sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | kraken2 2.0.8~beta-1 (armhf) Wed, 09 Oct 2019 14:07:51 +0000 | +==============================================================================+ Package: kraken2 Version: 2.0.8~beta-1 Source Version: 2.0.8~beta-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-0f016baa-7276-47c1-b671-df3620d31dc4' with '<>' I: NOTICE: Log filtering will replace 'build/kraken2-zQ64y2/resolver-MNTqIf' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-09-0814.31.pdiff [6263 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-10-09-0814.31.pdiff [6263 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-09-0814.31.pdiff [5268 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-10-09-0814.31.pdiff [5268 B] Get:6 http://debian.oregonstate.edu/debian unstable/main armhf Packages [7971 kB] Fetched 8177 kB in 2s (4332 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'kraken2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kraken2.git Please use: git clone https://salsa.debian.org/med-team/kraken2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 414 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main kraken2 2.0.8~beta-1 (dsc) [1993 B] Get:2 http://debian.oregonstate.edu/debian unstable/main kraken2 2.0.8~beta-1 (tar) [73.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main kraken2 2.0.8~beta-1 (diff) [338 kB] Fetched 414 kB in 0s (28.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/kraken2-zQ64y2/kraken2-2.0.8~beta' with '<>' I: NOTICE: Log filtering will replace 'build/kraken2-zQ64y2' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [404 B] Get:5 copy:/<>/apt_archive ./ Packages [491 B] Fetched 1852 B in 0s (93.3 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf libstdc++-9-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils ucf 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 62.0 MB of archives. After this operation, 238 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.7-3 [1300 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b5 [18.9 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.2.1-8 [193 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.33-1 [2721 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf-base amd64 9.2.1-8cross1 [193 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [6808 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [16.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-8cross1 [188 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.29-1cross7 [1122 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:9.2.1-8cross1 [37.3 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 9.2.1-8cross1 [73.3 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 9.2.1-8cross1 [6688 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 9.2.1-8cross1 [362 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 9.2.1-8cross1 [392 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 9.2.1-8cross1 [112 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armhf-cross all 9.2.1-8cross1 [665 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [7143 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1476 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 5.2.9-2cross7 [1312 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.29-1cross7 [2122 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armhf-cross all 9.2.1-8cross1 [1717 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [7385 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1184 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.8 [6644 B] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.66-2 [103 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.0-1 [23.3 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.0-1 [14.3 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-1 [81.8 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.6.1 [172 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.1-1 [1317 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190803-1 [102 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.6.1 [993 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:9.2.1-8 [37.3 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.29-2 [2341 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.2.1-8 [370 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 9.2.1-8 [6868 B] Get:79 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.2.17-1+b1 [1232 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.29-2 [2141 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 9.2.1-8 [75.3 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 9.2.1-8 [431 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 9.2.1-8 [113 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-9-dev armhf 9.2.1-8 [665 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-9-dev armhf 9.2.1-8 [1748 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.0 MB in 1s (66.6 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14991 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.7-3_amd64.deb ... Unpacking man-db (2.8.7-3) ... 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Selecting previously unselected package libgcc1:armhf. Preparing to unpack .../73-libgcc1_1%3a9.2.1-8_armhf.deb ... Unpacking libgcc1:armhf (1:9.2.1-8) ... Selecting previously unselected package libc6:armhf. Preparing to unpack .../74-libc6_2.29-2_armhf.deb ... Unpacking libc6:armhf (2.29-2) ... Selecting previously unselected package libasan5:armhf. Preparing to unpack .../75-libasan5_9.2.1-8_armhf.deb ... Unpacking libasan5:armhf (9.2.1-8) ... Selecting previously unselected package libatomic1:armhf. Preparing to unpack .../76-libatomic1_9.2.1-8_armhf.deb ... Unpacking libatomic1:armhf (9.2.1-8) ... Selecting previously unselected package linux-libc-dev:armhf. Preparing to unpack .../77-linux-libc-dev_5.2.17-1+b1_armhf.deb ... Unpacking linux-libc-dev:armhf (5.2.17-1+b1) ... Selecting previously unselected package libc6-dev:armhf. Preparing to unpack .../78-libc6-dev_2.29-2_armhf.deb ... Unpacking libc6-dev:armhf (2.29-2) ... Selecting previously unselected package libgomp1:armhf. 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Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.29-1cross7) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.66-2) ... Setting up libglib2.0-0:amd64 (2.62.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.6.1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up linux-libc-dev:armhf (5.2.17-1+b1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up gcc-9-arm-linux-gnueabihf-base:amd64 (9.2.1-8cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20190803-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up linux-libc-dev-armhf-cross (5.2.9-2cross7) ... Setting up autopoint (0.19.8.1-9) ... Setting up gcc-9-cross-base (9.2.1-8cross1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up binutils-arm-linux-gnueabihf (2.33-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b5) ... Setting up gcc-9-base:armhf (9.2.1-8) ... Setting up libgomp1-armhf-cross (9.2.1-8cross1) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up libtool (2.4.6-11) ... Setting up cpp-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libc6-dev-armhf-cross (2.29-1cross7) ... Setting up m4 (1.4.18-2) ... Setting up libatomic1-armhf-cross (9.2.1-8cross1) ... Setting up libgcc1-armhf-cross (1:9.2.1-8cross1) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up cpp-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan5-armhf-cross (9.2.1-8cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libstdc++6-armhf-cross (9.2.1-8cross1) ... Setting up libubsan1-armhf-cross (9.2.1-8cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-9-dev-armhf-cross (9.2.1-8cross1) ... Setting up po-debconf (1.0.21) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libstdc++-9-dev-armhf-cross (9.2.1-8cross1) ... Setting up gcc-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up g++-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.8) ... Setting up libgcc1:armhf (1:9.2.1-8) ... Setting up dh-autoreconf (19) ... Setting up libc6:armhf (2.29-2) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up libc6-dev:armhf (2.29-2) ... Setting up libstdc++6:armhf (9.2.1-8) ... Setting up debhelper (12.6.1) ... Setting up libgomp1:armhf (9.2.1-8) ... Setting up libasan5:armhf (9.2.1-8) ... Setting up libatomic1:armhf (9.2.1-8) ... Setting up libubsan1:armhf (9.2.1-8) ... Setting up libgcc-9-dev:armhf (9.2.1-8) ... Setting up libstdc++-9-dev:armhf (9.2.1-8) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.29-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.33-1 dpkg-dev_1.19.7 g++-8_8.3.0-23 g++-9_9.2.1-8 gcc-8_8.3.0-23 gcc-9_9.2.1-8 libc6-dev_2.29-2 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-8 libstdc++-9-dev-armhf-cross_9.2.1-8cross1 libstdc++6_9.2.1-8 libstdc++6-armhf-cross_9.2.1-8cross1 linux-libc-dev_5.2.17-1+b1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.33-1 binutils-arm-linux-gnueabihf_2.33-1 binutils-common_2.33-1 binutils-x86-64-linux-gnu_2.33-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-23 cpp-9_9.2.1-8 cpp-9-arm-linux-gnueabihf_9.2.1-8cross1 cpp-arm-linux-gnueabihf_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.6.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-23 g++-9_9.2.1-8 g++-9-arm-linux-gnueabihf_9.2.1-8cross1 g++-arm-linux-gnueabihf_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-23 gcc-8-base_8.3.0-23 gcc-9_9.2.1-8 gcc-9-arm-linux-gnueabihf_9.2.1-8cross1 gcc-9-arm-linux-gnueabihf-base_9.2.1-8cross1 gcc-9-base_9.2.1-8 gcc-9-cross-base_9.2.1-8cross1 gcc-arm-linux-gnueabihf_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.22+b1 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.66-2 libasan5_9.2.1-8 libasan5-armhf-cross_9.2.1-8cross1 libatomic1_9.2.1-8 libatomic1-armhf-cross_9.2.1-8cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2 libc-dev-bin_2.29-2 libc6_2.29-2 libc6-armhf-cross_2.29-1cross7 libc6-dev_2.29-2 libc6-dev-armhf-cross_2.29-1cross7 libcap-ng0_0.7.9-2+b1 libcc1-0_9.2.1-8 libcom-err2_1.45.4-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.6.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 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linux-libc-dev_5.2.17-1+b1 linux-libc-dev-armhf-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-6 perl-base_5.30.0-6 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-6 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kraken2 Binary: kraken2 Architecture: any Version: 2.0.8~beta-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.ccb.jhu.edu/software/kraken2/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/kraken2 Vcs-Git: https://salsa.debian.org/med-team/kraken2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12) Package-List: kraken2 deb science optional arch=any Checksums-Sha1: 82ca66617e3680475c35634125e35839201534c7 73570 kraken2_2.0.8~beta.orig.tar.gz 5dccbf46fcb99f426b3229e1be6dcdbeba685b49 338060 kraken2_2.0.8~beta-1.debian.tar.xz Checksums-Sha256: f2a91fc57a40b3e87df8ac2ea7c0ff1060cc9295c95de417ee53249ee3f7ad8e 73570 kraken2_2.0.8~beta.orig.tar.gz 06058c4ee869364108bfdd7c03417fc64d2f0ba85f5cf3d65e2af97ebc8851c9 338060 kraken2_2.0.8~beta-1.debian.tar.xz Files: dd0e9847ac0c1c35a4feda84a74c69a5 73570 kraken2_2.0.8~beta.orig.tar.gz d318d40bf33c1536b45e86b3afeef40d 338060 kraken2_2.0.8~beta-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl1Cz3oRHHRpbGxlQGRl 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F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kraken2_2.0.8~beta-1.dsc dpkg-source: info: extracting kraken2 in /<> dpkg-source: info: unpacking kraken2_2.0.8~beta.orig.tar.gz dpkg-source: info: unpacking kraken2_2.0.8~beta-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_install.patch dpkg-source: info: applying hardening+debug_options.patch dpkg-source: info: applying fix_reading_fasta.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-0f016baa-7276-47c1-b671-df3620d31dc4 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package kraken2 dpkg-buildpackage: info: source version 2.0.8~beta-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j1 clean make[1]: Entering directory '/<>/src' rm -f *.o estimate_capacity build_db classify dump_table lookup_accession_numbers make[1]: Leaving directory '/<>/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules build-arch dh build-arch --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src dh_auto_build -a -O--sourcedirectory=src cd src && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc make[1]: Entering directory '/<>/src' arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqreader.o seqreader.cc arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mmscanner.o mmscanner.cc In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/arm-linux-gnueabihf/include/c++/9/queue:61, from kraken2_headers.h:15, from mmscanner.h:10, from mmscanner.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const kraken2::MinimizerData&}; _Tp = kraken2::MinimizerData; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/arm-linux-gnueabihf/include/c++/9/queue:61, from kraken2_headers.h:15, from mmscanner.h:10, from mmscanner.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In member function ‘uint64_t* kraken2::MinimizerScanner::NextMinimizer(bool*)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o omp_hack.o omp_hack.cc arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utilities.o utilities.cc arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now estimate_capacity.cc seqreader.o mmscanner.o omp_hack.o utilities.o -o estimate_capacity arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mmap_file.o mmap_file.cc arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compact_hash.o compact_hash.cc compact_hash.cc: In constructor ‘kraken2::CompactHashTable::CompactHashTable(size_t, size_t, size_t)’: compact_hash.cc:32:27: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 32 | } catch (std::bad_alloc ex) { | ^~ compact_hash.cc: In member function ‘void kraken2::CompactHashTable::LoadTable(const char*, bool)’: compact_hash.cc:86:29: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 86 | } catch (std::bad_alloc ex) { | ^~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o taxonomy.o taxonomy.cc In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:60, from kraken2_headers.h:14, from mmap_file.h:10, from taxonomy.h:10, from taxonomy.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:61, from kraken2_headers.h:14, from mmap_file.h:10, from taxonomy.h:10, from taxonomy.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h: In member function ‘void kraken2::NCBITaxonomy::MarkNode(uint64_t)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h: In constructor ‘kraken2::NCBITaxonomy::NCBITaxonomy(std::string, std::string)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:60, from kraken2_headers.h:14, from mmap_file.h:10, from taxonomy.h:10, from taxonomy.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:61, from kraken2_headers.h:14, from mmap_file.h:10, from taxonomy.h:10, from taxonomy.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h: In member function ‘void kraken2::NCBITaxonomy::ConvertToKrakenTaxonomy(const char*)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now build_db.cc mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o -o build_db In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:60, from kraken2_headers.h:14, from build_db.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/map:61, from kraken2_headers.h:14, from build_db.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h: In function ‘void ReadIDToTaxonMap(std::map, long long unsigned int>&, std::string&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h: In function ‘_Z16ProcessSequencesR7OptionsRSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEySt4lessIS7_ESaISt4pairIKS7_yEEERN7kraken216CompactHashTableERNSG_8TaxonomyE._omp_fn.0’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reports.o reports.cc In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from kraken2_headers.h:1, from reports.h:10, from reports.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >&):: >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from kraken2_headers.h:1, from reports.h:10, from reports.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >&):: >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from kraken2_headers.h:1, from reports.h:10, from reports.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >&):: >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void kraken2::MpaReportDFS(taxid_t, std::ofstream&, bool, kraken2::Taxonomy&, taxon_counts_t&, std::vector >&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h: In function ‘void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, kraken2::Taxonomy&, taxon_counts_t&, taxon_counts_t&, uint64_t, char, int, int)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o aa_translate.o aa_translate.cc arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now classify.cc reports.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o -o classify classify.cc: In function ‘void ProcessFiles(const char*, const char*, kraken2::KeyValueStore*, kraken2::Taxonomy&, IndexOptions&, Options&, ClassificationStats&, OutputStreamData&, taxon_counts_t&)’: classify.cc:314:44: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 314 | sprintf(buffer, " kraken:taxid|%lu", tax.nodes()[call].external_id); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int uint64_t {aka long long unsigned int} | %llu In file included from /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/9/algorithm:62, from kraken2_headers.h:1, from classify.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_val >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 128 | __push_heap(_RandomAccessIterator __first, | ^~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:72, from /usr/arm-linux-gnueabihf/include/c++/9/queue:61, from kraken2_headers.h:15, from classify.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const OutputData&}; _Tp = OutputData; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/9/vector:67, from /usr/arm-linux-gnueabihf/include/c++/9/queue:61, from kraken2_headers.h:15, from classify.cc:7: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, taxon_counts_t&, std::vector >&)’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h: In function ‘_Z12ProcessFilesPKcS0_PN7kraken213KeyValueStoreERNS1_8TaxonomyER12IndexOptionsR7OptionsR19ClassificationStatsR16OutputStreamDataRSt13unordered_mapIyySt4hashIyESt8equal_toIyESaISt4pairIKyyEEE._omp_fn.0’: /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now dump_table.cc mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o -o dump_table arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now lookup_accession_numbers.cc mmap_file.o omp_hack.o utilities.o -o lookup_accession_numbers make[1]: Leaving directory '/<>/src' dh_auto_test -a -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=src dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_installdirs -a -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- KRAKEN2_DIR=/<>/debian/kraken2/usr/lib/kraken2 cd src && make -j1 install DESTDIR=/<>/kraken2-2.0.8\~beta/debian/kraken2 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" KRAKEN2_DIR=/<>/kraken2-2.0.8\~beta/debian/kraken2/usr/lib/kraken2 make[2]: Entering directory '/<>/src' cp estimate_capacity build_db classify dump_table lookup_accession_numbers /<>/debian/kraken2/usr/lib/kraken2/ make[2]: Leaving directory '/<>/src' ./install_kraken2.sh /<>/debian/kraken2/usr/lib/kraken2 make[2]: Entering directory '/<>/src' cp estimate_capacity build_db classify dump_table lookup_accession_numbers /<>/debian/kraken2/usr/lib/kraken2/ make[2]: Leaving directory '/<>/src' Kraken 2 installation complete. To make things easier for you, you may want to copy/symlink the following files into a directory in your PATH: /<>/debian/kraken2/usr/lib/kraken2/kraken2 /<>/debian/kraken2/usr/lib/kraken2/kraken2-build /<>/debian/kraken2/usr/lib/kraken2/kraken2-inspect make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src dh_installman -a -O--sourcedirectory=src dh_installinit -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link for file in /<>/debian/kraken2/usr/lib/kraken2/kraken* ; do \ if ! echo ${file} | grep -q '\.pm$' ; then \ ln -s ../lib/kraken2/`basename ${file}` /<>/debian/kraken2/usr/bin/`basename ${file}` ; \ fi \ done make[1]: Leaving directory '/<>' dh_strip_nondeterminism -a -O--sourcedirectory=src dh_compress -a -O--sourcedirectory=src dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/lookup_accession_numbers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/dump_table contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/estimate_capacity contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/build_db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/classify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dpkg-gencontrol: warning: package kraken2: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package kraken2: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src dpkg-deb: building package 'kraken2' in '../kraken2_2.0.8~beta-1_armhf.deb'. dpkg-deb: building package 'kraken2-dbgsym' in '../kraken2-dbgsym_2.0.8~beta-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../kraken2_2.0.8~beta-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-10-09T14:09:02Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kraken2_2.0.8~beta-1_armhf.changes: ----------------------------------- Format: 1.8 Date: Thu, 01 Aug 2019 13:36:17 +0200 Source: kraken2 Binary: kraken2 kraken2-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 2.0.8~beta-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: kraken2 - taxonomic classification system using exact k-mer matches Changes: kraken2 (2.0.8~beta-1) unstable; urgency=medium . * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 Checksums-Sha1: 5d98ed38fa32c44e5139dcce0b6fb04c5e0c3255 1312580 kraken2-dbgsym_2.0.8~beta-1_armhf.deb f5f38ef4f5a0f0c438cff914daeaf33f0edf5a16 4658 kraken2_2.0.8~beta-1_armhf.buildinfo fe4a1401b1f5462b075cccd3597a7197457676aa 761100 kraken2_2.0.8~beta-1_armhf.deb Checksums-Sha256: 5b02c67b417b16beba6ee7e59247404a0c2f6f88c4dfed676c446515c68a1bb7 1312580 kraken2-dbgsym_2.0.8~beta-1_armhf.deb cb7c59eddc02fadf3e1cf4bbe09e5157c9a31f8598046b8dd6aaa8a48ea3bdfd 4658 kraken2_2.0.8~beta-1_armhf.buildinfo df36c87de01114286d98b979ac9f00c5989a3888ac64bb1085d65951670a3be0 761100 kraken2_2.0.8~beta-1_armhf.deb Files: 7f6e49d031c5d6a500fe68191df8a3fd 1312580 debug optional kraken2-dbgsym_2.0.8~beta-1_armhf.deb dc8f3b541ff0a3388cd0693ff5b667e1 4658 science optional kraken2_2.0.8~beta-1_armhf.buildinfo 877fa6734e8082b0cc7f486d421b4148 761100 science optional kraken2_2.0.8~beta-1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kraken2 Binary: kraken2 Architecture: armhf Version: 2.0.8~beta-1 Checksums-Md5: 7f6e49d031c5d6a500fe68191df8a3fd 1312580 kraken2-dbgsym_2.0.8~beta-1_armhf.deb 877fa6734e8082b0cc7f486d421b4148 761100 kraken2_2.0.8~beta-1_armhf.deb Checksums-Sha1: 5d98ed38fa32c44e5139dcce0b6fb04c5e0c3255 1312580 kraken2-dbgsym_2.0.8~beta-1_armhf.deb fe4a1401b1f5462b075cccd3597a7197457676aa 761100 kraken2_2.0.8~beta-1_armhf.deb Checksums-Sha256: 5b02c67b417b16beba6ee7e59247404a0c2f6f88c4dfed676c446515c68a1bb7 1312580 kraken2-dbgsym_2.0.8~beta-1_armhf.deb df36c87de01114286d98b979ac9f00c5989a3888ac64bb1085d65951670a3be0 761100 kraken2_2.0.8~beta-1_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 09 Oct 2019 14:09:01 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.33-1), binutils-common (= 2.33-1), binutils-x86-64-linux-gnu (= 2.33-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-23), cpp-9 (= 9.2.1-8), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.6.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-8), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-23), gcc-8-base (= 8.3.0-23), gcc-9 (= 9.2.1-8), gcc-9-base (= 9.2.1-8), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3+b1), hostname (= 3.22+b1), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libarchive-zip-perl (= 1.66-2), libasan5 (= 9.2.1-8), libatomic1 (= 9.2.1-8), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.33-1), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-2), libc-dev-bin (= 2.29-2), libc6 (= 2.29-2), libc6-dev (= 2.29-2), libcap-ng0 (= 0.7.9-2+b1), libcc1-0 (= 9.2.1-8), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdebhelper-perl (= 12.6.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.0-1), libgcc-8-dev (= 8.3.0-23), libgcc-9-dev (= 9.2.1-8), libgcc1 (= 1:9.2.1-8), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.62.1-1), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-8), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-8), liblsan0 (= 9.2.1-8), liblz4-1 (= 1.9.1-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-23), libncurses6 (= 6.1+20190803-1), libncursesw6 (= 6.1+20190803-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-6), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.2.1-8), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-8), libstdc++6 (= 9.2.1-8), libsub-override-perl (= 0.09-2), libsystemd0 (= 242-7), libtinfo6 (= 6.1+20190803-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-8), libubsan1 (= 9.2.1-8), libuchardet0 (= 0.0.6-3), libudev1 (= 242-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.2.17-1+b1), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.7-3), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190803-1), ncurses-bin (= 6.1+20190803-1), patch (= 2.7.6-6), perl (= 5.30.0-6), perl-base (= 5.30.0-6), perl-modules-5.30 (= 5.30.0-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.96~beta-3), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1564659377" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kraken2-dbgsym_2.0.8~beta-1_armhf.deb ------------------------------------- new Debian package, version 2.0. size 1312580 bytes: control archive=808 bytes. 545 bytes, 12 lines control 617 bytes, 6 lines md5sums Package: kraken2-dbgsym Source: kraken2 Version: 2.0.8~beta-1 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1394 Depends: kraken2 (= 2.0.8~beta-1) Section: debug Priority: optional Description: debug symbols for kraken2 Build-Ids: 0224252369c1e92bff41357af3868e1054d582b0 0e9e81f78ad182ec6cdfde95fe4de6289bf0efaa 257ab1a86c23c4a5b67f25676812dd84dd339a50 ad659a381f56b952095c916364e2b3b0565a9403 cf173399c9a3951828baaba2ca2a325eac494247 drwxr-xr-x root/root 0 2019-08-01 11:36 ./ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/02/ -rw-r--r-- root/root 100996 2019-08-01 11:36 ./usr/lib/debug/.build-id/02/24252369c1e92bff41357af3868e1054d582b0.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/0e/ -rw-r--r-- root/root 300052 2019-08-01 11:36 ./usr/lib/debug/.build-id/0e/9e81f78ad182ec6cdfde95fe4de6289bf0efaa.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/25/ -rw-r--r-- root/root 489956 2019-08-01 11:36 ./usr/lib/debug/.build-id/25/7ab1a86c23c4a5b67f25676812dd84dd339a50.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/ad/ -rw-r--r-- root/root 235316 2019-08-01 11:36 ./usr/lib/debug/.build-id/ad/659a381f56b952095c916364e2b3b0565a9403.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.build-id/cf/ -rw-r--r-- root/root 96576 2019-08-01 11:36 ./usr/lib/debug/.build-id/cf/173399c9a3951828baaba2ca2a325eac494247.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 184828 2019-08-01 11:36 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/kraken2.debug drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/share/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-08-01 11:36 ./usr/share/doc/kraken2-dbgsym -> kraken2 kraken2_2.0.8~beta-1_armhf.deb ------------------------------ new Debian package, version 2.0. size 761100 bytes: control archive=3020 bytes. 2369 bytes, 41 lines control 4066 bytes, 54 lines md5sums Package: kraken2 Version: 2.0.8~beta-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1433 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 6), libstdc++6 (>= 5.2), ncbi-blast+ Section: science Priority: optional Homepage: https://www.ccb.jhu.edu/software/kraken2/ Description: taxonomic classification system using exact k-mer matches Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1's Webpage for more details]. . Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program: . 1. Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ≤ the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer's LCA. 2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy. 3. Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken's confidence scoring thresholds. 4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database. 5. 16S Databases: Kraken 2 also provides support for databases not based on NCBI's taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP. drwxr-xr-x root/root 0 2019-08-01 11:36 ./ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/bin/ lrwxrwxrwx root/root 0 2019-08-01 11:36 ./usr/bin/kraken2 -> ../lib/kraken2/kraken2 lrwxrwxrwx root/root 0 2019-08-01 11:36 ./usr/bin/kraken2-build -> ../lib/kraken2/kraken2-build lrwxrwxrwx root/root 0 2019-08-01 11:36 ./usr/bin/kraken2-inspect -> ../lib/kraken2/kraken2-inspect drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/ drwxr-xr-x root/root 0 2019-08-01 11:36 ./usr/lib/kraken2/ -rwxr-xr-x root/root 959 2019-08-01 11:36 ./usr/lib/kraken2/16S_gg_installation.sh -rwxr-xr-x root/root 956 2019-08-01 11:36 ./usr/lib/kraken2/16S_rdp_installation.sh -rwxr-xr-x root/root 1101 2019-08-01 11:36 ./usr/lib/kraken2/16S_silva_installation.sh -rwxr-xr-x root/root 947 2019-08-01 11:36 ./usr/lib/kraken2/add_to_library.sh -rwxr-xr-x root/root 54932 2019-08-01 11:36 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root/root 945 2019-08-01 11:36 ./usr/share/man/man1/kraken2.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. 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The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libclass-xsaccessor-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 18720 Build-Time: 42 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 17 Job: kraken2_2.0.8~beta-1 Lintian: pass Machine Architecture: amd64 Package: kraken2 Package-Time: 71 Source-Version: 2.0.8~beta-1 Space: 18720 Status: successful Version: 2.0.8~beta-1 -------------------------------------------------------------------------------- Finished at 2019-10-09T14:09:02Z Build needed 00:01:11, 18720k disk space