arm64.deb ... Unpacking sysvinit-utils (2.88dsf-59.10ubuntu1) over (2.88dsf-59.8git1) ... Setting up sysvinit-utils (2.88dsf-59.10ubuntu1) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libudev1_235-2ubuntu3_arm64.deb ... Unpacking libudev1:arm64 (235-2ubuntu3) over (234-2ubuntu10) ... Setting up libudev1:arm64 (235-2ubuntu3) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.6~alpha5_arm64.deb ... Unpacking libapt-pkg5.0:arm64 (1.6~alpha5) over (1.5~rc4) ... Setting up libapt-pkg5.0:arm64 (1.6~alpha5) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.27-5_arm64.deb ... Unpacking libgpg-error0:arm64 (1.27-5) over (1.27-3) ... Setting up libgpg-error0:arm64 (1.27-5) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.8.1-4_arm64.deb ... Unpacking libgcrypt20:arm64 (1.8.1-4) over (1.7.8-2ubuntu1) ... Setting up libgcrypt20:arm64 (1.8.1-4) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../gpgv_2.1.15-1ubuntu8_arm64.deb ... Unpacking gpgv (2.1.15-1ubuntu8) over (2.1.15-1ubuntu7) ... Setting up gpgv (2.1.15-1ubuntu8) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.3.1-2.1ubuntu3_arm64.deb ... Unpacking libseccomp2:arm64 (2.3.1-2.1ubuntu3) over (2.3.1-2.1ubuntu2) ... Setting up libseccomp2:arm64 (2.3.1-2.1ubuntu3) ... (Reading database ... 12580 files and directories currently installed.) Preparing to unpack .../apt_1.6~alpha5_arm64.deb ... Unpacking apt (1.6~alpha5) over (1.5~rc4) ... Setting up apt (1.6~alpha5) ... (Reading database ... 12576 files and directories currently installed.) Preparing to unpack .../libapparmor1_2.11.0-2ubuntu18_arm64.deb ... Unpacking libapparmor1:arm64 (2.11.0-2ubuntu18) over (2.11.0-2ubuntu17) ... Preparing to unpack .../libcap2_1%3a2.25-1.1_arm64.deb ... Unpacking libcap2:arm64 (1:2.25-1.1) over (1:2.25-1) ... Preparing to unpack .../libip4tc0_1.6.1-2ubuntu2_arm64.deb ... Unpacking libip4tc0:arm64 (1.6.1-2ubuntu2) over (1.6.1-2ubuntu1) ... Preparing to unpack .../libpcre3_2%3a8.39-5ubuntu3_arm64.deb ... Unpacking libpcre3:arm64 (2:8.39-5ubuntu3) over (2:8.39-4) ... Setting up libpcre3:arm64 (2:8.39-5ubuntu3) ... (Reading database ... 12576 files and directories currently installed.) Preparing to unpack .../libselinux1_2.7-2_arm64.deb ... Unpacking libselinux1:arm64 (2.7-2) over (2.7-1) ... Setting up libselinux1:arm64 (2.7-2) ... (Reading database ... 12576 files and directories currently installed.) Preparing to unpack .../systemd_235-2ubuntu3_arm64.deb ... Unpacking systemd (235-2ubuntu3) over (234-2ubuntu10) ... Preparing to unpack .../libsystemd0_235-2ubuntu3_arm64.deb ... Unpacking libsystemd0:arm64 (235-2ubuntu3) over (234-2ubuntu10) ... Setting up libsystemd0:arm64 (235-2ubuntu3) ... Setting up libapparmor1:arm64 (2.11.0-2ubuntu18) ... Setting up libcap2:arm64 (1:2.25-1.1) ... Setting up libip4tc0:arm64 (1.6.1-2ubuntu2) ... Setting up systemd (235-2ubuntu3) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/system.conf ... Removing empty /etc/rc.local Removed /etc/systemd/system/network-online.target.wants/systemd-networkd-wait-online.service. (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../systemd-sysv_235-2ubuntu3_arm64.deb ... Unpacking systemd-sysv (235-2ubuntu3) over (234-2ubuntu10) ... Preparing to unpack .../libcap-ng0_0.7.7-3.1_arm64.deb ... Unpacking libcap-ng0:arm64 (0.7.7-3.1) over (0.7.7-3build1) ... Setting up libcap-ng0:arm64 (0.7.7-3.1) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.7-2_all.deb ... Unpacking libsemanage-common (2.7-2) over (2.7-1) ... Setting up libsemanage-common (2.7-2) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.7-2_arm64.deb ... Unpacking libsemanage1:arm64 (2.7-2) over (2.7-1) ... Setting up libsemanage1:arm64 (2.7-2) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../libnettle6_3.3-2_arm64.deb ... Unpacking libnettle6:arm64 (3.3-2) over (3.3-1) ... Setting up libnettle6:arm64 (3.3-2) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.3-2_arm64.deb ... Unpacking libhogweed4:arm64 (3.3-2) over (3.3-1) ... Setting up libhogweed4:arm64 (3.3-2) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.9-2_arm64.deb ... Unpacking libp11-kit0:arm64 (0.23.9-2) over (0.23.7-3) ... Setting up libp11-kit0:arm64 (0.23.9-2) ... (Reading database ... 12582 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.11_all.deb ... Unpacking sensible-utils (0.0.11) over (0.0.10) ... Preparing to unpack .../01-pinentry-curses_1.0.0-3_arm64.deb ... Unpacking pinentry-curses (1.0.0-3) over (1.0.0-2) ... Preparing to unpack .../02-libnpth0_1.5-3_arm64.deb ... Unpacking libnpth0:arm64 (1.5-3) over (1.5-2) ... Preparing to unpack .../03-gnupg_2.1.15-1ubuntu8_arm64.deb ... Unpacking gnupg (2.1.15-1ubuntu8) over (2.1.15-1ubuntu7) ... Preparing to unpack .../04-gnupg-agent_2.1.15-1ubuntu8_arm64.deb ... Unpacking gnupg-agent (2.1.15-1ubuntu8) over (2.1.15-1ubuntu7) ... Preparing to unpack .../05-libsqlite3-0_3.20.1-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.20.1-2) over (3.19.3-3) ... Preparing to unpack .../06-multiarch-support_2.26-0ubuntu2_arm64.deb ... Unpacking multiarch-support (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../07-tzdata_2017c-1_all.deb ... Unpacking tzdata (2017c-1) over (2017b-2) ... Preparing to unpack .../08-libkeyutils1_1.5.9-9.1ubuntu1_arm64.deb ... Unpacking libkeyutils1:arm64 (1.5.9-9.1ubuntu1) over (1.5.9-9ubuntu1) ... Preparing to unpack .../09-libpng16-16_1.6.34-1_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.34-1) over (1.6.32-2) ... Preparing to unpack .../10-apt-transport-https_1.6~alpha5_all.deb ... Unpacking apt-transport-https (1.6~alpha5) over (1.5~rc4) ... Preparing to unpack .../11-dpkg-dev_1.19.0.4ubuntu1_all.deb ... Unpacking dpkg-dev (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Preparing to unpack .../12-libdpkg-perl_1.19.0.4ubuntu1_all.deb ... Unpacking libdpkg-perl (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Preparing to unpack .../13-build-essential_12.4ubuntu1_arm64.deb ... Unpacking build-essential (12.4ubuntu1) over (12.1ubuntu2) ... Preparing to unpack .../14-libpsl5_0.19.1-3_arm64.deb ... Unpacking libpsl5:arm64 (0.19.1-3) over (0.18.0-2) ... Preparing to unpack .../15-libcurl3-gnutls_7.55.1-1ubuntu2.1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.55.1-1ubuntu2.1) over (7.55.1-1ubuntu1) ... Setting up libnpth0:arm64 (1.5-3) ... Setting up libgomp1:arm64 (7.2.0-16ubuntu1) ... Setting up libatomic1:arm64 (7.2.0-16ubuntu1) ... Setting up libcc1-0:arm64 (7.2.0-16ubuntu1) ... Setting up apt-transport-https (1.6~alpha5) ... Setting up libasan4:arm64 (7.2.0-16ubuntu1) ... Setting up libpng16-16:arm64 (1.6.34-1) ... Setting up libpsl5:arm64 (0.19.1-3) ... Setting up multiarch-support (2.26-0ubuntu2) ... Setting up tzdata (2017c-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Nov 22 06:34:20 UTC 2017. Universal Time is now: Wed Nov 22 06:34:20 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (235-2ubuntu3) ... Setting up libubsan0:arm64 (7.2.0-16ubuntu1) ... Setting up libtsan0:arm64 (7.2.0-16ubuntu1) ... Setting up linux-libc-dev:arm64 (4.13.0-16.19) ... Setting up perl-modules-5.26 (5.26.1-2ubuntu1) ... Setting up cpp-7 (7.2.0-16ubuntu1) ... Setting up liblsan0:arm64 (7.2.0-16ubuntu1) ... Setting up binutils-common:arm64 (2.29.1-8ubuntu1) ... Setting up sensible-utils (0.0.11) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libperl5.26:arm64 (5.26.1-2ubuntu1) ... Setting up libsqlite3-0:arm64 (3.20.1-2) ... Setting up pinentry-curses (1.0.0-3) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:arm64 (1.5.9-9.1ubuntu1) ... Setting up gnupg-agent (2.1.15-1ubuntu8) ... Setting up libc6-dev:arm64 (2.26-0ubuntu2) ... Setting up libitm1:arm64 (7.2.0-16ubuntu1) ... Setting up libbinutils:arm64 (2.29.1-8ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.55.1-1ubuntu2.1) ... Setting up gnupg (2.1.15-1ubuntu8) ... Setting up libgcc-7-dev:arm64 (7.2.0-16ubuntu1) ... Setting up libstdc++-7-dev:arm64 (7.2.0-16ubuntu1) ... Setting up perl (5.26.1-2ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.29.1-8ubuntu1) ... Setting up binutils (2.29.1-8ubuntu1) ... Setting up gcc-7 (7.2.0-16ubuntu1) ... Setting up g++-7 (7.2.0-16ubuntu1) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13629024 arm64 bionic -c chroot:build-PACKAGEBUILD-13629024 --arch=arm64 --dist=bionic --nolog crac_2.5.0+dfsg-2.dsc Initiating build PACKAGEBUILD-13629024 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:30:44 UTC 2017 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-004.buildd +==============================================================================+ | crac 2.5.0+dfsg-2 (arm64) 22 Nov 2017 06:34 | +==============================================================================+ Package: crac Version: 2.5.0+dfsg-2 Source Version: 2.5.0+dfsg-2 Distribution: bionic Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/crac-ZHN20M/crac-2.5.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/crac-ZHN20M' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13629024/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- crac_2.5.0+dfsg-2.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-e10TFp/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-e10TFp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-e10TFp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-e10TFp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-e10TFp/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-e10TFp/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (47.7 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 libwind0-heimdal Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-e10TFp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (40.1 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12579 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), dh-autoreconf, zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config Filtered Build-Depends: debhelper (>= 9), dh-autoreconf, zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config dpkg-deb: building package 'sbuild-build-depends-crac-dummy' in '/<>/resolver-gzDLPB/apt_archive/sbuild-build-depends-crac-dummy.deb'. Ign:1 copy:/<>/resolver-gzDLPB/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gzDLPB/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-gzDLPB/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gzDLPB/apt_archive ./ Sources [264 B] Get:5 copy:/<>/resolver-gzDLPB/apt_archive ./ Packages [584 B] Fetched 2967 B in 0s (63.3 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install crac build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... 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 libgkarrays-dev libgkarrays1 libglib2.0-0 libgzstream-dev libgzstream0 libhts-dev libhts2 libicu60 libjellyfish-2.0-2 libjellyfish-2.0-dev liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db pkg-config po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur 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 intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libgkarrays-dev libgkarrays1 libglib2.0-0 libgzstream-dev libgzstream0 libhts-dev libhts2 libicu60 libjellyfish-2.0-2 libjellyfish-2.0-dev liblzma-dev libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-crac-dummy tabix zlib1g-dev 0 upgraded, 42 newly installed, 1 to remove and 0 not upgraded. Need to get 17.6 MB of archives. After this operation, 68.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-gzDLPB/apt_archive ./ sbuild-build-depends-crac-dummy 0.invalid.0 [912 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main arm64 groff-base arm64 1.22.3-9 [1129 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main arm64 libbsd0 arm64 0.8.6-3 [36.6 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main arm64 bsdmainutils arm64 9.0.14ubuntu1 [173 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main arm64 libpipeline1 arm64 1.5.0-1 [22.0 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main arm64 man-db arm64 2.7.6.1-2 [871 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main arm64 libmagic-mgc arm64 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main arm64 libmagic1 arm64 1:5.32-1 [61.7 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main arm64 file arm64 1:5.32-1 [21.6 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main arm64 libglib2.0-0 arm64 2.54.1-1ubuntu1 [980 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main arm64 libicu60 arm64 60.1-1ubuntu2 [7976 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main arm64 libxml2 arm64 2.9.4+dfsg1-5ubuntu2 [553 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main arm64 gettext-base arm64 0.19.8.1-4ubuntu1 [46.0 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main arm64 libsigsegv2 arm64 2.11-1 [12.5 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main arm64 m4 arm64 1.4.18-1 [185 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main arm64 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main arm64 autotools-dev all 20161112.1+nmu1 [40.2 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main arm64 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main arm64 autopoint all 0.19.8.1-4ubuntu1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main arm64 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-autoreconf all 15 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main arm64 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main arm64 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main arm64 libcroco3 arm64 0.6.12-1 [66.1 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main arm64 gettext arm64 0.19.8.1-4ubuntu1 [1020 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main arm64 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main arm64 debhelper all 10.10.5ubuntu1 [876 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/universe arm64 libgkarrays1 arm64 2.1.0+dfsg-1 [46.2 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/universe arm64 libgkarrays-dev arm64 2.1.0+dfsg-1 [74.0 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/universe arm64 libgzstream0 arm64 1.5+dfsg-2 [6192 B] Get:34 http://ftpmaster.internal/ubuntu bionic/universe arm64 libgzstream-dev arm64 1.5+dfsg-2 [6398 B] Get:35 http://ftpmaster.internal/ubuntu bionic/universe arm64 libhts2 arm64 1.5-1 [239 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main arm64 liblzma-dev arm64 5.2.2-1.3 [137 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/universe arm64 tabix arm64 1.5-1 [253 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/universe arm64 libhts-dev arm64 1.5-1 [345 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/universe arm64 libjellyfish-2.0-2 arm64 2.2.6-6 [59.5 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/universe arm64 libjellyfish-2.0-dev arm64 2.2.6-6 [128 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main arm64 pkg-config arm64 0.29.1-0ubuntu2 [42.8 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-0ubuntu2 [171 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.6 MB in 1s (9478 kB/s) (Reading database ... 12579 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12570 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_arm64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../01-libbsd0_0.8.6-3_arm64.deb ... Unpacking libbsd0:arm64 (0.8.6-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.14ubuntu1_arm64.deb ... Unpacking bsdmainutils (9.0.14ubuntu1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.0-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-2_arm64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_arm64.deb ... Unpacking libmagic-mgc (1:5.32-1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../06-libmagic1_1%3a5.32-1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.32-1) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.32-1_arm64.deb ... Unpacking file (1:5.32-1) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../08-libglib2.0-0_2.54.1-1ubuntu1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.54.1-1ubuntu1) ... Selecting previously unselected package libicu60:arm64. Preparing to unpack .../09-libicu60_60.1-1ubuntu2_arm64.deb ... Unpacking libicu60:arm64 (60.1-1ubuntu2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../10-libxml2_2.9.4+dfsg1-5ubuntu2_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-5ubuntu2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-4ubuntu1_arm64.deb ... Unpacking gettext-base (0.19.8.1-4ubuntu1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../12-libsigsegv2_2.11-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.11-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-1_arm64.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20161112.1+nmu1_all.deb ... Unpacking autotools-dev (20161112.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.15.1-3ubuntu1_all.deb ... Unpacking automake (1:1.15.1-3ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-4ubuntu1_all.deb ... Unpacking autopoint (0.19.8.1-4ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-2_all.deb ... Unpacking libtool (2.4.6-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_15_all.deb ... Unpacking dh-autoreconf (15) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.59-1_all.deb ... Unpacking libarchive-zip-perl (1.59-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_0.040-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.040-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../22-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_0.040-1_all.deb ... Unpacking dh-strip-nondeterminism (0.040-1) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../24-libcroco3_0.6.12-1_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-4ubuntu1_arm64.deb ... Unpacking gettext (0.19.8.1-4ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_10.10.5ubuntu1_all.deb ... Unpacking debhelper (10.10.5ubuntu1) ... Selecting previously unselected package libgkarrays1. Preparing to unpack .../29-libgkarrays1_2.1.0+dfsg-1_arm64.deb ... Unpacking libgkarrays1 (2.1.0+dfsg-1) ... Selecting previously unselected package libgkarrays-dev. Preparing to unpack .../30-libgkarrays-dev_2.1.0+dfsg-1_arm64.deb ... Unpacking libgkarrays-dev (2.1.0+dfsg-1) ... Selecting previously unselected package libgzstream0. Preparing to unpack .../31-libgzstream0_1.5+dfsg-2_arm64.deb ... Unpacking libgzstream0 (1.5+dfsg-2) ... Selecting previously unselected package libgzstream-dev. Preparing to unpack .../32-libgzstream-dev_1.5+dfsg-2_arm64.deb ... Unpacking libgzstream-dev (1.5+dfsg-2) ... Selecting previously unselected package libhts2:arm64. Preparing to unpack .../33-libhts2_1.5-1_arm64.deb ... Unpacking libhts2:arm64 (1.5-1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../34-liblzma-dev_5.2.2-1.3_arm64.deb ... Unpacking liblzma-dev:arm64 (5.2.2-1.3) ... Selecting previously unselected package tabix. Preparing to unpack .../35-tabix_1.5-1_arm64.deb ... Unpacking tabix (1.5-1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../36-libhts-dev_1.5-1_arm64.deb ... Unpacking libhts-dev:arm64 (1.5-1) ... Selecting previously unselected package libjellyfish-2.0-2. Preparing to unpack .../37-libjellyfish-2.0-2_2.2.6-6_arm64.deb ... Unpacking libjellyfish-2.0-2 (2.2.6-6) ... Selecting previously unselected package libjellyfish-2.0-dev. Preparing to unpack .../38-libjellyfish-2.0-dev_2.2.6-6_arm64.deb ... Unpacking libjellyfish-2.0-dev (2.2.6-6) ... Selecting previously unselected package pkg-config. Preparing to unpack .../39-pkg-config_0.29.1-0ubuntu2_arm64.deb ... Unpacking pkg-config (0.29.1-0ubuntu2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../40-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package sbuild-build-depends-crac-dummy. Preparing to unpack .../41-sbuild-build-depends-crac-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-crac-dummy (0.invalid.0) ... Setting up libicu60:arm64 (60.1-1ubuntu2) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libgzstream0 (1.5+dfsg-2) ... Setting up libgzstream-dev (1.5+dfsg-2) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:arm64 (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:arm64 (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up libgkarrays1 (2.1.0+dfsg-1) ... Setting up gettext-base (0.19.8.1-4ubuntu1) ... Setting up libpipeline1:arm64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:arm64 (0.8.6-3) ... Setting up libxml2:arm64 (2.9.4+dfsg1-5ubuntu2) ... Setting up libgkarrays-dev (2.1.0+dfsg-1) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:arm64 (1:5.32-1) ... Setting up libcroco3:arm64 (0.6.12-1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20161112.1+nmu1) ... Setting up tabix (1.5-1) ... Setting up liblzma-dev:arm64 (5.2.2-1.3) ... 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 libhts2:arm64 (1.5-1) ... Setting up autopoint (0.19.8.1-4ubuntu1) ... Setting up libjellyfish-2.0-2 (2.2.6-6) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libjellyfish-2.0-dev (2.2.6-6) ... Setting up libhts-dev:arm64 (1.5-1) ... 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 (2.7.6.1-2) ... 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 (10.10.5ubuntu1) ... Setting up sbuild-build-depends-crac-dummy (0.invalid.0) ... (Reading database ... 14658 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 (aarch64) 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_4.13.0-16.19 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-aarch64-linux-gnu_2.29.1-8ubuntu1 binutils-common_2.29.1-8ubuntu1 bsdmainutils_9.0.14ubuntu1 bsdutils_1:2.30.1-0ubuntu4 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_1.5.63 debhelper_10.10.5ubuntu1 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_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.1-0ubuntu4 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_2.30.1-0ubuntu4 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 libcomerr2_1.43.5-1 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_2.30.1-0ubuntu4 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 libgkarrays-dev_2.1.0+dfsg-1 libgkarrays1_2.1.0+dfsg-1 libglib2.0-0_2.54.1-1ubuntu1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-16ubuntu1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libgzstream-dev_1.5+dfsg-2 libgzstream0_1.5+dfsg-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 libhts-dev_1.5-1 libhts2_1.5-1 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 libitm1_7.2.0-16ubuntu1 libjellyfish-2.0-2_2.2.6-6 libjellyfish-2.0-dev_2.2.6-6 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9.1ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 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 liblsan0_7.2.0-16ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.1-0ubuntu4 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 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_2.30.1-0ubuntu4 libsqlite3-0_3.20.1-2 libss2_1.43.5-1 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-7-dev_7.2.0-16ubuntu1 libstdc++6_7.2.0-16ubuntu1 libsystemd0_235-2ubuntu3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.2.0-16ubuntu1 libubsan0_7.2.0-16ubuntu1 libudev1_235-2ubuntu3 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu4 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-5ubuntu2 linux-libc-dev_4.13.0-16.19 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_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mount_2.30.1-0ubuntu4 multiarch-support_2.26-0ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 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 pkg-config_0.29.1-0ubuntu2 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-crac-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-2ubuntu3 systemd-sysv_235-2ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.5-1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 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 Tue Aug 8 19:30:08 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./crac_2.5.0+dfsg-2.dsc dpkg-source: info: extracting crac in crac-2.5.0+dfsg dpkg-source: info: unpacking crac_2.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking crac_2.5.0+dfsg-2.debian.tar.xz dpkg-source: info: applying use_debian_packaged_libgzstream.patch dpkg-source: info: applying use_debian_packaged_libjellyfish.patch dpkg-source: info: applying fix_includes.patch dpkg-source: info: applying skip_failed_test_bug-14958.patch dpkg-source: info: applying use_debian_packages_libgtarrays.patch dpkg-source: info: applying reproducible_build.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-13629024 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13629024 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13629024 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build crac-2.5.0+dfsg dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with autoreconf dh_auto_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_update_autotools_config -a dh_autoreconf -a aclocal: warning: couldn't open directory 'config/m4': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'. libtoolize: copying file 'config/m4/libtool.m4' libtoolize: copying file 'config/m4/ltoptions.m4' libtoolize: copying file 'config/m4/ltsugar.m4' libtoolize: copying file 'config/m4/ltversion.m4' libtoolize: copying file 'config/m4/lt~obsolete.m4' configure.ac:147: installing 'config/compile' configure.ac:139: installing 'config/config.guess' configure.ac:139: installing 'config/config.sub' configure.ac:137: installing 'config/install-sh' configure.ac:137: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' test_f/Makefile.am:109: warning: shell find . -name "*.should_get": non-POSIX variable name test_f/Makefile.am:109: (probably a GNU make extension) test_f/Makefile.am:110: warning: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name test_f/Makefile.am:110: (probably a GNU make extension) test_f/Makefile.am:111: warning: shell find . -name "*.fastq" -o -name "*.fq": non-POSIX variable name test_f/Makefile.am:111: (probably a GNU make extension) parallel-tests: installing 'config/test-driver' dh_auto_configure -a ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for gawk... (cached) mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C preprocessor... gcc -E checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for ld used by gcc... (cached) /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes checking for dpkg... /usr/bin/dpkg checking for rpmbuild... no checking for sqrt in -lm... yes checking for pthread_join in -lpthread... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether sys/types.h defines makedev... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for memory.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking sys/file.h usability... yes checking sys/file.h presence... yes checking for sys/file.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for int64_t... yes checking for off_t... yes checking for size_t... (cached) yes checking for struct stat.st_blksize... yes checking for uint32_t... yes checking for uint8_t... yes checking for ptrdiff_t... no checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for gettimeofday... yes checking for memchr... yes checking for memmove... yes checking for memset... yes checking for mkfifo... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strrchr... yes checking for strstr... yes checking for strtol... yes checking for gzread in -lz... yes checking for hts_open in -lhts... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating control config.status: creating crac.spec config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating src/libReadsInfo/Makefile config.status: creating src/libSSA/Makefile config.status: creating src/libReadsReader/Makefile config.status: creating src/libReadsReader/kseq/Makefile config.status: creating man/Makefile config.status: creating man/crac.1 config.status: creating scripts/crac-client config.status: creating test_f/Makefile config.status: creating test_f/bug/Makefile config.status: creating test_f/causes/Makefile config.status: creating test_f/cigar/Makefile config.status: creating test_f/splices_adjust/Makefile config.status: creating config/config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build -a make -j1 make[1]: Entering directory '/<>/crac-2.5.0+dfsg' Making all in src make[2]: Entering directory '/<>/crac-2.5.0+dfsg/src' Making all in libReadsInfo make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioTagIndelInfo.o `test -f 'BioTagIndelInfo.cpp' || echo './'`BioTagIndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioUndeterminedInfo.o `test -f 'BioUndeterminedInfo.cpp' || echo './'`BioUndeterminedInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-cigarTypes.o `test -f 'cigarTypes.cpp' || echo './'`cigarTypes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-Cigar.o `test -f 'Cigar.cpp' || echo './'`Cigar.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-DuplicationInfo.o `test -f 'DuplicationInfo.cpp' || echo './'`DuplicationInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-genericInfo.o `test -f 'genericInfo.cpp' || echo './'`genericInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-IndelInfo.o `test -f 'IndelInfo.cpp' || echo './'`IndelInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-repetitionInfo.o `test -f 'repetitionInfo.cpp' || echo './'`repetitionInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SeqErrInfo.o `test -f 'SeqErrInfo.cpp' || echo './'`SeqErrInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo './'`SNPInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo './'`SpliceInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo './'`SpliceInterInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo './'`SpliceIntraInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo './'`SpliceNoCoverInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo './'`SplicingInfo.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp samHeader.cpp: In member function ‘bam_hdr_t* SamHeader::writeBamHeader(samFile*)’: samHeader.cpp:160:15: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] sam_hdr_write(out,h); ~~~~~~~~~~~~~^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp In file included from ../libReadsReader/readsReader.h:57:0, from ../Read.h:55, from ../ReadIndex.h:52, from ../Support.h:59, from tagInfo.h:71, from tagInfo.cpp:53: ../libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ ../libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp rm -f libReadsInfo.a ar cru libReadsInfo.a libReadsInfo_a-BioTagIndelInfo.o libReadsInfo_a-BioUndeterminedInfo.o libReadsInfo_a-cigarTypes.o libReadsInfo_a-Cigar.o libReadsInfo_a-DuplicationInfo.o libReadsInfo_a-genericInfo.o libReadsInfo_a-IndelInfo.o libReadsInfo_a-repetitionInfo.o libReadsInfo_a-SeqErrInfo.o libReadsInfo_a-SNPInfo.o libReadsInfo_a-SpliceInfo.o libReadsInfo_a-SpliceInterInfo.o libReadsInfo_a-SpliceIntraInfo.o libReadsInfo_a-SpliceNoCoverInfo.o libReadsInfo_a-SplicingInfo.o libReadsInfo_a-samLine.o libReadsInfo_a-samHeader.o libReadsInfo_a-bamUtils.o libReadsInfo_a-tagInfo.o libReadsInfo_a-undeterminedErrorInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsInfo.a make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' Making all in libSSA make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libSSA' g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitarray.o bitarray.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitrankw32int.o bitrankw32int.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o chrPosition.o chrPosition.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Huffman_Codes.o Huffman_Codes.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateOnGenome.o locateOnGenome.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateTags.o locateTags.cpp In file included from /usr/include/libGkArrays/readsReader.h:109:0, from locateTags.h:60, from locateTags.cpp:53: /usr/include/libGkArrays/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ /usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ /usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp rm -f libSSA.a ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libSSA.a g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt `pkg-config --cflags libGkArrays` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cracIndex.o cracIndex.cpp cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "\tCompiled on " <<__DATE__ << endl << endl; ^~~~~~~~ In file included from ./seqan/basic.h:64:0, from ./seqan/sequence.h:27, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./seqan/sequence.h:38:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./seqan/sequence.h:51:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./seqan/sequence.h:53:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./seqan/sequence.h:57:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./seqan/sequence.h:62:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ In file included from ./seqan/index.h:82:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_base.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)’: ./seqan/index/shape_base.h:273:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)’: ./seqan/index/shape_base.h:309:65: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h:310:64: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< Shape > >::Type TSize; ^~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:322:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:424:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_base.h: In function ‘typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)’: ./seqan/index/shape_base.h:492:56: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ In file included from ./seqan/index.h:83:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11, from cracIndex.cpp:67: ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)’: ./seqan/index/shape_gapped.h:370:62: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape >::Type THValue; ^~~~~~~ ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)’: ./seqan/index/shape_gapped.h:387:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ ./seqan/index/shape_gapped.h: In function ‘typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)’: ./seqan/index/shape_gapped.h:415:75: warning: typedef ‘THValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value< Shape > >::Type THValue; ^~~~~~~ In file included from ./seqan/file.h:66:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align&, FastaAlign)’: ./seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ ./seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)’: ./seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^~~~~~~~~ In file included from ./seqan/file.h:69:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13, from cracIndex.cpp:67: ./seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)’: ./seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ In file included from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13:0, from cracIndex.cpp:67: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from cracIndex.cpp:67:0: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor ‘KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()’: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample ^~~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::buildSamples()’: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^~~~~~~~~ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA::nextBlock()’: /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:745:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TAlphabet; ^~~~~~~~~ In file included from ./seqan/sequence.h:57:0, from /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10, from cracIndex.cpp:67: ./seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts, seqan::Packed<> > >’: ./seqan/sequence/string_packed.h:906:43: required from ‘typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]’ ./seqan/sequence/string_packed.h:1237:17: required from ‘typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]’ ./seqan/sequence/string_base.h:181:29: required from ‘typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]’ /<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:354:32: required from here ./seqan/sequence/string_packed.h:294:37: warning: comparison between ‘enum seqan::BitsPerValue >::’ and ‘enum seqan::BitsPerValue::’ [-Wenum-compare] VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./seqan/sequence/string_packed.h: In instantiation of ‘struct seqan::_PackedConsts, seqan::Packed<> > >’: ./seqan/sequence/string_packed.h:958:50: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Iter >&) [with TContainer = seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::GetValue > >::Type = seqan::SimpleType]’ ./seqan/basic/basic_proxy.h:242:17: required from ‘typename seqan::GetValue >::Type seqan::getValue(const seqan::Proxy&) [with TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::GetValue >::Type = seqan::SimpleType]’ ./seqan/basic/basic_proxy.h:272:34: required from ‘typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; TSpec = seqan::IteratorProxy, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::Convert >::Type = char]’ ./seqan/basic/basic_converter.h:111:20: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Packed<> >, seqan::Packed<> > > >; typename seqan::Convert::Type = char]’ cracIndex.cpp:224:50: required from here ./seqan/sequence/string_packed.h:294:37: warning: comparison between ‘enum seqan::BitsPerValue >::’ and ‘enum seqan::BitsPerValue::’ [-Wenum-compare] /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/<>/crac-2.5.0+dfsg/src/libSSA/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/<>/crac-2.5.0+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libSSA' Making all in libReadsReader make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' Making all in kseq make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' g++ -DHAVE_CONFIG_H -I. -I../../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsReader_a-readsReader.o `test -f 'readsReader.cpp' || echo './'`readsReader.cpp rm -f libReadsReader.a ar cru libReadsReader.a libReadsReader_a-readsReader.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libReadsReader.a make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Classifier.o Classifier.cpp In file included from ./libReadsReader/readsReader.h:57:0, from ./Read.h:55, from ./ReadIndex.h:52, from ./Classifier.h:56, from Classifier.cpp:52: ./libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ ./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ ./libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ Classifier.cpp: In member function ‘virtual void SingleReadClassifier::classify()’: Classifier.cpp:203:33: warning: ‘bioundetermined_type’ may be used uninitialized in this function [-Wmaybe-uninitialized] taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ suppoBreak->getPositionStartBreak(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bioundetermined_type, ~~~~~~~~~~~~~~~~~~~~~ message.c_str()); ~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o classifyTags.o classifyTags.cpp classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl; ^~~~~~~~ In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from classifyTags.cpp:52: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GkReadIndex.o GkReadIndex.cpp In file included from /usr/include/libGkArrays/bitvector.hxx:104:0, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104:0, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline bool operator[](const CountWordSize i) const throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator--() throw (BinVectOverflow); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241:0, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241:0, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112:0, from GkReadIndex.h:60, from GkReadIndex.cpp:55: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void realloc(uintSA nbElements) throw (logic_error); ^~~~~ In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from GkReadIndex.h:59, from GkReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o JellyReadIndex.o JellyReadIndex.cpp In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from JellyReadIndex.h:59, from JellyReadIndex.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o crac.o crac.cpp crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] printf("\tCompiled on %s.\n\n",__DATE__); ^~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104:0, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator=(const LargeBinVect &v) throw (std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104:0, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline bool operator[](const CountWordSize i) const throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline bool GetBit(const CountWordSize i) const throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Append(const bool value) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator++() throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator++(int) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect &operator--() throw (BinVectOverflow); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); ^~~~~ /usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] inline LargeBinVect Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc); ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241:0, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc) ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/largebinvect.hxx:241:0, from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, from crac.cpp:69: /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool LargeBinVect::GetBit(const CountWordSize i) const throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator+=(const LargeBinVect &v) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator++() throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator++(int) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect &LargeBinVect::operator--() throw (BinVectOverflow) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::operator--(int) throw (BinVectOverflow, std::bad_alloc) { ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LargeBinVect LargeBinVect::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) { ^~~~~ In file included from /usr/include/libGkArrays/gkArrays.h:112:0, from crac.cpp:69: /usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument); ^~~~~ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void realloc(uintSA nbElements) throw (logic_error); ^~~~~ In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from crac.cpp:66: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Parameters.o Parameters.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SupportBreak.o SupportBreak.cpp In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from SupportBreak.cpp:55: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BreakList.o BreakList.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.cpp In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from Support.h:59, from Support.cpp:57: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp locateServer.cpp: In function ‘void* launchSubServer(void*)’: locateServer.cpp:464:8: warning: unused variable ‘threshold’ [-Wunused-variable] uint threshold = indexTags->getFactorLength(); ^~~~~~~~~ locateServer.cpp:466:9: warning: variable ‘dontCare’ set but not used [-Wunused-but-set-variable] char *dontCare, *variable, *tag_length, *factor; ^~~~~~~~ locateServer.cpp: In function ‘void locateServer(ClassifyTags*, const char*, const char*)’: locateServer.cpp:717:9: warning: variable ‘dontCare’ set but not used [-Wunused-but-set-variable] char *dontCare; ^~~~~~~~ In file included from libReadsReader/readsReader.h:57:0, from Read.h:55, from ReadIndex.h:52, from classifyTags.h:53, from locateServer.cpp:59: libReadsReader/readsReader.h: At global scope: libReadsReader/kseq/kseq.h:169:14: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] static int kseq_read(kseq_t *seq) \ ^ libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro ‘__KSEQ_READ’ __KSEQ_READ ^~~~~~~~~~~ libReadsReader/readsReader.h:59:1: note: in expansion of macro ‘KSEQ_INIT’ KSEQ_INIT(gzFile, gzread) ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/<>/crac-2.5.0+dfsg -I/<>/crac-2.5.0+dfsg/src -I/<>/crac-2.5.0+dfsg/src/libSSA -I/<>/crac-2.5.0+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish `pkg-config --cflags libGkArrays` `pkg-config --cflags libProgressBar` -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/<>/crac-2.5.0+dfsg/src/libSSA -L/<>/crac-2.5.0+dfsg/src/libReadsInfo -L/<>/crac-2.5.0+dfsg/src/libReadsReader -ljellyfish-2.0 `pkg-config --libs libGkArrays` `pkg-config --libs libProgressBar` -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /<>/crac-2.5.0+dfsg/src/libSSA/libSSA.a /<>/crac-2.5.0+dfsg/src/libReadsInfo/libReadsInfo.a /<>/crac-2.5.0+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/crac-2.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/<>/crac-2.5.0+dfsg/src/libSSA -L/<>/crac-2.5.0+dfsg/src/libReadsInfo -L/<>/crac-2.5.0+dfsg/src/libReadsReader /usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /<>/crac-2.5.0+dfsg/src/libSSA/libSSA.a /<>/crac-2.5.0+dfsg/src/libReadsInfo/libReadsInfo.a /<>/crac-2.5.0+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm ln -s -f /<>/crac-2.5.0+dfsg/src/libSSA/crac-index crac-index make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/src' Making all in man make[2]: Entering directory '/<>/crac-2.5.0+dfsg/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/man' Making all in scripts make[2]: Entering directory '/<>/crac-2.5.0+dfsg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/scripts' Making all in test_f make[2]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' Making all in causes make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/causes' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/causes' Making all in bug make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/bug' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/bug' Making all in cigar make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/cigar' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/cigar' Making all in splices_adjust make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Entering directory '/<>/crac-2.5.0+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg' make[1]: Leaving directory '/<>/crac-2.5.0+dfsg' dh_auto_test -a make -j1 check VERBOSE=1 make[1]: Entering directory '/<>/crac-2.5.0+dfsg' Making check in src make[2]: Entering directory '/<>/crac-2.5.0+dfsg/src' Making check in libReadsInfo make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' Making check in libSSA make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libSSA' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libSSA' Making check in libReadsReader make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' Making check in kseq make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/src' Making check in man make[2]: Entering directory '/<>/crac-2.5.0+dfsg/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/man' Making check in scripts make[2]: Entering directory '/<>/crac-2.5.0+dfsg/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/scripts' Making check in test_f make[2]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' Making check in causes make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/causes' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/causes' Making check in bug make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/bug' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/bug' Making check in cigar make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/cigar' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/cigar' Making check in splices_adjust make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' make check-TESTS make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' make[5]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' PASS: index_genomes.sh PASS: launch_sg.sh PASS: test_index.sh ============================================================================ Testsuite summary for crac 2.5.0 ============================================================================ # TOTAL: 3 # PASS: 3 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Entering directory '/<>/crac-2.5.0+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/<>/crac-2.5.0+dfsg' make[1]: Leaving directory '/<>/crac-2.5.0+dfsg' fakeroot debian/rules binary-arch dh binary-arch --with autoreconf dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/crac-2.5.0\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/crac-2.5.0+dfsg' Making install in src make[2]: Entering directory '/<>/crac-2.5.0+dfsg/src' Making install in libReadsInfo make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsInfo' Making install in libSSA make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libSSA' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libSSA' /bin/mkdir -p '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /<>/crac-2.5.0+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libSSA' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libSSA' Making install in libReadsReader make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' Making install in kseq make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/crac-2.5.0+dfsg/debian/crac/usr/include/crac-2.5.0/kseq' /usr/bin/install -c -m 644 kseq.h '/<>/crac-2.5.0+dfsg/debian/crac/usr/include/crac-2.5.0/kseq' make[5]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader/kseq' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[5]: Entering directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src/libReadsReader' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/src' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/src' /bin/mkdir -p '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /<>/crac-2.5.0+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/src' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/src' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/src' Making install in man make[2]: Entering directory '/<>/crac-2.5.0+dfsg/man' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/crac-2.5.0+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/<>/crac-2.5.0+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/man' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/man' Making install in scripts make[2]: Entering directory '/<>/crac-2.5.0+dfsg/scripts' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/scripts' /bin/mkdir -p '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/<>/crac-2.5.0+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/scripts' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/scripts' Making install in test_f make[2]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' Making install in causes make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/causes' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/causes' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/causes' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/causes' Making install in bug make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/bug' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/bug' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/bug' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/bug' Making install in cigar make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/cigar' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/cigar' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/cigar' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/cigar' Making install in splices_adjust make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f/splices_adjust' make[3]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' make[4]: Entering directory '/<>/crac-2.5.0+dfsg/test_f' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[3]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg/test_f' make[2]: Entering directory '/<>/crac-2.5.0+dfsg' make[3]: Entering directory '/<>/crac-2.5.0+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/crac-2.5.0+dfsg' make[2]: Leaving directory '/<>/crac-2.5.0+dfsg' make[1]: Leaving directory '/<>/crac-2.5.0+dfsg' 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 crac (in debian/crac); do_strip: , oemstrip: pkgstriptranslations: processing crac-dbgsym (in debian/.debhelper/crac/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/crac/DEBIAN/control, package crac, directory debian/crac pkgstripfiles: Running PNG optimization (using 4 cpus) for package crac ... pkgstripfiles: processing control file: debian/.debhelper/crac/dbgsym-root/DEBIAN/control, package crac-dbgsym, directory debian/.debhelper/crac/dbgsym-root pkgstripfiles: No PNG files. pkgstripfiles: Running PNG optimization (using 4 cpus) for package crac-dbgsym ... dpkg-deb: building package 'crac' in '../crac_2.5.0+dfsg-2_arm64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'crac-dbgsym' in 'debian/.debhelper/scratch-space/build-crac/crac-dbgsym_2.5.0+dfsg-2_arm64.deb'. Renaming crac-dbgsym_2.5.0+dfsg-2_arm64.deb to crac-dbgsym_2.5.0+dfsg-2_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../crac_2.5.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build crac-2.5.0+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171122-0637 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ crac_2.5.0+dfsg-2_arm64.changes: -------------------------------- Format: 1.8 Date: Tue, 08 Aug 2017 21:16:46 +0200 Source: crac Binary: crac Architecture: arm64 Version: 2.5.0+dfsg-2 Distribution: bionic Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: crac - integrated RNA-Seq read analysis Closes: 859300 Changes: crac (2.5.0+dfsg-2) unstable; urgency=low . [ Steffen Moeller ] * debian/upstream/metadata: Added reference to registries * debian/copyright: Corrected upstream name to CRAC . [ Sascha Steinbiss ] * Make build reproducible. Thanks to Chris Lamb for the patch. Closes: #859300 Checksums-Sha1: a5a2aeb9d104fcce7f766333c4cd0323f8ef8b32 1552872 crac-dbgsym_2.5.0+dfsg-2_arm64.ddeb 3cd68c4fb3c4fbd95d76b397b599787ff9805604 6302 crac_2.5.0+dfsg-2_arm64.buildinfo 4c03c1e2dd6d937957a8bb701a6078879e5afbf1 244172 crac_2.5.0+dfsg-2_arm64.deb Checksums-Sha256: 7baab5dee57a15449b700e8af1b0fcdd0745c1061c69a034c9329eb8d8c6ff06 1552872 crac-dbgsym_2.5.0+dfsg-2_arm64.ddeb 8479c3eb6c5859744daebd89653879cf2347d188496aa28082883778fa65eca8 6302 crac_2.5.0+dfsg-2_arm64.buildinfo f6775d68e85f3da31ad521a2f3fe2aee0cb477d2c797a60c97e3ed4c2944f0e2 244172 crac_2.5.0+dfsg-2_arm64.deb Files: 33c563314007e2e9346e63f07c2499bb 1552872 debug optional crac-dbgsym_2.5.0+dfsg-2_arm64.ddeb 0f15572301aeb7e5d632e6251016cb5b 6302 science optional crac_2.5.0+dfsg-2_arm64.buildinfo 35429970bd329cfbfe47afd401a99405 244172 science optional crac_2.5.0+dfsg-2_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ crac_2.5.0+dfsg-2_arm64.deb --------------------------- new debian package, version 2.0. size 244172 bytes: control archive=1380 bytes. 1524 bytes, 26 lines control 485 bytes, 8 lines md5sums Package: crac Version: 2.5.0+dfsg-2 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 654 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.0), libgkarrays1, libgzstream0, libhts2, libjellyfish-2.0-2, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://crac.gforge.inria.fr/ Description: integrated RNA-Seq read analysis CRAC is a tool to analyze High Throughput Sequencing (HTS) data in comparison to a reference genome. It is intended for transcriptomic and genomic sequencing reads. More precisely, with transcriptomic reads as input, it predicts point mutations, indels, splice junction, and chimeric RNAs (ie, non colinear splice junctions). CRAC can also output positions and nature of sequence error that it detects in the reads. CRAC uses a genome index. This index must be computed before running the read analysis. For this sake, use the command "crac-index" on your genome files. You can then process the reads using the command crac. See the man page of CRAC (help file) by typing "man crac". CRAC requires large amount of main memory on your computer. For processing against the Human genome, say 50 million reads of 100 nucleotide each, CRAC requires about 40 gigabytes of main memory. Check whether the system of your computing server is equipped with sufficient amount of memory before launching an analysis. drwxr-xr-x root/root 0 2017-08-08 19:16 ./ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/bin/ -rwxr-xr-x root/root 439048 2017-08-08 19:16 ./usr/bin/crac -rwxr-xr-x root/root 11120 2017-08-08 19:16 ./usr/bin/crac-client -rwxr-xr-x root/root 156464 2017-08-08 19:16 ./usr/bin/crac-index drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/include/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/include/crac-2.5.0/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/include/crac-2.5.0/kseq/ -rw-r--r-- root/root 12765 2017-08-08 19:16 ./usr/include/crac-2.5.0/kseq/kseq.h drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/share/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/share/doc/crac/ -rw-r--r-- root/root 2004 2015-07-10 14:36 ./usr/share/doc/crac/README.gz -rw-r--r-- root/root 338 2017-08-08 19:16 ./usr/share/doc/crac/changelog.Debian.gz -rw-r--r-- root/root 25986 2017-08-08 19:14 ./usr/share/doc/crac/copyright drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/share/man/ drwxr-xr-x root/root 0 2017-08-08 19:16 ./usr/share/man/man1/ -rw-r--r-- root/root 6448 2017-08-08 19:16 ./usr/share/man/man1/crac.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 37748 Build-Time: 182 Distribution: bionic Host Architecture: arm64 Install-Time: 21 Job: crac_2.5.0+dfsg-2.dsc Machine Architecture: arm64 Package: crac Package-Time: 205 Source-Version: 2.5.0+dfsg-2 Space: 37748 Status: successful Version: 2.5.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 20171122-0637 Build needed 00:03:25, 37748k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 Scanning for processes to kill in build PACKAGEBUILD-13629024 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 Stopping target for build PACKAGEBUILD-13629024 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-13629024 Removing build PACKAGEBUILD-13629024