RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-019 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:29:59 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_157 python-lpbuildd_157 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.3 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 12 Feb 05:09:49 ntpdate[1803]: adjust time server 10.211.37.1 offset 0.008260 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 /home/buildd/filecache-default/b6762bcd0bec7d108ffb0fb3fb0b7d1ce32df8bb Creating target for build PACKAGEBUILD-14340990 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 Starting target for build PACKAGEBUILD-14340990 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14340990 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 Updating target for build PACKAGEBUILD-14340990 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 Packages [1007 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe i386 Packages [8334 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4920 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 Packages [129 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [51.1 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe i386 Packages [554 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [158 kB] Fetched 16.3 MB in 4s (3414 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libustr-1.0-1 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: dirmngr gcc-8-base gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm libargon2-0 libcom-err2 libcryptsetup12 libext2fs2 libgdbm5 libjson-c3 libmpfr6 libnghttp2-14 libssl1.1 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd bash binutils binutils-common binutils-i686-linux-gnu bsdutils build-essential coreutils cpp-7 dash debconf debianutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi6 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 libmount1 libmpc3 libmpx2 libncurses5 libncursesw5 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libprocps6 libpsl5 libquadmath0 libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login lsb-base mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata ubuntu-keyring util-linux 145 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 71.2 MB of archives. After this operation, 12.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main i386 perl-modules-5.26 all 5.26.1-4build1 [2760 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main i386 libgdbm5 i386 1.14.1-3 [30.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main i386 libperl5.26 i386 5.26.1-4build1 [3173 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 perl i386 5.26.1-4build1 [201 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 perl-base i386 5.26.1-4build1 [1494 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libc6-dev i386 2.26-0ubuntu4 [2143 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libc-dev-bin i386 2.26-0ubuntu4 [67.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 linux-libc-dev i386 4.15.0-9.10 [964 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gcc-8-base i386 8-20180208-0ubuntu1 [18.0 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libgcc1 i386 1:8-20180208-0ubuntu1 [48.3 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libc6 i386 2.26-0ubuntu4 [2530 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main i386 init-system-helpers all 1.51 [37.3 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main i386 base-files i386 10ubuntu1 [55.9 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main i386 debianutils i386 4.8.4 [86.2 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main i386 bash i386 4.4.18-1ubuntu1 [662 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main i386 bsdutils i386 1:2.30.2-0.1ubuntu2 [62.6 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main i386 coreutils i386 8.28-1ubuntu1 [1306 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main i386 dpkg i386 1.19.0.5ubuntu1 [1162 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main i386 dash i386 0.5.8-2.10 [93.2 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main i386 libcom-err2 i386 1.43.9-1 [11.7 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main i386 libcomerr2 all 1.43.9-1 [7368 B] Get:22 http://ftpmaster.internal/ubuntu bionic/main i386 libext2fs2 i386 1.43.9-1 [184 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main i386 e2fslibs all 1.43.9-1 [7368 B] Get:24 http://ftpmaster.internal/ubuntu bionic/main i386 e2fsprogs i386 1.43.9-1 [537 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main i386 findutils i386 4.6.0+git+20170828-2 [305 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main i386 hostname i386 3.20 [11.7 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main i386 login i386 1:4.5-1ubuntu1 [309 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main i386 libncurses5 i386 6.0+20171125-1ubuntu1 [101 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main i386 libtinfo5 i386 6.0+20171125-1ubuntu1 [80.6 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main i386 libncursesw5 i386 6.0+20171125-1ubuntu1 [128 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main i386 ncurses-bin i386 6.0+20171125-1ubuntu1 [165 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main i386 sed i386 4.4-2 [185 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main i386 libuuid1 i386 2.30.2-0.1ubuntu2 [16.1 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main i386 libblkid1 i386 2.30.2-0.1ubuntu2 [133 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main i386 libsmartcols1 i386 2.30.2-0.1ubuntu2 [85.7 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main i386 libfdisk1 i386 2.30.2-0.1ubuntu2 [173 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main i386 libpcre3 i386 2:8.39-9 [228 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main i386 libselinux1 i386 2.7-2build1 [73.0 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main i386 libmount1 i386 2.30.2-0.1ubuntu2 [143 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main i386 fdisk i386 2.30.2-0.1ubuntu2 [115 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main i386 util-linux i386 2.30.2-0.1ubuntu2 [905 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main i386 base-passwd i386 3.5.44 [47.8 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libc-bin i386 2.26-0ubuntu4 [571 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main i386 ncurses-base all 6.0+20171125-1ubuntu1 [17.3 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main i386 sysvinit-utils i386 2.88dsf-59.10ubuntu1 [19.3 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libstdc++6 i386 8-20180208-0ubuntu1 [432 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libudev1 i386 237-1ubuntu3 [58.3 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main i386 libapt-pkg5.0 i386 1.6~alpha7ubuntu1 [869 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main i386 libaudit-common all 1:2.8.2-1ubuntu1 [4132 B] Get:50 http://ftpmaster.internal/ubuntu bionic/main i386 libcap-ng0 i386 0.7.7-3.1 [11.2 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main i386 libaudit1 i386 1:2.8.2-1ubuntu1 [40.1 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main i386 libsemanage-common all 2.7-2build1 [6944 B] Get:53 http://ftpmaster.internal/ubuntu bionic/main i386 libsemanage1 i386 2.7-2build1 [93.3 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main i386 passwd i386 1:4.5-1ubuntu1 [818 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main i386 debconf all 1.5.65 [124 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main i386 adduser all 3.116ubuntu1 [163 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main i386 libgpg-error0 i386 1.27-6 [41.4 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main i386 libgcrypt20 i386 1.8.1-4 [398 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpgv i386 2.2.4-1ubuntu1 [216 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main i386 ubuntu-keyring all 2018.02.06 [20.7 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main i386 libgmp10 i386 2:6.1.2+dfsg-2 [246 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main i386 libnettle6 i386 3.4-1 [127 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main i386 libhogweed4 i386 3.4-1 [139 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main i386 libidn2-0 i386 2.0.4-1 [94.8 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main i386 libffi6 i386 3.2.1-8 [17.2 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main i386 libp11-kit0 i386 0.23.9-2 [185 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main i386 libtasn1-6 i386 4.13-2 [38.8 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main i386 libgnutls30 i386 3.5.17-1ubuntu1 [701 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main i386 libseccomp2 i386 2.3.1-2.1ubuntu3 [35.4 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main i386 apt i386 1.6~alpha7ubuntu1 [1179 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main i386 libargon2-0 i386 0~20161029-1.1 [24.9 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main i386 libjson-c3 i386 0.12.1-1.3 [23.3 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main i386 libdevmapper1.02.1 i386 2:1.02.145-4.1ubuntu2 [126 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libcryptsetup12 i386 2:2.0.1-0ubuntu1 [151 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main i386 libapparmor1 i386 2.11.0-2ubuntu19 [30.4 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main i386 libcap2 i386 1:2.25-1.2 [13.4 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main i386 libidn11 i386 1.33-2.1 [46.8 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main i386 libip4tc0 i386 1.6.1-2ubuntu2 [20.4 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main i386 libkmod2 i386 24-1ubuntu3 [46.4 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main i386 mount i386 2.30.2-0.1ubuntu2 [116 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main i386 libprocps6 i386 2:3.3.12-3ubuntu1 [32.3 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main i386 lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main i386 procps i386 2:3.3.12-3ubuntu1 [224 kB] Get:84 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 systemd i386 237-1ubuntu3 [2949 kB] Get:85 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libsystemd0 i386 237-1ubuntu3 [222 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main i386 init i386 1.51 [5864 B] Get:87 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 systemd-sysv i386 237-1ubuntu3 [12.6 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main i386 libss2 i386 1.43.9-1 [11.6 kB] Get:89 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 multiarch-support i386 2.26-0ubuntu4 [6908 B] Get:90 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libitm1 i386 8-20180208-0ubuntu1 [31.0 kB] Get:91 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libmpx2 i386 8-20180208-0ubuntu1 [12.9 kB] Get:92 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libmpc3 i386 1.1.0-1 [46.1 kB] Get:93 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libmpfr6 i386 4.0.1-1 [246 kB] Get:94 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 g++-7 i386 7.3.0-3ubuntu1 [7815 kB] Get:95 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gcc-7 i386 7.3.0-3ubuntu1 [7683 kB] Get:96 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 cpp-7 i386 7.3.0-3ubuntu1 [6968 kB] Get:97 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libcc1-0 i386 8-20180208-0ubuntu1 [41.5 kB] Get:98 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libbinutils i386 2.30-4ubuntu1 [545 kB] Get:99 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 binutils i386 2.30-4ubuntu1 [3392 B] Get:100 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 binutils-common i386 2.30-4ubuntu1 [193 kB] Get:101 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 binutils-i686-linux-gnu i386 2.30-4ubuntu1 [2026 kB] Get:102 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libgomp1 i386 8-20180208-0ubuntu1 [80.9 kB] Get:103 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libatomic1 i386 8-20180208-0ubuntu1 [9684 B] Get:104 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libasan4 i386 7.3.0-3ubuntu1 [361 kB] Get:105 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libubsan0 i386 7.3.0-3ubuntu1 [141 kB] Get:106 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libcilkrts5 i386 7.3.0-3ubuntu1 [47.2 kB] Get:107 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libquadmath0 i386 8-20180208-0ubuntu1 [208 kB] Get:108 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libstdc++-7-dev i386 7.3.0-3ubuntu1 [1486 kB] Get:109 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 libgcc-7-dev i386 7.3.0-3ubuntu1 [2396 kB] Get:110 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gcc-7-base i386 7.3.0-3ubuntu1 [18.9 kB] Get:111 http://ftpmaster.internal/ubuntu bionic/main i386 sensible-utils all 0.0.11 [14.8 kB] Get:112 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gnupg-l10n all 2.2.4-1ubuntu1 [48.6 kB] Get:113 http://ftpmaster.internal/ubuntu bionic/main i386 libassuan0 i386 2.5.1-2 [37.0 kB] Get:114 http://ftpmaster.internal/ubuntu bionic/main i386 readline-common all 7.0-3 [52.9 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main i386 libreadline7 i386 7.0-3 [128 kB] Get:116 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gnupg i386 2.2.4-1ubuntu1 [249 kB] Get:117 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gnupg-agent all 2.2.4-1ubuntu1 [4544 B] Get:118 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpgconf i386 2.2.4-1ubuntu1 [130 kB] Get:119 http://ftpmaster.internal/ubuntu bionic/main i386 pinentry-curses i386 1.1.0-1 [37.8 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/main i386 libnpth0 i386 1.5-3 [7988 B] Get:121 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpg-agent i386 2.2.4-1ubuntu1 [246 kB] Get:122 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gnupg-utils i386 2.2.4-1ubuntu1 [138 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main i386 libsqlite3-0 i386 3.22.0-1 [531 kB] Get:124 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpg i386 2.2.4-1ubuntu1 [507 kB] Get:125 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpg-wks-client i386 2.2.4-1ubuntu1 [102 kB] Get:126 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpg-wks-server i386 2.2.4-1ubuntu1 [94.6 kB] Get:127 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 gpgsm i386 2.2.4-1ubuntu1 [235 kB] Get:128 http://ftpmaster.internal/ubuntu bionic-proposed/main i386 dirmngr i386 2.2.4-1ubuntu1 [342 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main i386 dmsetup i386 2:1.02.145-4.1ubuntu2 [70.5 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/main i386 libroken18-heimdal i386 7.5.0+dfsg-1 [44.8 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/main i386 libasn1-8-heimdal i386 7.5.0+dfsg-1 [183 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-1 [32.1 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-1 [92.6 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/main i386 libwind0-heimdal i386 7.5.0+dfsg-1 [48.3 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-1 [118 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-1 [232 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-1 [16.4 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-1 [106 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [15.6 kB] Get:140 http://ftpmaster.internal/ubuntu bionic/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [52.8 kB] Get:141 http://ftpmaster.internal/ubuntu bionic/main i386 libslang2 i386 2.3.1a-1ubuntu1 [423 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main i386 libssl1.0.0 i386 1.0.2n-1ubuntu2 [913 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/main i386 libssl1.1 i386 1.1.0g-2ubuntu1 [1122 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main i386 openssl i386 1.1.0g-2ubuntu1 [541 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main i386 tzdata all 2018c-1 [188 kB] Get:146 http://ftpmaster.internal/ubuntu bionic/main i386 libgssapi-krb5-2 i386 1.16-2build1 [132 kB] Get:147 http://ftpmaster.internal/ubuntu bionic/main i386 libkrb5-3 i386 1.16-2build1 [303 kB] Get:148 http://ftpmaster.internal/ubuntu bionic/main i386 libk5crypto3 i386 1.16-2build1 [90.0 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/main i386 libkrb5support0 i386 1.16-2build1 [32.8 kB] Get:150 http://ftpmaster.internal/ubuntu bionic/main i386 libkeyutils1 i386 1.5.9-9.2ubuntu1 [9544 B] Get:151 http://ftpmaster.internal/ubuntu bionic/main i386 libpng16-16 i386 1.6.34-1 [183 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/universe i386 apt-transport-https all 1.6~alpha7ubuntu1 [1692 B] Get:153 http://ftpmaster.internal/ubuntu bionic/main i386 dpkg-dev all 1.19.0.5ubuntu1 [607 kB] Get:154 http://ftpmaster.internal/ubuntu bionic/main i386 libdpkg-perl all 1.19.0.5ubuntu1 [211 kB] Get:155 http://ftpmaster.internal/ubuntu bionic/main i386 build-essential i386 12.4ubuntu1 [4752 B] Get:156 http://ftpmaster.internal/ubuntu bionic/main i386 libfakeroot i386 1.22-2ubuntu1 [27.1 kB] Get:157 http://ftpmaster.internal/ubuntu bionic/main i386 fakeroot i386 1.22-2ubuntu1 [63.6 kB] Get:158 http://ftpmaster.internal/ubuntu bionic/main i386 libnghttp2-14 i386 1.29.0-1build1 [82.9 kB] Get:159 http://ftpmaster.internal/ubuntu bionic/main 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Setting up systemd-sysv (237-1ubuntu3) ... Setting up liblockfile1:i386 (1.14-1.1) ... Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up linux-libc-dev:i386 (4.15.0-9.10) ... Setting up libmpfr6:i386 (4.0.1-1) ... Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libroken18-heimdal:i386 (7.5.0+dfsg-1) ... Setting up perl-modules-5.26 (5.26.1-4build1) ... Setting up libgdbm5:i386 (1.14.1-3) ... Setting up libkrb5support0:i386 (1.16-2build1) ... Setting up optipng (0.7.6-1.1) ... Setting up gnupg-l10n (2.2.4-1ubuntu1) ... Setting up gcc-7-base:i386 (7.3.0-3ubuntu1) ... Setting up binutils-common:i386 (2.30-4ubuntu1) ... Setting up libmpx2:i386 (8-20180208-0ubuntu1) ... Setting up sensible-utils (0.0.11) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... Setting up libperl5.26:i386 (5.26.1-4build1) ... Setting up libssl1.1:i386 (1.1.0g-2ubuntu1) ... Setting up libheimbase1-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libfakeroot:i386 (1.22-2ubuntu1) ... Setting up openssl (1.1.0g-2ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libsqlite3-0:i386 (3.22.0-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu2) ... Setting up libmpc3:i386 (1.1.0-1) ... Setting up libc-dev-bin (2.26-0ubuntu4) ... Setting up libcomerr2 (1.43.9-1) ... Setting up libkeyutils1:i386 (1.5.9-9.2ubuntu1) ... Setting up libc6-dev:i386 (2.26-0ubuntu4) ... Setting up libslang2:i386 (2.3.1a-1ubuntu1) ... Setting up libassuan0:i386 (2.5.1-2) ... Setting up libitm1:i386 (8-20180208-0ubuntu1) ... Setting up libk5crypto3:i386 (1.16-2build1) ... Setting up pkgbinarymangler (134) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libasan4:i386 (7.3.0-3ubuntu1) ... Setting up libbinutils:i386 (2.30-4ubuntu1) ... Setting up libcilkrts5:i386 (7.3.0-3ubuntu1) ... Setting up init (1.51) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libubsan0:i386 (7.3.0-3ubuntu1) ... Setting up gpgconf (2.2.4-1ubuntu1) ... Setting up libhcrypto4-heimdal:i386 (7.5.0+dfsg-1) ... Setting up fakeroot (1.22-2ubuntu1) ... Setting up libhx509-5-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libgcc-7-dev:i386 (7.3.0-3ubuntu1) ... Setting up cpp-7 (7.3.0-3ubuntu1) ... Setting up libstdc++-7-dev:i386 (7.3.0-3ubuntu1) ... Setting up perl (5.26.1-4build1) ... Setting up binutils-i686-linux-gnu (2.30-4ubuntu1) ... Setting up gpgsm (2.2.4-1ubuntu1) ... Setting up gnupg-utils (2.2.4-1ubuntu1) ... Setting up pinentry-curses (1.1.0-1) ... Setting up libkrb5-3:i386 (1.16-2build1) ... Setting up binutils (2.30-4ubuntu1) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-1) ... Setting up dirmngr (2.2.4-1ubuntu1) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up gpg (2.2.4-1ubuntu1) ... Setting up gcc-7 (7.3.0-3ubuntu1) ... Setting up g++-7 (7.3.0-3ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu1) ... Setting up gpg-agent (2.2.4-1ubuntu1) ... Installing new version of config file /etc/X11/Xsession.d/90gpg-agent ... Setting up gpg-wks-server (2.2.4-1ubuntu1) ... Setting up gpg-wks-client (2.2.4-1ubuntu1) ... Setting up libgssapi-krb5-2:i386 (1.16-2build1) ... Setting up dpkg-dev (1.19.0.5ubuntu1) ... Setting up gnupg-agent (2.2.4-1ubuntu1) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-1) ... Setting up build-essential (12.4ubuntu1) ... Setting up libcurl3-gnutls:i386 (7.58.0-2ubuntu1) ... Setting up gnupg (2.2.4-1ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14340990 i386 bionic-proposed -c chroot:build-PACKAGEBUILD-14340990 --arch=i386 --dist=bionic-proposed --nolog 'centrifuge_1.0.3~beta-1.dsc' Initiating build PACKAGEBUILD-14340990 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-101-generic #124-Ubuntu SMP Fri Nov 10 18:29:59 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-019.buildd +==============================================================================+ | centrifuge 1.0.3~beta-1 (i386) 12 Feb 2018 05:10 | +==============================================================================+ Package: centrifuge Version: 1.0.3~beta-1 Source Version: 1.0.3~beta-1 Distribution: bionic-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/centrifuge-YjxSS_/centrifuge-1.0.3~beta' with '<>' I: NOTICE: Log filtering will replace 'build/centrifuge-YjxSS_' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14340990/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- centrifuge_1.0.3~beta-1.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-D4OaQD/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-D4OaQD/apt_archive ./ InRelease Get:2 copy:/<>/resolver-D4OaQD/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-D4OaQD/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-D4OaQD/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-D4OaQD/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (104 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libustr-1.0-1 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-D4OaQD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12967 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10) Filtered Build-Depends: debhelper (>= 10) dpkg-deb: building package 'sbuild-build-depends-centrifuge-dummy' in '/<>/resolver-HxUgjU/apt_archive/sbuild-build-depends-centrifuge-dummy.deb'. Ign:1 copy:/<>/resolver-HxUgjU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HxUgjU/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-HxUgjU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HxUgjU/apt_archive ./ Sources [210 B] Get:5 copy:/<>/resolver-HxUgjU/apt_archive ./ Packages [527 B] Fetched 2856 B in 0s (122 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install centrifuge build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gnupg-agent libcryptsetup4 libcurl3-gnutls libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libustr-1.0-1 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-centrifuge-dummy 0 upgraded, 34 newly installed, 1 to remove and 0 not upgraded. Need to get 17.8 MB of archives. After this operation, 65.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-HxUgjU/apt_archive ./ sbuild-build-depends-centrifuge-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main i386 libbsd0 i386 0.8.7-1 [44.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main i386 bsdmainutils i386 11.1.2ubuntu1 [184 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main i386 groff-base i386 1.22.3-10 [1169 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main i386 libpipeline1 i386 1.5.0-1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main i386 man-db i386 2.8.1-1 [1028 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main i386 libmagic-mgc i386 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main i386 libmagic1 i386 1:5.32-1 [75.0 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main i386 file i386 1:5.32-1 [21.9 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main i386 libglib2.0-0 i386 2.54.1-1ubuntu1 [1231 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main i386 libfreetype6 i386 2.8.1-0.1ubuntu2 [351 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main i386 libgraphite2-3 i386 1.3.10-8 [80.8 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main i386 libharfbuzz0b i386 1.7.2-1 [240 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main i386 libicu-le-hb0 i386 1.0.3+git161113-4 [15.6 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main i386 libicu60 i386 60.2-3ubuntu1 [8205 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main i386 libxml2 i386 2.9.4+dfsg1-6.1ubuntu1 [697 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main i386 gettext-base i386 0.19.8.1-4ubuntu2 [50.9 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main i386 libsigsegv2 i386 2.12-1 [15.0 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main i386 m4 i386 1.4.18-1 [196 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main i386 autoconf all 2.69-11 [322 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main i386 autotools-dev all 20171216.1 [39.7 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main i386 automake all 1:1.15.1-3ubuntu1 [509 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main i386 autopoint all 0.19.8.1-4ubuntu2 [412 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main i386 libtool all 2.4.6-2 [194 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main i386 dh-autoreconf all 16 [15.8 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main i386 libarchive-zip-perl all 1.60-1 [83.9 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main i386 libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main i386 dh-strip-nondeterminism all 0.040-1 [5196 B] Get:30 http://ftpmaster.internal/ubuntu bionic/main i386 libcroco3 i386 0.6.12-2 [87.7 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main i386 gettext i386 0.19.8.1-4ubuntu2 [1095 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main i386 po-debconf all 1.0.20 [232 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main i386 debhelper all 11.1.4ubuntu1 [900 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.8 MB in 1s (17.8 MB/s) (Reading database ... 12967 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package libbsd0:i386. (Reading database ... 12958 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_i386.deb ... Unpacking libbsd0:i386 (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu1_i386.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_i386.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.0-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.1-1_i386.deb ... Unpacking man-db (2.8.1-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_i386.deb ... 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Setting up gettext-base (0.19.8.1-4ubuntu2) ... Setting up libpipeline1:i386 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:i386 (0.8.7-1) ... Setting up libfreetype6:i386 (2.8.1-0.1ubuntu2) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:i386 (1:5.32-1) ... Setting up libgraphite2-3:i386 (1.3.10-8) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... Setting up autotools-dev (20171216.1) ... Setting up bsdmainutils (11.1.2ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-4ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up libharfbuzz0b:i386 (1.7.2-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... 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 (2.8.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libicu-le-hb0:i386 (1.0.3+git161113-4) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up libicu60:i386 (60.2-3ubuntu1) ... Setting up libxml2:i386 (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libcroco3:i386 (0.6.12-2) ... Setting up gettext (0.19.8.1-4ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.20) ... Setting up debhelper (11.1.4ubuntu1) ... Setting up dh-autoreconf (16) ... Setting up sbuild-build-depends-centrifuge-dummy (0.invalid.0) ... (Reading database ... 14850 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu4) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-101-generic amd64 (i686) Toolchain package versions: binutils_2.30-4ubuntu1 dpkg-dev_1.19.0.5ubuntu1 g++-7_7.3.0-3ubuntu1 gcc-7_7.3.0-3ubuntu1 libc6-dev_2.26-0ubuntu4 libstdc++-7-dev_7.3.0-3ubuntu1 libstdc++6_8-20180208-0ubuntu1 linux-libc-dev_4.15.0-9.10 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 apt_1.6~alpha7ubuntu1 apt-transport-https_1.6~alpha7ubuntu1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu2 autotools-dev_20171216.1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4.18-1ubuntu1 binutils_2.30-4ubuntu1 binutils-common_2.30-4ubuntu1 binutils-i686-linux-gnu_2.30-4ubuntu1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.30.2-0.1ubuntu2 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 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ncurses-bin_6.0+20171125-1ubuntu1 openssl_1.1.0g-2ubuntu1 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.5-1build1 perl_5.26.1-4build1 perl-base_5.26.1-4build1 perl-modules-5.26_5.26.1-4build1 pinentry-curses_1.1.0-1 pkgbinarymangler_134 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1 readline-common_7.0-3 sbuild-build-depends-centrifuge-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 systemd_237-1ubuntu3 systemd-sysv_237-1ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2018c-1 ubuntu-keyring_2018.02.06 util-linux_2.30.2-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jan 6 11:13:40 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./centrifuge_1.0.3~beta-1.dsc dpkg-source: info: extracting centrifuge in centrifuge-1.0.3~beta dpkg-source: info: unpacking centrifuge_1.0.3~beta.orig.tar.gz dpkg-source: info: unpacking centrifuge_1.0.3~beta-1.debian.tar.xz dpkg-source: info: applying fix_auto_ptr_usage_in_gcc-7.patch dpkg-source: info: applying 0002-Fix-build-with-rank.patch dpkg-source: info: applying 0003-Fix-make-install-DESTDIR.patch dpkg-source: info: applying hardening.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-14340990 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14340990 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14340990 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package centrifuge dpkg-buildpackage: info: source version 1.0.3~beta-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build centrifuge-1.0.3~beta dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' rm -f centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge-build-bin-debug centrifuge-class-debug centrifuge-inspect-bin-debug \ centrifuge-build-bin.exe centrifuge-class.exe centrifuge-inspect-bin.exe centrifuge-build-bin-debug.exe centrifuge-class-debug.exe centrifuge-inspect-bin-debug.exe \ centrifuge-src.zip centrifuge-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 make[1]: Entering directory '/<>' /usr/bin/g++ -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ \ -o centrifuge-build-bin centrifuge_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp centrifuge_build_main.cpp \ -lpthread /usr/bin/g++ -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ \ -o centrifuge-class centrifuge.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp ref_coord.cpp mask.cpp pe.cpp aligner_seed_policy.cpp scoring.cpp presets.cpp simple_func.cpp random_util.cpp outq.cpp centrifuge_main.cpp \ -lpthread /usr/bin/g++ -O3 -m32 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m32 -msse2 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \ -I . \ -o centrifuge-inspect-bin centrifuge_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from centrifuge.cpp:34: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: 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 blockwise_sa.h:29:0, from bt2_idx.h:44, from centrifuge_build.cpp:27: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: 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 bt2_idx.h:44:0, from centrifuge_build.cpp:27: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from bt2_idx.h:44:0, from centrifuge.cpp:34: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge_build.cpp:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from hier_idx.h:24, from centrifuge_inspect.cpp:28: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from centrifuge_build.cpp:27:0: bt2_idx.h: In instantiation of ‘void Ebwt::buildToDisk(InorderBlockwiseSA&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList&, int) [with TStr = SString; index_t = long long unsigned int; std::ostream = std::basic_ostream]’: bt2_idx.h:1492:16: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here bt2_idx.h:3452:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t k = 0; k < kmer_size; k++) { ~~^~~~~~~~~~~ bt2_idx.h:3641:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t k = 0; k < kmer_size; k++) { ~~^~~~~~~~~~~ bt2_idx.h: In instantiation of ‘void Ebwt::buildToDisk(InorderBlockwiseSA&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList&, int) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ostream = std::basic_ostream]’: bt2_idx.h:1492:16: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:706:54: required from here bt2_idx.h:3452:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t k = 0; k < kmer_size; k++) { ~~^~~~~~~~~~~ bt2_idx.h:3641:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t k = 0; k < kmer_size; k++) { ~~^~~~~~~~~~~ In file included from bt2_idx.h:44:0, from hier_idx.h:24, from centrifuge_inspect.cpp:28: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from centrifuge_build.cpp:27: diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = SString]’: blockwise_sa.h:383:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here diff_sample.h:813:43: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:813:43: warning: large integer implicitly truncated to unsigned type [-Woverflow] diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = S2bDnaString]’: blockwise_sa.h:383:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:706:54: required from here diff_sample.h:813:43: warning: large integer implicitly truncated to unsigned type [-Woverflow] diff_sample.h:813:43: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge_build.cpp:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ blockwise_sa.h:383:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:661:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:661:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from bt2_idx.h:44:0, from centrifuge_build.cpp:27: blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’: blockwise_sa.h:607:9: required from ‘void KarkkainenBlockwiseSA::buildSamples() [with TStr = SString]’ blockwise_sa.h:388:16: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here blockwise_sa.h:460:15: warning: large integer implicitly truncated to unsigned type [-Woverflow] mkeyQSortSuf(t, s, slen, 4, ~~~~~~~~~~~~^~~~~~~~~~~~~~~ this->verbose(), this->sanityCheck()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:460:15: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge_build.cpp:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = S2bDnaString]’ blockwise_sa.h:383:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:706:54: required from here multikey_qsort.h:661:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:661:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:454:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:607:9: required from ‘void KarkkainenBlockwiseSA::buildSamples() [with TStr = SString]’ blockwise_sa.h:388:16: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:460:15: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:607:9: required from ‘void KarkkainenBlockwiseSA::buildSamples() [with TStr = SString]’ blockwise_sa.h:388:16: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:454:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:607:9: required from ‘void KarkkainenBlockwiseSA::buildSamples() [with TStr = SString]’ blockwise_sa.h:388:16: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:454:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:607:9: required from ‘void KarkkainenBlockwiseSA::buildSamples() [with TStr = SString]’ blockwise_sa.h:388:16: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:454:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:607:9: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] blockwise_sa.h:362:9: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:215:34: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::__cxx11::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::__cxx11::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ bt2_idx.h:1488:33: required from ‘void Ebwt::initFromVector(TStr&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ bt2_idx.h:881:23: required from ‘Ebwt::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList&, EList&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ centrifuge_build.cpp:472:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’ centrifuge_build.cpp:686:60: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge.cpp:34: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from centrifuge.cpp:47:0: classifier.h: In instantiation of ‘int Classifier::go(const Scoring&, const Ebwt&, const Ebwt&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: centrifuge.cpp:2660:94: required from here classifier.h:411:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(i + 1 < _hitMap.size()) { classifier.h:429:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(_hitMap[i].rank + 1 >= _hitMap[i].path.size()) { classifier.h:439:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] uint64_t parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]); classifier.h:472:63: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] uint64_t cur_parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]); In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge.cpp:34: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from centrifuge.cpp:47:0: classifier.h: In instantiation of ‘void Classifier::searchForwardAndReverse(index_t, const Ebwt&, const Scoring&, RandomSource&, const ReportingParams&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: classifier.h:238:36: required from ‘int Classifier::go(const Scoring&, const Ebwt&, const Ebwt&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ centrifuge.cpp:2660:94: required from here classifier.h:839:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] hit.size() + rchit.size() > rp.ihits) { classifier.h:636:16: warning: variable ‘cur’ set but not used [-Wunused-but-set-variable] size_t cur[2] = {0, 0} ; ^~~ In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge.cpp:34: multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from centrifuge.cpp:41:0: aln_sink.h: In instantiation of ‘void AlnSinkSam::appendMate(Ebwt&, BTString&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; TReadId = long long unsigned int; size_t = unsigned int]’: aln_sink.h:1407:19: required from ‘void AlnSinkSam::append(BTString&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, bool, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; size_t = unsigned int; TReadId = long long unsigned int]’ centrifuge.cpp:3301:1: required from here aln_sink.h:2302:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i=0; i < this->tab_fmt_cols_.size(); ++i) { In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from hier_idx.h:24, from centrifuge_inspect.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: 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 bt2_idx.h:44:0, from bt2_idx.cpp:25: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from bt2_idx.cpp:25: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: 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 bt2_idx.h:44:0, from bt2_idx.cpp:25: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from bt2_idx.cpp:25: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:29:0, from bt2_idx.h:44, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: 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 bt2_idx.h:44:0, from bt2_idx.cpp:25: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] this->verbose(), this->sanityCheck()); ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:491:52: warning: large integer implicitly truncated to unsigned type [-Woverflow] In file included from diff_sample.h:26:0, from blockwise_sa.h:29, from bt2_idx.h:44, from bt2_idx.cpp:25: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:485:56: required from here multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h:764:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:491:52: required from here multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:496:40: warning: large integer implicitly truncated to unsigned type [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1155:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:26: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:1065:39: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1062:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1161:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:485:56: required from here multikey_qsort.h:914:8: warning: large integer implicitly truncated to unsigned type [-Woverflow] off = OFF_MASK; multikey_qsort.h:922:28: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:25: warning: large integer implicitly truncated to unsigned type [-Woverflow] sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from diff_sample.cpp:20:0: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- prefix=/usr/lib/centrifuge make -j4 install DESTDIR=/<>/centrifuge-1.0.3\~beta/debian/centrifuge AM_UPDATE_INFO_DIR=no prefix=/usr/lib/centrifuge make[2]: Entering directory '/<>' mkdir -p /<>/debian/centrifuge/usr/lib/centrifuge/bin mkdir -p /<>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices install -m 0644 indices/Makefile /<>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices install -d -m 0755 /<>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc install -m 0644 doc/* /<>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc for file in centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge centrifuge-build centrifuge-inspect centrifuge-download centrifuge-RemoveEmptySequence.pl centrifuge-compress.pl centrifuge-sort-nt.pl centrifuge-RemoveN.pl centrifuge-BuildSharedSequence.pl; do \ install -m 0755 $file /<>/debian/centrifuge/usr/lib/centrifuge/bin ; \ done make[2]: Leaving directory '/<>' mv debian/centrifuge/usr/lib/centrifuge/bin/* debian/centrifuge/usr/lib/centrifuge/ rmdir debian/centrifuge/usr/lib/centrifuge/bin # move documentation to correct location mkdir -p debian/centrifuge/usr/share/doc/centrifuge/html mv debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*html \ debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*css \ debian/centrifuge/usr/share/doc/centrifuge/html # remove useless stuff in documentation dir rm -rf debian/centrifuge/usr/lib/centrifuge/share/doc/ make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package centrifuge: unused substitution variable ${perl:Depends} dpkg-gencontrol: warning: package centrifuge: unused substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 134 INFO: pkgstriptranslations version 134 pkgstriptranslations: processing centrifuge (in debian/centrifuge); do_strip: , oemstrip: pkgstriptranslations: processing centrifuge-dbgsym (in debian/.debhelper/centrifuge/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/centrifuge/DEBIAN/control, package centrifuge, directory debian/centrifuge pkgstripfiles: Running PNG optimization (using 4 cpus) for package centrifuge ... pkgstripfiles: No PNG files. dpkg-deb: building package 'centrifuge' in '../centrifuge_1.0.3~beta-1_i386.deb'. pkgstripfiles: processing control file: debian/.debhelper/centrifuge/dbgsym-root/DEBIAN/control, package centrifuge-dbgsym, directory debian/.debhelper/centrifuge/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package centrifuge-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'centrifuge-dbgsym' in 'debian/.debhelper/scratch-space/build-centrifuge/centrifuge-dbgsym_1.0.3~beta-1_i386.deb'. Renaming centrifuge-dbgsym_1.0.3~beta-1_i386.deb to centrifuge-dbgsym_1.0.3~beta-1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../centrifuge_1.0.3~beta-1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build centrifuge-1.0.3~beta dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180212-0511 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ centrifuge_1.0.3~beta-1_i386.changes: ------------------------------------- Format: 1.8 Date: Sat, 06 Jan 2018 12:11:48 +0100 Source: centrifuge Binary: centrifuge Architecture: i386 Version: 1.0.3~beta-1 Distribution: bionic-proposed Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: centrifuge - rapid and memory-efficient system for classification of DNA seque Closes: 886463 Changes: centrifuge (1.0.3~beta-1) unstable; urgency=low . * Initial release (Closes: #886463) Checksums-Sha1: 74d739c88ef582a16800b246b5e0a873a2dbd143 3097712 centrifuge-dbgsym_1.0.3~beta-1_i386.ddeb 0592cb3a1f8dcc1b2a4112016dad9962a906b33e 5214 centrifuge_1.0.3~beta-1_i386.buildinfo c59aa15ffc0baf0fb6d95b78c8ed1216200ddc85 567196 centrifuge_1.0.3~beta-1_i386.deb Checksums-Sha256: a3ce57125f482894eedd36fbd161f47c9e3038976b3fd676b863983cfee9fcd4 3097712 centrifuge-dbgsym_1.0.3~beta-1_i386.ddeb b0680c4a7793776ac97fb916fbe3ad1ba75010784f57762d397ece8eb6ab2e30 5214 centrifuge_1.0.3~beta-1_i386.buildinfo 9bc7ae2adc4917c77cc96db1d7008b40918d7565ce4d208992b5631ded02bf10 567196 centrifuge_1.0.3~beta-1_i386.deb Files: 5de4649358faed3b93c7d88a53ac3a0d 3097712 debug optional centrifuge-dbgsym_1.0.3~beta-1_i386.ddeb 280772612beb233fe2434f4a5e361357 5214 science optional centrifuge_1.0.3~beta-1_i386.buildinfo 45f5b4a3dcda40de5c5330be5d2b7f46 567196 science optional centrifuge_1.0.3~beta-1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ centrifuge_1.0.3~beta-1_i386.deb -------------------------------- new debian package, version 2.0. size 567196 bytes: control archive=1916 bytes. 1236 bytes, 22 lines control 2528 bytes, 33 lines md5sums Package: centrifuge Version: 1.0.3~beta-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1906 Depends: libc6 (>= 2.7), libgcc1 (>= 1:4.2), libstdc++6 (>= 5.2), python, hisat2, jellyfish Section: science Priority: optional Homepage: https://ccb.jhu.edu/software/centrifuge/ Description: rapid and memory-efficient system for classification of DNA sequences Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification speed, allowing it to process a typical DNA sequencing run within an hour. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. drwxr-xr-x root/root 0 2018-01-06 11:11 ./ drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/ drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/bin/ -rwxr-xr-x root/root 312 2018-01-06 11:11 ./usr/bin/centrifuge lrwxrwxrwx root/root 0 2018-01-06 11:11 ./usr/bin/centrifuge-build -> centrifuge lrwxrwxrwx root/root 0 2018-01-06 11:11 ./usr/bin/centrifuge-compress -> centrifuge lrwxrwxrwx root/root 0 2018-01-06 11:11 ./usr/bin/centrifuge-download -> centrifuge lrwxrwxrwx root/root 0 2018-01-06 11:11 ./usr/bin/centrifuge-inspect -> centrifuge drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/lib/ drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/lib/centrifuge/ -rwxr-xr-x root/root 16775 2018-01-06 11:11 ./usr/lib/centrifuge/centrifuge -rwxr-xr-x root/root 12130 2018-01-06 11:11 ./usr/lib/centrifuge/centrifuge-BuildSharedSequence.pl -rwxr-xr-x root/root 411 2018-01-06 11:11 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2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/doc/ -rw-r--r-- root/root 151 2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/doc/README -rw-r--r-- root/root 82391 2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/doc/manual.inc.html.old -rw-r--r-- root/root 778 2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/doc/strip_markdown.pl drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/indices/ -rw-r--r-- root/root 11711 2018-01-06 11:11 ./usr/lib/centrifuge/share/centrifuge/indices/Makefile drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/share/ drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/share/doc/centrifuge/ -rw-r--r-- root/root 159 2018-01-06 11:11 ./usr/share/doc/centrifuge/changelog.Debian.gz -rw-r--r-- root/root 1053 2018-01-06 11:11 ./usr/share/doc/centrifuge/copyright drwxr-xr-x root/root 0 2018-01-06 11:11 ./usr/share/doc/centrifuge/html/ -rw-r--r-- root/root 1234 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2018-01-06 11:11 ./usr/share/man/man1/centrifuge-compress.1.gz -rw-r--r-- root/root 847 2018-01-06 11:11 ./usr/share/man/man1/centrifuge-download.1.gz -rw-r--r-- root/root 422 2018-01-06 11:11 ./usr/share/man/man1/centrifuge-inspect.1.gz -rw-r--r-- root/root 398 2018-01-06 11:11 ./usr/share/man/man1/centrifuge.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 30700 Build-Time: 69 Distribution: bionic-proposed Host Architecture: i386 Install-Time: 11 Job: centrifuge_1.0.3~beta-1.dsc Machine Architecture: amd64 Package: centrifuge Package-Time: 82 Source-Version: 1.0.3~beta-1 Space: 30700 Status: successful Version: 1.0.3~beta-1 -------------------------------------------------------------------------------- Finished at 20180212-0511 Build needed 00:01:22, 30700k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 Scanning for processes to kill in build PACKAGEBUILD-14340990 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 Stopping target for build PACKAGEBUILD-14340990 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=i386 PACKAGEBUILD-14340990 Removing build PACKAGEBUILD-14340990