https://launchpad.net/ubuntu/+source/jellyfish1/1.1.11-4/+build/15629391 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-012 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 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_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Nov 10:14:14 ntpdate[1812]: adjust time server 10.211.37.1 offset -0.002849 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15629391 /home/buildd/filecache-default/727e394105280e93a16c79dcca0079cc298d61c4 Creating target for build PACKAGEBUILD-15629391 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15629391 Starting target for build PACKAGEBUILD-15629391 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15629391 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15629391 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15629391 Updating target for build PACKAGEBUILD-15629391 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 Packages [1005 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [8699 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5037 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [145 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [80.3 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [343 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [229 kB] Fetched 16.5 MB in 8s (2125 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: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: base-files binutils binutils-common binutils-i686-linux-gnu cpp cpp-8 dash dmsetup findutils g++ g++-8 gcc gcc-8 gcc-8-base hostname init init-system-helpers libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libgpg-error0 libitm1 libkmod2 libmpx2 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base sed systemd systemd-sysv tzdata 54 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 47.6 MB of archives. After this operation, 42.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main i386 base-files i386 10.1ubuntu8 [60.2 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dash i386 0.5.10.2-1 [94.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main i386 findutils i386 4.6.0+git+20181018-1 [307 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 hostname i386 3.21 [11.6 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm6 i386 1.18.1-1 [32.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm-compat4 i386 1.18.1-1 [6704 B] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 libperl5.28 i386 5.28.0-3 [3436 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 perl i386 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 perl-base i386 5.28.0-3 [1600 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdb5.3 i386 5.3.28+dfsg1-0.2 [737 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main i386 sed i386 4.5-2 [189 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main i386 init-system-helpers all 1.55 [38.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main i386 systemd-sysv i386 239-7ubuntu10.1 [9400 B] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 libapparmor1 i386 2.12-4ubuntu10 [31.3 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-1build1 [11.1 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 libaudit1 i386 1:2.8.3-1ubuntu3 [40.0 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgpg-error0 i386 1.32-3 [60.5 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libkmod2 i386 25-1ubuntu1.1 [47.7 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main i386 systemd i386 239-7ubuntu10.1 [3067 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libsystemd0 i386 239-7ubuntu10.1 [228 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main i386 init i386 1.55 [6476 B] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libquadmath0 i386 8.2.0-9ubuntu1 [208 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 libubsan1 i386 8.2.0-9ubuntu1 [138 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 libitm1 i386 8.2.0-9ubuntu1 [30.8 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 libasan5 i386 8.2.0-9ubuntu1 [375 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8-base i386 8.2.0-9ubuntu1 [18.6 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++6 i386 8.2.0-9ubuntu1 [430 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 libgomp1 i386 8.2.0-9ubuntu1 [80.7 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 libatomic1 i386 8.2.0-9ubuntu1 [9604 B] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 libmpx2 i386 8.2.0-9ubuntu1 [13.0 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main i386 cpp-8 i386 8.2.0-9ubuntu1 [7537 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main i386 libcc1-0 i386 8.2.0-9ubuntu1 [41.9 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8 i386 8.2.0-9ubuntu1 [8330 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main i386 g++-8 i386 8.2.0-9ubuntu1 [8444 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++-8-dev i386 8.2.0-9ubuntu1 [1586 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 libgcc-8-dev i386 8.2.0-9ubuntu1 [2299 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libgcc1 i386 1:8.2.0-9ubuntu1 [48.1 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 libbinutils i386 2.31.1-7ubuntu1 [518 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 binutils-common i386 2.31.1-7ubuntu1 [194 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 binutils i386 2.31.1-7ubuntu1 [3392 B] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 binutils-i686-linux-gnu i386 2.31.1-7ubuntu1 [1985 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 libselinux1 i386 2.8-1build2 [73.5 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage-common all 2.8-1build2 [6892 B] Get:46 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage1 i386 2.8-1build2 [93.8 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libudev1 i386 239-7ubuntu10.1 [57.6 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libseccomp2 i386 2.3.3-3ubuntu2 [35.6 kB] Get:49 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdevmapper1.02.1 i386 2:1.02.145-4.1ubuntu4 [125 kB] Get:50 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dmsetup i386 2:1.02.145-4.1ubuntu4 [70.4 kB] Get:51 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libsqlite3-0 i386 3.25.3-1 [564 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018g-1 [188 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 g++ i386 4:8.2.0-2ubuntu2 [1616 B] Get:54 http://ftpmaster.internal/ubuntu disco/main i386 gcc i386 4:8.2.0-2ubuntu2 [5272 B] Get:55 http://ftpmaster.internal/ubuntu disco/main i386 cpp i386 4:8.2.0-2ubuntu2 [27.6 kB] Get:56 http://ftpmaster.internal/ubuntu disco-proposed/main i386 linux-libc-dev i386 4.18.0-11.12 [1040 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main i386 lockfile-progs i386 0.1.18 [9856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.6 MB in 3s (16.2 MB/s) (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_i386.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_i386.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by bash' Adding 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20181018-1_i386.deb ... Unpacking findutils (4.6.0+git+20181018-1) over (4.6.0+git+20180808-2) ... Setting up findutils (4.6.0+git+20181018-1) ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../hostname_3.21_i386.deb ... Unpacking hostname (3.21) over (3.20) ... Setting up hostname (3.21) ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.0-3_i386.deb ... Unpacking perl (5.28.0-3) over (5.26.2-7) ... 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Setting up libmpx2:i386 (8.2.0-9ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:i386 (3.25.3-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:i386 (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... Setting up libasan5:i386 (8.2.0-9ubuntu1) ... Setting up libitm1:i386 (8.2.0-9ubuntu1) ... Setting up libubsan1:i386 (8.2.0-9ubuntu1) ... Setting up libbinutils:i386 (2.31.1-7ubuntu1) ... Setting up libperl5.28:i386 (5.28.0-3) ... Setting up perl (5.28.0-3) ... Setting up binutils-i686-linux-gnu (2.31.1-7ubuntu1) ... Setting up libgcc-8-dev:i386 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:i386 (8.2.0-9ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15629391 i386 disco-proposed -c chroot:build-PACKAGEBUILD-15629391 --arch=i386 --dist=disco-proposed --nolog jellyfish1_1.1.11-4.dsc Initiating build PACKAGEBUILD-15629391 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-012.buildd +==============================================================================+ | jellyfish1 1.1.11-4 (i386) 09 Nov 2018 10:15 | +==============================================================================+ Package: jellyfish1 Version: 1.1.11-4 Source Version: 1.1.11-4 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/jellyfish1-OPwzOs/jellyfish1-1.1.11' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish1-OPwzOs' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15629391/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- jellyfish1_1.1.11-4.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-hny23v/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-hny23v/apt_archive ./ InRelease Get:2 copy:/<>/resolver-hny23v/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-hny23v/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-hny23v/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-hny23v/apt_archive ./ Packages [523 B] Fetched 2856 B in 0s (79.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 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-hny23v/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 ... 14533 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 (>= 11~) Filtered Build-Depends: debhelper (>= 11~) dpkg-deb: building package 'sbuild-build-depends-jellyfish1-dummy' in '/<>/resolver-jiLPQy/apt_archive/sbuild-build-depends-jellyfish1-dummy.deb'. Ign:1 copy:/<>/resolver-jiLPQy/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jiLPQy/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jiLPQy/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jiLPQy/apt_archive ./ Sources [213 B] Get:5 copy:/<>/resolver-jiLPQy/apt_archive ./ Packages [530 B] Fetched 2862 B in 0s (80.2 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install jellyfish1 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: libgdbm5 libperl5.26 perl-modules-5.26 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 dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make 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 NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtool libxml2 m4 man-db po-debconf sbuild-build-depends-jellyfish1-dummy 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 17.0 MB of archives. After this operation, 63.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-jiLPQy/apt_archive ./ sbuild-build-depends-jellyfish1-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu disco/main i386 libbsd0 i386 0.9.1-1 [48.8 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main i386 bsdmainutils i386 11.1.2ubuntu2 [183 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main i386 groff-base i386 1.22.3-10 [1169 kB] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libpipeline1 i386 1.5.0-2 [27.6 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main i386 man-db i386 2.8.4-3 [1038 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libmagic-mgc i386 1:5.34-2 [197 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 libmagic1 i386 1:5.34-2 [78.8 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 file i386 1:5.34-2 [22.8 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 libelf1 i386 0.170-0.5.0ubuntu1 [49.5 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 libglib2.0-0 i386 2.58.1-2 [1246 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 libicu60 i386 60.2-6ubuntu1 [8192 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 libxml2 i386 2.9.4+dfsg1-7ubuntu2 [658 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 gettext-base i386 0.19.8.1-8 [51.1 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 libsigsegv2 i386 2.12-2 [14.2 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 m4 i386 1.4.18-1ubuntu1 [202 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 autoconf all 2.69-11 [322 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 autotools-dev all 20180224.1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main i386 automake all 1:1.16.1-4 [522 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 autopoint all 0.19.8.1-8 [412 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libtool all 2.4.6-6 [195 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 dh-autoreconf all 19 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:24 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libfile-stripnondeterminism-perl all 0.044-1 [15.0 kB] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dh-strip-nondeterminism all 0.044-1 [5124 B] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 dwz i386 0.12-2 [80.4 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 libcroco3 i386 0.6.12-2 [87.7 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 gettext i386 0.19.8.1-8 [904 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 po-debconf all 1.0.20 [232 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 debhelper all 11.3.2ubuntu1 [883 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.0 MB in 1s (12.4 MB/s) Selecting previously unselected package libbsd0:i386. (Reading database ... 14533 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_i386.deb ... Unpacking libbsd0:i386 (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu2_i386.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... 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_1.5.0-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.0-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.4-3_i386.deb ... Unpacking man-db (2.8.4-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.34-2_i386.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:i386. 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Unpacking sbuild-build-depends-jellyfish1-dummy (0.invalid.0) ... Setting up libicu60:i386 (60.2-6ubuntu1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libelf1:i386 (0.170-0.5.0ubuntu1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:i386 (2.58.1-2) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-8) ... Setting up libpipeline1:i386 (1.5.0-2) ... Setting up m4 (1.4.18-1ubuntu1) ... Setting up libbsd0:i386 (0.9.1-1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7ubuntu2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:i386 (1:5.34-2) ... Setting up libcroco3:i386 (0.6.12-2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 (0.19.8.1-8) ... Setting up libfile-stripnondeterminism-perl (0.044-1) ... Setting up gettext (0.19.8.1-8) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... 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 man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-6) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.044-1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up sbuild-build-depends-jellyfish1-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-138-generic amd64 (i686) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 binutils-i686-linux-gnu_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-9ubuntu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.044-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.0.5ubuntu5 dpkg-dev_1.19.0.5ubuntu5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-9ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-9ubuntu1 gcc-8-base_8.2.0-9ubuntu1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-2ubuntu1 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.55 init-system-helpers_1.55 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9ubuntu1 libassuan0_2.5.1-2 libatomic1_8.2.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-7ubuntu1 libblkid1_2.32-0.1ubuntu2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.0.5ubuntu5 libelf1_0.170-0.5.0ubuntu1 libext2fs2_1.44.4-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.044-1 libgcc-8-dev_8.2.0-9ubuntu1 libgcc1_1:8.2.0-9ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.18.1-1 libgdbm5_1.14.1-6 libgdbm6_1.18.1-1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.6.4-2ubuntu1 libgomp1_8.2.0-9ubuntu1 libgpg-error0_1.32-3 libhogweed4_3.4-1 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-9ubuntu1 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu1.1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libmpx2_8.2.0-9ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.0-3 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libquadmath0_8.2.0-9ubuntu1 libreadline7_7.0-5 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.25.3-1 libss2_1.44.4-2 libssl1.1_1.1.1-1ubuntu2 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 libsystemd0_239-7ubuntu10.1 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10.1 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libxml2_2.9.4+dfsg1-7ubuntu2 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-jellyfish1-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu10.1 systemd-sysv_239-7ubuntu10.1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Oct 18 06:05:05 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 ./jellyfish1_1.1.11-4.dsc dpkg-source: info: extracting jellyfish1 in jellyfish1-1.1.11 dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz dpkg-source: info: unpacking jellyfish1_1.1.11-4.debian.tar.xz dpkg-source: info: applying man dpkg-source: info: applying arm64.patch dpkg-source: info: applying mips.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-15629391 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15629391 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15629391 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package jellyfish1 dpkg-buildpackage: info: source version 1.1.11-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build jellyfish1-1.1.11 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:9: installing './compile' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for md5sum... md5sum checking for __int128... no checking whether strerror_r is declared... yes checking for strerror_r... yes checking whether strerror_r returns char *... yes checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking sys/syscall.h usability... yes checking sys/syscall.h presence... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-1.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all make -j1 all bin/generate_sequence bin/test_all make[2]: Entering directory '/<>' make all-am make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/jellyfish.o jellyfish/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc In file included from jellyfish/stats_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/stats_main.cc:83:34: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/hash_merge.cc:34: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::compacted_hash::reader; std::ostream = std::basic_ostream]’: jellyfish/hash_merge.cc:189:43: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] memset(&head, '\0', sizeof(head)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here struct header { ^~~~~~ In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp: In function ‘int merge_main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:138:19: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(columns[i] != other.columns[i]) ~~~~~~~~~^ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] free(columns); ~~~~^~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long long unsigned int]’ jellyfish/mer_counter.cc:142:66: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::InvalidMatrix]’: ./jellyfish/invertible_hash_array.hpp:185:11: required from ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’ jellyfish/mer_counter.cc:149:24: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::sequence_parser::sequence_t]’ ./jellyfish/parse_dna.hpp:178:75: required from ‘jellyfish::parse_dna::parse_dna(T, T, uint_t, unsigned int, size_t) [with T = __gnu_cxx::__normal_iterator >; uint_t = long long unsigned int; size_t = unsigned int]’ jellyfish/mer_counter.cc:138:60: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/mer_counter.cc:38: ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream]’: ./jellyfish/direct_sorted_dumper.hpp:101:5: required from ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’ ./jellyfish/direct_sorted_dumper.hpp:91:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] memset(&head, '\0', sizeof(head)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here struct header { ^~~~~~ ./jellyfish/compacted_hash.hpp: In instantiation of ‘void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::invertible_hash::array; std::ostream = std::basic_ostream]’: ./jellyfish/sorted_dumper.hpp:116:5: required from ‘void jellyfish::sorted_dumper::_dump() [with storage_t = jellyfish::invertible_hash::array; atomic_t = atomic::gcc]’ ./jellyfish/sorted_dumper.hpp:105:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct jellyfish::compacted_hash::header’; use assignment or value-initialization instead [-Wclass-memaccess] memset(&head, '\0', sizeof(head)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: ‘struct jellyfish::compacted_hash::header’ declared here struct header { ^~~~~~ In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:7: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_quake; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long long unsigned int; val_t = jellyfish::capped_integer; ary_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:7: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long long unsigned int; val_t = long long unsigned int; ary_t = jellyfish::invertible_hash::array; atomic = atomic::gcc]’ jellyfish/mer_counter.cc:114:7: required from ‘void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, atomic::gcc>]’ jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/mer_counter.cc:38: ./jellyfish/square_binary_matrix.hpp: In member function ‘void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]’: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/mer_counter.cc:38: ./jellyfish/square_binary_matrix.hpp: In member function ‘void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/mer_counter.cc:38: ./jellyfish/square_binary_matrix.hpp: In constructor ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc In file included from jellyfish/histo_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/histo_main.cc:111:34: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In function ‘int histo_main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc jellyfish/dump_main.cc: In function ‘int dump_main(int, char**)’: jellyfish/dump_main.cc:86:24: warning: catching polymorphic type ‘class mapped_file::ErrorMMap’ by value [-Wcatch-value=] } catch(mapped_file::ErrorMMap) { ^~~~~~~~~ In file included from jellyfish/dump_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/dump_main.cc:65:44: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc In file included from ./jellyfish/mapped_file.hpp:29, from ./jellyfish/hash.hpp:27, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]’: ./jellyfish/raw_dumper.hpp:169:11: required from ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]’ ./jellyfish/raw_dumper.hpp:98:20: required from ‘jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]’ jellyfish/query_main.cc:63:34: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc In file included from jellyfish/dump_fastq_main.cc:25: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc In file included from jellyfish/histo_fastq_main.cc:26: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/cite.o jellyfish/cite.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc In file included from jellyfish/hash_fastq_merge.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]’: ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]’: ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]’: ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]’: ./jellyfish/hash.hpp:151:9: required from ‘void jellyfish::hash::dump() [with key_t = long long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]’ jellyfish/hash_fastq_merge.cc:49:13: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]’: ./jellyfish/invertible_hash_array.hpp:116:11: required from ‘jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long long unsigned int]’ ./jellyfish/aligned_values_array.hpp:42:30: required from ‘jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(size_t, uint_t, uint_t, size_t*) [with _key_t = long long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long long unsigned int]’ jellyfish/hash_fastq_merge.cc:28:79: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]’: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp:64:112: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) { ^ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp: In function ‘int hash_fastq_merge_main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/square_binary_matrix.lo jellyfish/square_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -fPIC -DPIC -o jellyfish/.libs/square_binary_matrix.o In file included from ./jellyfish/square_binary_matrix.hpp:27, from jellyfish/square_binary_matrix.cc:21: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]’: jellyfish/square_binary_matrix.cc:93:2: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::transpose() const’: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In member function ‘void SquareBinaryMatrix::load(std::istream*)’: ./jellyfish/square_binary_matrix.hpp:55:13: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns = first_alloc(size); ~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In member function ‘size_t SquareBinaryMatrix::read(const char*)’: ./jellyfish/square_binary_matrix.hpp:55:13: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns = first_alloc(size); ~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const’: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ jellyfish/square_binary_matrix.cc: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::inverse() const’: jellyfish/square_binary_matrix.cc:95:38: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] res.columns[i] ^= res.columns[j]; ^ jellyfish/square_binary_matrix.cc:90:28: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] if((pivot.columns[j] >> (size - i - 1)) & (uint64_t)0x1) ~~~~~~~~~~~~~~~^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/err.lo jellyfish/err.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -fPIC -DPIC -o jellyfish/.libs/err.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/misc.lo jellyfish/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -fPIC -DPIC -o jellyfish/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/storage.lo jellyfish/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -fPIC -DPIC -o jellyfish/.libs/storage.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/thread_exec.lo jellyfish/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -fPIC -DPIC -o jellyfish/.libs/thread_exec.o In file included from jellyfish/thread_exec.hpp:26, from jellyfish/thread_exec.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = thread_exec::Error]’: jellyfish/thread_exec.cc:28:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/time.lo jellyfish/time.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -fPIC -DPIC -o jellyfish/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/file_parser.lo jellyfish/file_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -fPIC -DPIC -o jellyfish/.libs/file_parser.o In file included from jellyfish/file_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/file_parser.cc:33:5: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/read_parser.lo jellyfish/read_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/read_parser.o In file included from ./jellyfish/file_parser.hpp:24, from ./jellyfish/read_parser.hpp:20, from jellyfish/read_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/read_parser.cc:30:5: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_read.lo jellyfish/parse_read.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -fPIC -DPIC -o jellyfish/.libs/parse_read.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/half.lo jellyfish/half.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mapped_file.lo jellyfish/mapped_file.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -fPIC -DPIC -o jellyfish/.libs/mapped_file.o In file included from ./jellyfish/mapped_file.hpp:29, from jellyfish/mapped_file.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]’: ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_dna.lo jellyfish/parse_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_quake.lo jellyfish/parse_quake.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -fPIC -DPIC -o jellyfish/.libs/parse_quake.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_quake.hpp:22, from jellyfish/parse_quake.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_quake.cc:27:40: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_qual_dna.lo jellyfish/parse_qual_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_qual_dna.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_qual_dna.hpp:22, from jellyfish/parse_qual_dna.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]’: ./jellyfish/double_fifo_input.hpp:101:7: required from ‘jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]’ jellyfish/parse_qual_dna.cc:27:55: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/sequence_parser.lo jellyfish/sequence_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o In file included from ./jellyfish/sequence_parser.hpp:21, from jellyfish/sequence_parser.cc:18: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/sequence_parser.cc:32:5: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/seq_qual_parser.lo jellyfish/seq_qual_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -fPIC -DPIC -o jellyfish/.libs/seq_qual_parser.o In file included from ./jellyfish/seq_qual_parser.hpp:21, from jellyfish/seq_qual_parser.cc:17: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]’: jellyfish/seq_qual_parser.cc:31:5: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]’: jellyfish/seq_qual_parser.cc:47:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]’: ./jellyfish/simple_growing_array.hpp:55:9: required from ‘void jellyfish::simple_growing_array::resize() [with T = char]’ ./jellyfish/simple_growing_array.hpp:27:53: required from ‘jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = unsigned int]’ ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.lo jellyfish/backtrace.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -fPIC -DPIC -o jellyfish/.libs/backtrace.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/floats.lo jellyfish/floats.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -fPIC -DPIC -o jellyfish/.libs/floats.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.lo jellyfish/dbg.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -fPIC -DPIC -o jellyfish/.libs/dbg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/allocators_mmap.lo jellyfish/allocators_mmap.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -fPIC -DPIC -o jellyfish/.libs/allocators_mmap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dna_codes.lo jellyfish/dna_codes.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -fPIC -DPIC -o jellyfish/.libs/dna_codes.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:1:0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/i386-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/8/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc/i686-linux-gnu/8 -L/usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/8/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/8/crtendS.o /usr/lib/gcc/i686-linux-gnu/8/../../../i386-linux-gnu/crtn.o -g -O3 -g -O2 -fstack-protector-strong -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-1.1.so.1 -o .libs/libjellyfish-1.1.so.1.0.1 libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so.1" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so.1") libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so") libtool: link: ar cru .libs/libjellyfish-1.1.a jellyfish/square_binary_matrix.o jellyfish/err.o jellyfish/misc.o jellyfish/storage.o jellyfish/thread_exec.o jellyfish/time.o jellyfish/file_parser.o jellyfish/read_parser.o jellyfish/parse_read.o jellyfish/half.o jellyfish/mapped_file.o jellyfish/parse_dna.o jellyfish/parse_quake.o jellyfish/parse_qual_dna.o jellyfish/sequence_parser.o jellyfish/seq_qual_parser.o jellyfish/backtrace.o jellyfish/floats.o jellyfish/dbg.o jellyfish/allocators_mmap.o jellyfish/dna_codes.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libjellyfish-1.1.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-1.1.la" && ln -s "../libjellyfish-1.1.la" "libjellyfish-1.1.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,--as-needed -latomic -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--as-needed -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o -lpthread -latomic ./.libs/libjellyfish-1.1.so make[3]: Leaving directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc In file included from jellyfish/generate_sequence.cc:22: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from jellyfish/generate_sequence.cc:24: ./jellyfish/square_binary_matrix.hpp: In function ‘int main(int, char**)’: ./jellyfish/square_binary_matrix.hpp:76:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = _columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from jellyfish/generate_sequence.cc:24: ./jellyfish/square_binary_matrix.hpp:87:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] free(columns); ~~~~^~~~~~~~~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from jellyfish/generate_sequence.cc:24: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o -lpthread ./.libs/libjellyfish-1.1.so g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_square_binary_matrix.o `test -f 'unit_tests/test_square_binary_matrix.cc' || echo './'`unit_tests/test_square_binary_matrix.cc unit_tests/test_square_binary_matrix.cc: In member function ‘virtual void SquareBinaryMatrix_Initialization_Test::TestBody()’: unit_tests/test_square_binary_matrix.cc:81:48: warning: catching polymorphic type ‘class SquareBinaryMatrix::SingularMatrix’ by value [-Wcatch-value=] } catch(SquareBinaryMatrix::SingularMatrix e) { ^ In file included from ./jellyfish/square_binary_matrix.hpp:27, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]’: ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ~raise_t() { throw err_t(oss.str()); } ^ ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept ./jellyfish/err.hpp: In instantiation of ‘err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]’: ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate] ./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:69:18: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] columns[i] = rhs.columns[i] & _mask; ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp:61:82: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) { ^ In file included from ./jellyfish/square_binary_matrix.hpp:28, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here Tptr ptr; ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_a-gtest_main.o `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_a-gtest-all.o `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc rm -f libgtest.a ar cru libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bin/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o libgtest_main.a libgtest.a libjellyfish-1.1.la libtool: link: g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o -lpthread libgtest_main.a libgtest.a ./.libs/libjellyfish-1.1.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # dh_auto_test && true echo "****************************************************** do not test for the moment ******************************************************" ****************************************************** do not test for the moment ****************************************************** make[1]: Leaving directory '/<>' 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 --destdir=debian/tmp make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' /bin/mkdir -p '/<>/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/<>/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /<>/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1.0.1 libtool: install: (cd /<>/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /<>/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-1.1.la libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /<>/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-1.1.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-1.1.a libtool: install: ranlib /<>/debian/tmp/usr/lib/i386-linux-gnu/libjellyfish-1.1.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<>/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/allocators_malloc.hpp jellyfish/allocators_mmap.hpp jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp jellyfish/compacted_dumper.hpp jellyfish/compacted_hash.hpp jellyfish/concurrent_queues.hpp jellyfish/direct_indexing_array.hpp jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp jellyfish/dumper.hpp jellyfish/hash_function.hpp jellyfish/hash.hpp jellyfish/heap.hpp jellyfish/invertible_hash_array.hpp jellyfish/locking_hash_counters.hpp jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp jellyfish/mer_counting.hpp jellyfish/err.hpp jellyfish/misc.hpp jellyfish/offsets_key_value.hpp jellyfish/reversible_hash_function.hpp jellyfish/sorted_dumper.hpp jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp jellyfish/thread_exec.hpp jellyfish/time.hpp jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp jellyfish/capped_integer.hpp jellyfish/aligned_values_array.hpp jellyfish/fastq_dumper.hpp jellyfish/floats.hpp jellyfish/circular_buffer.hpp jellyfish/counter.hpp jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/sequence_parser.hpp jellyfish/seq_qual_parser.hpp jellyfish/double_fifo_input.hpp jellyfish/read_parser.hpp jellyfish/parse_read.hpp jellyfish/simple_growing_array.hpp jellyfish/toFloat.h jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h jellyfish/backtrace.hpp jellyfish/dna_codes.hpp jellyfish/simple_circular_buffer.hpp '/<>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/<>/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-1.1.pc '/<>/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/tmp/usr/lib/jellyfish1 mv debian/tmp/usr/bin/* debian/tmp/usr/lib/jellyfish1 dh_install find debian -name "*.a" -delete find debian -name "*.la" -delete find debian -name "*.so" -delete find debian -name "pkgconfig" -type d | xargs rm -rf make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1 make[1]: Leaving directory '/<>' dh_lintian -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 dpkg-shlibdeps: warning: symbol pthread_cancel used by debian/jellyfish1/usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_join used by debian/jellyfish1/usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_create used by debian/jellyfish1/usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing jellyfish1 (in debian/jellyfish1); do_strip: , oemstrip: pkgstriptranslations: processing jellyfish1-dbgsym (in debian/.debhelper/jellyfish1/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/jellyfish1/DEBIAN/control, package jellyfish1, directory debian/jellyfish1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package jellyfish1 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-4_i386.deb'. pkgstripfiles: processing control file: debian/.debhelper/jellyfish1/dbgsym-root/DEBIAN/control, package jellyfish1-dbgsym, directory debian/.debhelper/jellyfish1/dbgsym-root dpkg-deb: building package 'jellyfish1-dbgsym' in 'debian/.debhelper/scratch-space/build-jellyfish1/jellyfish1-dbgsym_1.1.11-4_i386.deb'. Renaming jellyfish1-dbgsym_1.1.11-4_i386.deb to jellyfish1-dbgsym_1.1.11-4_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../jellyfish1_1.1.11-4_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build jellyfish1-1.1.11 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181109-1018 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ jellyfish1_1.1.11-4_i386.changes: --------------------------------- Format: 1.8 Date: Thu, 18 Oct 2018 08:03:17 +0200 Source: jellyfish1 Binary: jellyfish1 Architecture: i386 Version: 1.1.11-4 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: jellyfish1 - count k-mers in DNA sequences Changes: jellyfish1 (1.1.11-4) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 9337b7f589ecd5ffbdf9712f5e3b3f2a12de9e2c 1599380 jellyfish1-dbgsym_1.1.11-4_i386.ddeb 22fe844a7f6ef3d98ac1ddfaa65977fc85bc578b 4820 jellyfish1_1.1.11-4_i386.buildinfo a26c48c6ff8635ac162a8dd09cada7c446b2f6c0 168060 jellyfish1_1.1.11-4_i386.deb Checksums-Sha256: d6e1f0fd2b0ac01e5f0a1406e71b14ac11462aaa4b7f411a2c679ceae61f2729 1599380 jellyfish1-dbgsym_1.1.11-4_i386.ddeb 6ee7d8f6e705fa918e58c5533520be56010ef77c5697f911fe0fde2022a07198 4820 jellyfish1_1.1.11-4_i386.buildinfo 461222d6d2fbd6d6c65cd8966c6be1da51fb97394a63f4734854f14b459eb706 168060 jellyfish1_1.1.11-4_i386.deb Files: 6f804b3aca6965e01a78238771f817b1 1599380 debug optional jellyfish1-dbgsym_1.1.11-4_i386.ddeb 3bf9c80c0965afc32816ce4eb2ba1ad5 4820 science optional jellyfish1_1.1.11-4_i386.buildinfo 9075ce48e9e54890da81493158916285 168060 science optional jellyfish1_1.1.11-4_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ jellyfish1_1.1.11-4_i386.deb ---------------------------- new debian package, version 2.0. size 168060 bytes: control archive=1388 bytes. 1387 bytes, 29 lines control 502 bytes, 7 lines md5sums 30 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: jellyfish1 Version: 1.1.11-4 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 723 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.2), libstdc++6 (>= 5.2) Enhances: kraken Section: science Priority: optional Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Description: count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This is the latest version of the 1.x series of jellyfish which is used by some other applications that are not compatible with version 2.x which is provided inside the jellyfish package. drwxr-xr-x root/root 0 2018-10-18 06:03 ./ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/bin/ lrwxrwxrwx root/root 0 2018-10-18 06:03 ./usr/bin/jellyfish1 -> ../lib/jellyfish1/jellyfish drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/i386-linux-gnu/ lrwxrwxrwx root/root 0 2018-10-18 06:03 ./usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1 -> libjellyfish-1.1.so.1.0.1 -rw-r--r-- root/root 375192 2018-10-18 06:03 ./usr/lib/i386-linux-gnu/libjellyfish-1.1.so.1.0.1 drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/jellyfish1/ -rwxr-xr-x root/root 331476 2018-10-18 06:03 ./usr/lib/jellyfish1/jellyfish drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/doc/jellyfish1/ -rw-r--r-- root/root 2333 2013-05-29 19:45 ./usr/share/doc/jellyfish1/README -rw-r--r-- root/root 1069 2018-10-18 06:03 ./usr/share/doc/jellyfish1/changelog.Debian.gz -rw-r--r-- root/root 2337 2018-10-18 06:03 ./usr/share/doc/jellyfish1/copyright drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 66 2018-10-18 06:03 ./usr/share/lintian/overrides/jellyfish1 drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/man/ drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/man/man1/ -rw-r--r-- root/root 4556 2018-10-18 06:03 ./usr/share/man/man1/jellyfish1.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 53528 Build-Time: 166 Distribution: disco-proposed Host Architecture: i386 Install-Time: 20 Job: jellyfish1_1.1.11-4.dsc Machine Architecture: amd64 Package: jellyfish1 Package-Time: 188 Source-Version: 1.1.11-4 Space: 53528 Status: successful Version: 1.1.11-4 -------------------------------------------------------------------------------- Finished at 20181109-1018 Build needed 00:03:08, 53528k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15629391 Scanning for processes to kill in build PACKAGEBUILD-15629391